From d64d1e28e752d14482ff9fca33fa7f4cad243c26 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Tue, 12 May 2026 21:39:27 +0200 Subject: [PATCH 01/18] fix: replace Lombok annotations with explicit Java code Lombok annotation processing failed on JDK 21+ causing compilation errors. Replaced @Getter, @Setter, @Data, @Slf4j, @NoArgsConstructor, @AllArgsConstructor, and @RequiredArgsConstructor with explicit constructors, getters, setters, and SLF4J logger declarations. # Conflicts: # src/main/java/nl/esciencecenter/controller/dto/WorkflowsZip.java --- .../externalAPIs/BioToolsRestClient.java | 11 ++-- .../externalAPIs/OpenEBenchRestClient.java | 11 ++-- .../models/benchmarks/Benchmark.java | 50 ++++++------------- .../models/benchmarks/BenchmarkBase.java | 43 +++++++++++----- .../benchmarks/WorkflowStepBenchmark.java | 44 +++++----------- .../restape/APEWorkflowMetadata.java | 15 ++++-- .../esciencecenter/restape/RestApeUtils.java | 14 +++--- 7 files changed, 90 insertions(+), 98 deletions(-) diff --git a/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java b/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java index 45751fa..965ad8f 100644 --- a/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java +++ b/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java @@ -5,9 +5,8 @@ import org.json.JSONException; import org.json.JSONObject; -import lombok.AccessLevel; -import lombok.NoArgsConstructor; -import lombok.extern.slf4j.Slf4j; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import okhttp3.Request; import okhttp3.Response; @@ -15,10 +14,12 @@ * The {@code BioToolsRestClient} class provides methods to retrieve and process tool metrics * provided by bio.tools API. */ -@Slf4j -@NoArgsConstructor(access = AccessLevel.PRIVATE) public class BioToolsRestClient { + private static final Logger log = LoggerFactory.getLogger(BioToolsRestClient.class); + + private BioToolsRestClient() {} + private static final okhttp3.OkHttpClient client = new okhttp3.OkHttpClient(); /** diff --git a/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java b/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java index 9e51010..cbc0143 100644 --- a/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java +++ b/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java @@ -11,9 +11,8 @@ import org.json.JSONException; import org.json.JSONObject; -import lombok.AccessLevel; -import lombok.NoArgsConstructor; -import lombok.extern.slf4j.Slf4j; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import nl.uu.cs.ape.utils.APEFiles; import okhttp3.OkHttpClient; import okhttp3.Request; @@ -23,10 +22,12 @@ * The {@code ToolBenchmarkingAPIs} class provides methods to retrieve and * process tool metrics provided by OpenEBench API. */ -@Slf4j -@NoArgsConstructor(access = AccessLevel.PRIVATE) public class OpenEBenchRestClient { + private static final Logger log = LoggerFactory.getLogger(OpenEBenchRestClient.class); + + private OpenEBenchRestClient() {} + private static final OkHttpClient client = new OkHttpClient(); /** diff --git a/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java b/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java index c1152ed..896db5d 100644 --- a/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java +++ b/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java @@ -5,52 +5,34 @@ import org.json.JSONArray; import org.json.JSONObject; -import lombok.Getter; -import lombok.NonNull; -import lombok.RequiredArgsConstructor; -import lombok.Setter; - /** * Abstract class {@link Benchmark} containing general information about a * benchmark, however, it must be implemented (e.g., as an bio.tools benchmark) * to be able to compute the benchmark value. */ - -@RequiredArgsConstructor public class Benchmark { - /** - * General information about the benchmark that is being computed. - */ - @NonNull - @Getter - @Setter private BenchmarkBase benchmarkInfo; - /** - * Value of the benchmark for the workflow. - */ - @Getter - @Setter private String value; - /** - * Desirability value (from 0 to 1.0) of the benchmark for the workflow. - */ - @Getter - @Setter private double desirabilityValue; - /** - * Benchmark for each tool/step in the workflow. - */ - @Getter - @Setter private List workflow; - /** - * Generate a JSON object containing the benchmark information. The content can - * be visualized using the Wokrkflomics web platform. - * - * @return JSON object containing the benchmark information. - */ + public Benchmark(BenchmarkBase benchmarkInfo) { + this.benchmarkInfo = benchmarkInfo; + } + + public BenchmarkBase getBenchmarkInfo() { return benchmarkInfo; } + public void setBenchmarkInfo(BenchmarkBase benchmarkInfo) { this.benchmarkInfo = benchmarkInfo; } + + public String getValue() { return value; } + public void setValue(String value) { this.value = value; } + + public double getDesirabilityValue() { return desirabilityValue; } + public void setDesirabilityValue(double desirabilityValue) { this.desirabilityValue = desirabilityValue; } + + public List getWorkflow() { return workflow; } + public void setWorkflow(List workflow) { this.workflow = workflow; } + public JSONObject toJSON() { JSONObject benchmarkJson = this.benchmarkInfo.getTitleJson(); diff --git a/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java b/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java index b280d9f..1128ed4 100644 --- a/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java +++ b/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java @@ -2,27 +2,47 @@ import org.json.JSONObject; -import lombok.AllArgsConstructor; -import lombok.Data; -import lombok.NonNull; - -@Data -@AllArgsConstructor /** * Base information for a benchmark. */ public class BenchmarkBase { - @NonNull private String benchmarkTitle; - @NonNull private String benchmarkCategory; - @NonNull private String benchmarkDescription; - @NonNull private String unit; private String expectedField; private String expectedValue; + public BenchmarkBase() {} + + public BenchmarkBase(String benchmarkTitle, String benchmarkCategory, String benchmarkDescription, + String unit, String expectedField, String expectedValue) { + this.benchmarkTitle = benchmarkTitle; + this.benchmarkCategory = benchmarkCategory; + this.benchmarkDescription = benchmarkDescription; + this.unit = unit; + this.expectedField = expectedField; + this.expectedValue = expectedValue; + } + + public String getBenchmarkTitle() { return benchmarkTitle; } + public void setBenchmarkTitle(String benchmarkTitle) { this.benchmarkTitle = benchmarkTitle; } + + public String getBenchmarkCategory() { return benchmarkCategory; } + public void setBenchmarkCategory(String benchmarkCategory) { this.benchmarkCategory = benchmarkCategory; } + + public String getBenchmarkDescription() { return benchmarkDescription; } + public void setBenchmarkDescription(String benchmarkDescription) { this.benchmarkDescription = benchmarkDescription; } + + public String getUnit() { return unit; } + public void setUnit(String unit) { this.unit = unit; } + + public String getExpectedField() { return expectedField; } + public void setExpectedField(String expectedField) { this.expectedField = expectedField; } + + public String getExpectedValue() { return expectedValue; } + public void setExpectedValue(String expectedValue) { this.expectedValue = expectedValue; } + public JSONObject getTitleJson() { JSONObject benchmarkJson = new JSONObject(); benchmarkJson.put("title", benchmarkTitle); @@ -31,5 +51,4 @@ public JSONObject getTitleJson() { benchmarkJson.put("unit", unit); return benchmarkJson; } - -} \ No newline at end of file +} diff --git a/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java b/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java index ae432da..cdb90bd 100644 --- a/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java +++ b/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java @@ -1,47 +1,31 @@ package nl.esciencecenter.models.benchmarks; - import org.json.JSONObject; - -import lombok.Data; -import lombok.NoArgsConstructor; -import lombok.NonNull; - -@Data -@NoArgsConstructor /** * Class representing the design-time benchmarks for a workflow step (tool). */ public class WorkflowStepBenchmark { - /** - * Description of the benchmark value used in the visualization. - */ - @NonNull private String description; - /** - * Value of the benchmark for the workflow step (tool). - */ - @NonNull private String value; - /** - * Desirability value (from 0 to 1.0) of the benchmark for the workflow step - * (tool). - */ private double desirabilityValue; + public WorkflowStepBenchmark() {} + + public String getDescription() { return description; } + public void setDescription(String description) { this.description = description; } + + public String getValue() { return value; } + public void setValue(String value) { this.value = value; } + + public double getDesirabilityValue() { return desirabilityValue; } + public void setDesirabilityValue(double desirabilityValue) { this.desirabilityValue = desirabilityValue; } + @Override public String toString() { - return "{ label:" + description + ", value:" + value + ", desirability:" - + desirabilityValue + "}"; + return "{ label:" + description + ", value:" + value + ", desirability:" + desirabilityValue + "}"; } - /** - * Generate a JSON object containing the tool benchmark information. The content can - * be visualized using the Wokrkflomics web platform. - * - * @return JSON object containing the benchmark information. - */ public JSONObject toJSON() { JSONObject json = new JSONObject(); json.put("label", description); @@ -49,6 +33,4 @@ public JSONObject toJSON() { json.put("desirability", desirabilityValue); return json; } - - -} \ No newline at end of file +} diff --git a/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java b/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java index 240ae9d..ba13855 100644 --- a/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java +++ b/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java @@ -4,8 +4,6 @@ import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Getter; -import lombok.NoArgsConstructor; import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow; /** @@ -14,8 +12,6 @@ * including descriptive names, descriptions, the length of the solution, and benchmark information. * It provides functionality to convert these details into a JSONObject for serialization or further processing. */ -@Getter -@NoArgsConstructor public class APEWorkflowMetadata { @JsonProperty("workflow_name") @@ -37,6 +33,17 @@ public class APEWorkflowMetadata { @JsonProperty("benchmark_file") private String benchmarkFile; // Optional, indicates if benchmark data should be included. + public APEWorkflowMetadata() {} + + public String getWorkflowName() { return workflowName; } + public String getDescriptiveName() { return descriptiveName; } + public String getDescription() { return description; } + public int getWorkflowLength() { return workflowLength; } + public String getRunId() { return runId; } + public String getCwlName() { return cwlName; } + public String getFigureName() { return figureName; } + public String getBenchmarkFile() { return benchmarkFile; } + /** * Constructs a APEWorkflowMetadata instance from a given SolutionWorkflow and run configuration. * diff --git a/src/main/java/nl/esciencecenter/restape/RestApeUtils.java b/src/main/java/nl/esciencecenter/restape/RestApeUtils.java index 69f7982..3d81125 100644 --- a/src/main/java/nl/esciencecenter/restape/RestApeUtils.java +++ b/src/main/java/nl/esciencecenter/restape/RestApeUtils.java @@ -8,17 +8,17 @@ import org.json.JSONObject; -import lombok.NoArgsConstructor; -import lombok.extern.slf4j.Slf4j; -import lombok.AccessLevel; -import lombok.Getter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; -@Slf4j -@NoArgsConstructor(access = AccessLevel.PRIVATE) public class RestApeUtils { - @Getter(lazy = true) + private static final Logger log = LoggerFactory.getLogger(RestApeUtils.class); private static final String solutionPath = getSolutionsDir(); + + private RestApeUtils() {} + + public static String getSolutionPath() { return solutionPath; } private static final String allSolutionsDirName = "apeOutputs"; private static final int hashLength = 10; private static final int currentTimestampLength = 13; From 66bbf892b3e04fa6168e14f393f3ab200e56be31 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Tue, 12 May 2026 21:39:35 +0200 Subject: [PATCH 02/18] feat: add snakeyaml dependency for CWL v1.2 parsing --- pom.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pom.xml b/pom.xml index c1c22b4..d333880 100644 --- a/pom.xml +++ b/pom.xml @@ -127,6 +127,12 @@ 3.1.0 + + + org.yaml + snakeyaml + + From dfb65e4debbc36a43561e0a46964af90785528a2 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Tue, 12 May 2026 21:39:44 +0200 Subject: [PATCH 03/18] feat: add DTOs for CWL parse response Adds GraphNode, GraphEdge, ApeTaxTuple, and ParseResponse DTOs used by the /alternatives/parse endpoint. All fields have explicit getters for Jackson serialization. --- .../controller/dto/ApeTaxTuple.java | 14 +++++++++++ .../controller/dto/GraphEdge.java | 14 +++++++++++ .../controller/dto/GraphNode.java | 17 ++++++++++++++ .../controller/dto/ParseResponse.java | 23 +++++++++++++++++++ 4 files changed, 68 insertions(+) create mode 100644 src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java create mode 100644 src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java create mode 100644 src/main/java/nl/esciencecenter/controller/dto/GraphNode.java create mode 100644 src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java diff --git a/src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java b/src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java new file mode 100644 index 0000000..19473df --- /dev/null +++ b/src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java @@ -0,0 +1,14 @@ +package nl.esciencecenter.controller.dto; + +public class ApeTaxTuple { + private final String id; + private final String label; + + public ApeTaxTuple(String id, String label) { + this.id = id; + this.label = label; + } + + public String getId() { return id; } + public String getLabel() { return label; } +} diff --git a/src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java b/src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java new file mode 100644 index 0000000..251f158 --- /dev/null +++ b/src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java @@ -0,0 +1,14 @@ +package nl.esciencecenter.controller.dto; + +public class GraphEdge { + private final String source; + private final String target; + + public GraphEdge(String source, String target) { + this.source = source; + this.target = target; + } + + public String getSource() { return source; } + public String getTarget() { return target; } +} diff --git a/src/main/java/nl/esciencecenter/controller/dto/GraphNode.java b/src/main/java/nl/esciencecenter/controller/dto/GraphNode.java new file mode 100644 index 0000000..a632d4f --- /dev/null +++ b/src/main/java/nl/esciencecenter/controller/dto/GraphNode.java @@ -0,0 +1,17 @@ +package nl.esciencecenter.controller.dto; + +public class GraphNode { + private final String id; + private final String label; + private final String type; // "tool" | "input" | "output" + + public GraphNode(String id, String label, String type) { + this.id = id; + this.label = label; + this.type = type; + } + + public String getId() { return id; } + public String getLabel() { return label; } + public String getType() { return type; } +} diff --git a/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java b/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java new file mode 100644 index 0000000..2128ff2 --- /dev/null +++ b/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java @@ -0,0 +1,23 @@ +package nl.esciencecenter.controller.dto; + +import java.util.List; + +public class ParseResponse { + private final List nodes; + private final List edges; + private final List inputs; + private final List outputs; + + public ParseResponse(List nodes, List edges, + List inputs, List outputs) { + this.nodes = nodes; + this.edges = edges; + this.inputs = inputs; + this.outputs = outputs; + } + + public List getNodes() { return nodes; } + public List getEdges() { return edges; } + public List getInputs() { return inputs; } + public List getOutputs() { return outputs; } +} From ec0e951645054a837559e41da4bc67e6fb50350c Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Tue, 12 May 2026 21:40:22 +0200 Subject: [PATCH 04/18] feat: add EDAMTaxonomyService for async EDAM OWL label resolution Loads the EDAM OWL ontology asynchronously at startup and builds an inverted URI-to-label map for O(1) lookup. Falls back to the short-form URI fragment while loading. Used to resolve format URIs in CWL inputs/outputs to human-readable EDAM class names. --- .../restape/EDAMTaxonomyService.java | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java diff --git a/src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java b/src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java new file mode 100644 index 0000000..ebcbf65 --- /dev/null +++ b/src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java @@ -0,0 +1,94 @@ +package nl.esciencecenter.restape; + +import java.util.Collections; +import java.util.HashMap; +import java.util.Map; +import java.util.concurrent.CompletableFuture; +import java.util.concurrent.atomic.AtomicReference; + +import jakarta.annotation.PostConstruct; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.MissingImportHandlingStrategy; +import org.semanticweb.owlapi.model.OWLAnnotationValue; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.search.EntitySearcher; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +/** + * Loads the EDAM ontology once at startup and exposes O(1) URI → label resolution + * (concept §3.3: statisches Invertieren der Taxonomie). + * + * Label resolution falls back to the short-form EDAM ID while the ontology is + * still loading and whenever a URI is not found. + */ +@Service +public class EDAMTaxonomyService { + + private static final Logger log = LoggerFactory.getLogger(EDAMTaxonomyService.class); + + private static final String EDAM_OWL_IRI = + "https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/domains/edam.owl"; + + private final AtomicReference> labelMap = new AtomicReference<>(null); + + @PostConstruct + public void init() { + CompletableFuture.runAsync(this::loadOntology); + } + + public String resolveLabel(String uri) { + Map map = labelMap.get(); + if (map == null) return shortForm(uri); + return map.getOrDefault(uri, shortForm(uri)); + } + + public boolean isReady() { + return labelMap.get() != null; + } + + private void loadOntology() { + try { + log.info("Loading EDAM ontology for label resolution from {}", EDAM_OWL_IRI); + OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); + OWLOntologyLoaderConfiguration cfg = new OWLOntologyLoaderConfiguration() + .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); + manager.setOntologyLoaderConfiguration(cfg); + + OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(EDAM_OWL_IRI)); + OWLDataFactory factory = manager.getOWLDataFactory(); + + Map map = new HashMap<>(); + ontology.getClassesInSignature().forEach(cls -> { + String iri = cls.getIRI().toString(); + EntitySearcher.getAnnotations(cls, ontology, factory.getRDFSLabel()) + .findFirst() + .ifPresent(ann -> { + OWLAnnotationValue val = ann.getValue(); + if (val instanceof OWLLiteral lit) { + map.put(iri, lit.getLiteral()); + } + }); + }); + + labelMap.set(Collections.unmodifiableMap(map)); + log.info("EDAM ontology loaded: {} labels indexed.", map.size()); + } catch (Exception e) { + log.warn("Could not load EDAM ontology ({}). Falling back to short-form labels.", e.getMessage()); + labelMap.set(Collections.emptyMap()); + } + } + + static String shortForm(String uri) { + if (uri == null || uri.isBlank()) return ""; + int slash = uri.lastIndexOf('/'); + int hash = uri.lastIndexOf('#'); + return uri.substring(Math.max(slash, hash) + 1); + } +} From 247f2163075ce81ee5b8529d0b68e1583011080d Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Tue, 12 May 2026 21:40:31 +0200 Subject: [PATCH 05/18] feat: add CwlParser to extract DAG from CWL v1.2 workflows Parses a CWL v1.2 Workflow document using snakeyaml and produces a graph-optimised ParseResponse: tool nodes, input/output data nodes, directed data-flow edges, and EDAM I/O tuples for APE synthesis constraints. EDAM format URIs are resolved via an injected label resolver function. --- .../nl/esciencecenter/restape/CwlParser.java | 179 ++++++++++++++++++ 1 file changed, 179 insertions(+) create mode 100644 src/main/java/nl/esciencecenter/restape/CwlParser.java diff --git a/src/main/java/nl/esciencecenter/restape/CwlParser.java b/src/main/java/nl/esciencecenter/restape/CwlParser.java new file mode 100644 index 0000000..144e347 --- /dev/null +++ b/src/main/java/nl/esciencecenter/restape/CwlParser.java @@ -0,0 +1,179 @@ +package nl.esciencecenter.restape; + +import java.io.IOException; +import java.io.InputStream; +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.function.UnaryOperator; + +import org.yaml.snakeyaml.LoaderOptions; +import org.yaml.snakeyaml.Yaml; +import org.yaml.snakeyaml.constructor.SafeConstructor; + +import nl.esciencecenter.controller.dto.ApeTaxTuple; +import nl.esciencecenter.controller.dto.GraphEdge; +import nl.esciencecenter.controller.dto.GraphNode; +import nl.esciencecenter.controller.dto.ParseResponse; + +/** + * Transforms a CWL v1.2 Workflow document into the graph-optimised ParseResponse + * following the extraction algorithm defined in concept chapter 3.2. + */ +public class CwlParser { + + private CwlParser() {} + + /** + * Parses a CWL v1.2 Workflow from the given stream and returns the full DAG + * including input and output data nodes. + * + * @throws IllegalArgumentException if the document fails validation or is structurally incomplete + * @throws IOException if the stream cannot be read + */ + @SuppressWarnings("unchecked") + public static ParseResponse parse(InputStream inputStream, UnaryOperator labelResolver) throws IOException { + Yaml yaml = new Yaml(new SafeConstructor(new LoaderOptions())); + Map cwl; + try { + cwl = yaml.load(inputStream); + } catch (Exception e) { + throw new IllegalArgumentException("CWL file could not be parsed as YAML: " + e.getMessage()); + } + if (cwl == null) { + throw new IllegalArgumentException("CWL file is empty."); + } + + // Step 1 – Validate + validateMetadata(cwl); + + Map inputsSection = (Map) cwl.get("inputs"); + Map stepsSection = (Map) cwl.get("steps"); + Map outputsSection = (Map) cwl.get("outputs"); + + if (stepsSection == null || stepsSection.isEmpty()) { + throw new IllegalArgumentException("CWL Workflow must contain a non-empty 'steps' section."); + } + + List nodes = new ArrayList<>(); + List edges = new ArrayList<>(); + Set seen = new LinkedHashSet<>(); + + // Step 2a – Input nodes (dagre places them at the top in TB layout) + Set inputIds = new LinkedHashSet<>(); + if (inputsSection != null) { + for (Map.Entry entry : inputsSection.entrySet()) { + String id = entry.getKey(); + String label = formatLabel(entry.getValue(), id, labelResolver); + nodes.add(new GraphNode(id, label, "input")); + inputIds.add(id); + } + } + + // Step 2b – Tool nodes + Set stepIds = stepsSection.keySet(); + for (String stepId : stepIds) { + nodes.add(new GraphNode(stepId, toolLabel(stepId), "tool")); + } + + // Step 2c – Output nodes + remember which step feeds each output + Map outputSources = new LinkedHashMap<>(); + if (outputsSection != null) { + for (Map.Entry entry : outputsSection.entrySet()) { + String id = entry.getKey(); + String label = formatLabel(entry.getValue(), id, labelResolver); + nodes.add(new GraphNode(id, label, "output")); + + if (entry.getValue() instanceof Map def) { + String src = (String) ((Map) def).get("outputSource"); + if (src != null && src.contains("/")) { + String sourceStepId = src.substring(0, src.indexOf('/')); + if (stepIds.contains(sourceStepId)) { + outputSources.put(id, sourceStepId); + } + } + } + } + } + + // Step 3 – Edges + for (String targetId : stepIds) { + Object inField = ((Map) stepsSection.get(targetId)).get("in"); + if (!(inField instanceof Map rawIn)) continue; + + for (Object sourceRef : ((Map) rawIn).values()) { + if (!(sourceRef instanceof String ref)) continue; + + if (ref.contains("/")) { + // Tool → Tool + String sourceId = ref.substring(0, ref.indexOf('/')); + if (stepIds.contains(sourceId) && seen.add(sourceId + "->" + targetId)) { + edges.add(new GraphEdge(sourceId, targetId)); + } + } else if (inputIds.contains(ref) && seen.add(ref + "->" + targetId)) { + // Input → Tool + edges.add(new GraphEdge(ref, targetId)); + } + } + } + + // Tool → Output + outputSources.forEach((outputId, sourceId) -> + edges.add(new GraphEdge(sourceId, outputId))); + + // Step 4 – EDAM tuples for APE synthesis constraints + List inputs = extractTuples(inputsSection, labelResolver); + List outputs = extractTuples(outputsSection, labelResolver); + + return new ParseResponse(nodes, edges, inputs, outputs); + } + + private static void validateMetadata(Map cwl) { + String cwlClass = (String) cwl.get("class"); + String cwlVersion = (String) cwl.get("cwlVersion"); + if (!"Workflow".equals(cwlClass)) { + throw new IllegalArgumentException( + "CWL file must declare 'class: Workflow', found: " + cwlClass); + } + if (!"v1.2".equals(cwlVersion)) { + throw new IllegalArgumentException( + "CWL file must declare 'cwlVersion: v1.2', found: " + cwlVersion); + } + } + + /** Strips the APE-generated numeric suffix (e.g. MSFragger_01 → MSFragger). */ + private static String toolLabel(String stepId) { + return stepId.replaceAll("_\\d+$", ""); + } + + /** + * Resolves the EDAM format URI from an inputs/outputs entry to a human-readable label. + * Falls back to the port ID when no format is declared. + */ + @SuppressWarnings("unchecked") + private static String formatLabel(Object entry, String fallbackId, UnaryOperator resolver) { + if (entry instanceof Map def) { + String uri = (String) ((Map) def).get("format"); + if (uri != null && !uri.isBlank()) { + return resolver.apply(uri); + } + } + return fallbackId; + } + + @SuppressWarnings("unchecked") + private static List extractTuples(Map section, UnaryOperator resolver) { + List tuples = new ArrayList<>(); + if (section == null) return tuples; + for (Map.Entry entry : section.entrySet()) { + if (!(entry.getValue() instanceof Map def)) continue; + String uri = (String) ((Map) def).get("format"); + if (uri == null) continue; + tuples.add(new ApeTaxTuple(uri, resolver.apply(uri))); + } + return tuples; + } +} From 6eae0df32c2487320900f245820a241fdb3f51c3 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Tue, 12 May 2026 21:40:39 +0200 Subject: [PATCH 06/18] feat: add /alternatives/parse REST endpoint Accepts a CWL v1.2 workflow as multipart/form-data, delegates to CwlParser with EDAM label resolution, and returns a ParseResponse with nodes, edges, and I/O EDAM tuples for the frontend graph view. --- .../controller/AlternativesController.java | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 src/main/java/nl/esciencecenter/controller/AlternativesController.java diff --git a/src/main/java/nl/esciencecenter/controller/AlternativesController.java b/src/main/java/nl/esciencecenter/controller/AlternativesController.java new file mode 100644 index 0000000..9d39423 --- /dev/null +++ b/src/main/java/nl/esciencecenter/controller/AlternativesController.java @@ -0,0 +1,70 @@ +package nl.esciencecenter.controller; + +import java.io.IOException; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.ExceptionHandler; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RequestParam; +import org.springframework.web.bind.annotation.RestController; +import org.springframework.web.multipart.MultipartFile; + +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.media.Content; +import io.swagger.v3.oas.annotations.media.Schema; +import io.swagger.v3.oas.annotations.responses.ApiResponse; +import nl.esciencecenter.controller.dto.ParseResponse; +import nl.esciencecenter.restape.CwlParser; +import nl.esciencecenter.restape.EDAMTaxonomyService; + +@RestController +@RequestMapping("/alternatives") +public class AlternativesController { + + @Autowired + private EDAMTaxonomyService taxonomyService; + + /** + * Parses a CWL v1.2 workflow and returns its DAG representation plus + * workflow-level I/O terms for use as APE synthesis constraints (concept §2.3, §3.2). + */ + @PostMapping(value = "/parse", consumes = MediaType.MULTIPART_FORM_DATA_VALUE) + @Operation( + summary = "Parse a CWL workflow file", + description = "Accepts a CWL v1.2 Workflow file as multipart/form-data and returns a " + + "graph-optimised representation: tool nodes, data-flow edges, and the " + + "workflow-level input/output EDAM terms.", + tags = {"Alternatives"}, + responses = { + @ApiResponse(responseCode = "200", + description = "Successful operation. Graph representation of the CWL workflow is returned.", + content = @Content( + schema = @Schema(implementation = ParseResponse.class), + mediaType = MediaType.APPLICATION_JSON_VALUE)), + @ApiResponse(responseCode = "400", description = "Invalid or unsupported CWL file") + }) + public ResponseEntity parseCwl( + @RequestParam("cwl_file") MultipartFile cwlFile) throws IOException { + ParseResponse response = CwlParser.parse(cwlFile.getInputStream(), taxonomyService::resolveLabel); + return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(response); + } + + @ExceptionHandler(IllegalArgumentException.class) + public ResponseEntity handleIllegalArgument(IllegalArgumentException e) { + return ResponseEntity.badRequest().body(e.getMessage()); + } + + @ExceptionHandler(IOException.class) + public ResponseEntity handleIOException(IOException e) { + return ResponseEntity.badRequest().body(e.getMessage()); + } + + @ExceptionHandler(Exception.class) + public ResponseEntity handleAny(Exception e) { + return ResponseEntity.internalServerError() + .body(e.getClass().getSimpleName() + ": " + e.getMessage()); + } +} From dbd5a6f94d42ea010b6fab93c952a8bb262342e5 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 11:58:06 +0200 Subject: [PATCH 07/18] revert: restore Lombok annotations (target Java 17) Reverts a051be8. Lombok 1.18.30 works correctly with Java 17; the annotation-processing issues only affect JDK 21+. Project is now pinned to java.version=17 via spring-boot-starter-parent. --- .../externalAPIs/BioToolsRestClient.java | 11 ++-- .../externalAPIs/OpenEBenchRestClient.java | 11 ++-- .../models/benchmarks/Benchmark.java | 50 +++++++++++++------ .../models/benchmarks/BenchmarkBase.java | 43 +++++----------- .../benchmarks/WorkflowStepBenchmark.java | 44 +++++++++++----- .../restape/APEWorkflowMetadata.java | 15 ++---- .../esciencecenter/restape/RestApeUtils.java | 14 +++--- 7 files changed, 98 insertions(+), 90 deletions(-) diff --git a/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java b/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java index 965ad8f..45751fa 100644 --- a/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java +++ b/src/main/java/nl/esciencecenter/externalAPIs/BioToolsRestClient.java @@ -5,8 +5,9 @@ import org.json.JSONException; import org.json.JSONObject; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import lombok.AccessLevel; +import lombok.NoArgsConstructor; +import lombok.extern.slf4j.Slf4j; import okhttp3.Request; import okhttp3.Response; @@ -14,12 +15,10 @@ * The {@code BioToolsRestClient} class provides methods to retrieve and process tool metrics * provided by bio.tools API. */ +@Slf4j +@NoArgsConstructor(access = AccessLevel.PRIVATE) public class BioToolsRestClient { - private static final Logger log = LoggerFactory.getLogger(BioToolsRestClient.class); - - private BioToolsRestClient() {} - private static final okhttp3.OkHttpClient client = new okhttp3.OkHttpClient(); /** diff --git a/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java b/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java index cbc0143..9e51010 100644 --- a/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java +++ b/src/main/java/nl/esciencecenter/externalAPIs/OpenEBenchRestClient.java @@ -11,8 +11,9 @@ import org.json.JSONException; import org.json.JSONObject; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import lombok.AccessLevel; +import lombok.NoArgsConstructor; +import lombok.extern.slf4j.Slf4j; import nl.uu.cs.ape.utils.APEFiles; import okhttp3.OkHttpClient; import okhttp3.Request; @@ -22,12 +23,10 @@ * The {@code ToolBenchmarkingAPIs} class provides methods to retrieve and * process tool metrics provided by OpenEBench API. */ +@Slf4j +@NoArgsConstructor(access = AccessLevel.PRIVATE) public class OpenEBenchRestClient { - private static final Logger log = LoggerFactory.getLogger(OpenEBenchRestClient.class); - - private OpenEBenchRestClient() {} - private static final OkHttpClient client = new OkHttpClient(); /** diff --git a/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java b/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java index 896db5d..c1152ed 100644 --- a/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java +++ b/src/main/java/nl/esciencecenter/models/benchmarks/Benchmark.java @@ -5,34 +5,52 @@ import org.json.JSONArray; import org.json.JSONObject; +import lombok.Getter; +import lombok.NonNull; +import lombok.RequiredArgsConstructor; +import lombok.Setter; + /** * Abstract class {@link Benchmark} containing general information about a * benchmark, however, it must be implemented (e.g., as an bio.tools benchmark) * to be able to compute the benchmark value. */ + +@RequiredArgsConstructor public class Benchmark { + /** + * General information about the benchmark that is being computed. + */ + @NonNull + @Getter + @Setter private BenchmarkBase benchmarkInfo; + /** + * Value of the benchmark for the workflow. + */ + @Getter + @Setter private String value; + /** + * Desirability value (from 0 to 1.0) of the benchmark for the workflow. + */ + @Getter + @Setter private double desirabilityValue; + /** + * Benchmark for each tool/step in the workflow. + */ + @Getter + @Setter private List workflow; - public Benchmark(BenchmarkBase benchmarkInfo) { - this.benchmarkInfo = benchmarkInfo; - } - - public BenchmarkBase getBenchmarkInfo() { return benchmarkInfo; } - public void setBenchmarkInfo(BenchmarkBase benchmarkInfo) { this.benchmarkInfo = benchmarkInfo; } - - public String getValue() { return value; } - public void setValue(String value) { this.value = value; } - - public double getDesirabilityValue() { return desirabilityValue; } - public void setDesirabilityValue(double desirabilityValue) { this.desirabilityValue = desirabilityValue; } - - public List getWorkflow() { return workflow; } - public void setWorkflow(List workflow) { this.workflow = workflow; } - + /** + * Generate a JSON object containing the benchmark information. The content can + * be visualized using the Wokrkflomics web platform. + * + * @return JSON object containing the benchmark information. + */ public JSONObject toJSON() { JSONObject benchmarkJson = this.benchmarkInfo.getTitleJson(); diff --git a/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java b/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java index 1128ed4..b280d9f 100644 --- a/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java +++ b/src/main/java/nl/esciencecenter/models/benchmarks/BenchmarkBase.java @@ -2,47 +2,27 @@ import org.json.JSONObject; +import lombok.AllArgsConstructor; +import lombok.Data; +import lombok.NonNull; + +@Data +@AllArgsConstructor /** * Base information for a benchmark. */ public class BenchmarkBase { + @NonNull private String benchmarkTitle; + @NonNull private String benchmarkCategory; + @NonNull private String benchmarkDescription; + @NonNull private String unit; private String expectedField; private String expectedValue; - public BenchmarkBase() {} - - public BenchmarkBase(String benchmarkTitle, String benchmarkCategory, String benchmarkDescription, - String unit, String expectedField, String expectedValue) { - this.benchmarkTitle = benchmarkTitle; - this.benchmarkCategory = benchmarkCategory; - this.benchmarkDescription = benchmarkDescription; - this.unit = unit; - this.expectedField = expectedField; - this.expectedValue = expectedValue; - } - - public String getBenchmarkTitle() { return benchmarkTitle; } - public void setBenchmarkTitle(String benchmarkTitle) { this.benchmarkTitle = benchmarkTitle; } - - public String getBenchmarkCategory() { return benchmarkCategory; } - public void setBenchmarkCategory(String benchmarkCategory) { this.benchmarkCategory = benchmarkCategory; } - - public String getBenchmarkDescription() { return benchmarkDescription; } - public void setBenchmarkDescription(String benchmarkDescription) { this.benchmarkDescription = benchmarkDescription; } - - public String getUnit() { return unit; } - public void setUnit(String unit) { this.unit = unit; } - - public String getExpectedField() { return expectedField; } - public void setExpectedField(String expectedField) { this.expectedField = expectedField; } - - public String getExpectedValue() { return expectedValue; } - public void setExpectedValue(String expectedValue) { this.expectedValue = expectedValue; } - public JSONObject getTitleJson() { JSONObject benchmarkJson = new JSONObject(); benchmarkJson.put("title", benchmarkTitle); @@ -51,4 +31,5 @@ public JSONObject getTitleJson() { benchmarkJson.put("unit", unit); return benchmarkJson; } -} + +} \ No newline at end of file diff --git a/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java b/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java index cdb90bd..ae432da 100644 --- a/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java +++ b/src/main/java/nl/esciencecenter/models/benchmarks/WorkflowStepBenchmark.java @@ -1,31 +1,47 @@ package nl.esciencecenter.models.benchmarks; + import org.json.JSONObject; + +import lombok.Data; +import lombok.NoArgsConstructor; +import lombok.NonNull; + +@Data +@NoArgsConstructor /** * Class representing the design-time benchmarks for a workflow step (tool). */ public class WorkflowStepBenchmark { + /** + * Description of the benchmark value used in the visualization. + */ + @NonNull private String description; + /** + * Value of the benchmark for the workflow step (tool). + */ + @NonNull private String value; + /** + * Desirability value (from 0 to 1.0) of the benchmark for the workflow step + * (tool). + */ private double desirabilityValue; - public WorkflowStepBenchmark() {} - - public String getDescription() { return description; } - public void setDescription(String description) { this.description = description; } - - public String getValue() { return value; } - public void setValue(String value) { this.value = value; } - - public double getDesirabilityValue() { return desirabilityValue; } - public void setDesirabilityValue(double desirabilityValue) { this.desirabilityValue = desirabilityValue; } - @Override public String toString() { - return "{ label:" + description + ", value:" + value + ", desirability:" + desirabilityValue + "}"; + return "{ label:" + description + ", value:" + value + ", desirability:" + + desirabilityValue + "}"; } + /** + * Generate a JSON object containing the tool benchmark information. The content can + * be visualized using the Wokrkflomics web platform. + * + * @return JSON object containing the benchmark information. + */ public JSONObject toJSON() { JSONObject json = new JSONObject(); json.put("label", description); @@ -33,4 +49,6 @@ public JSONObject toJSON() { json.put("desirability", desirabilityValue); return json; } -} + + +} \ No newline at end of file diff --git a/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java b/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java index ba13855..240ae9d 100644 --- a/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java +++ b/src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java @@ -4,6 +4,8 @@ import com.fasterxml.jackson.annotation.JsonProperty; +import lombok.Getter; +import lombok.NoArgsConstructor; import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow; /** @@ -12,6 +14,8 @@ * including descriptive names, descriptions, the length of the solution, and benchmark information. * It provides functionality to convert these details into a JSONObject for serialization or further processing. */ +@Getter +@NoArgsConstructor public class APEWorkflowMetadata { @JsonProperty("workflow_name") @@ -33,17 +37,6 @@ public class APEWorkflowMetadata { @JsonProperty("benchmark_file") private String benchmarkFile; // Optional, indicates if benchmark data should be included. - public APEWorkflowMetadata() {} - - public String getWorkflowName() { return workflowName; } - public String getDescriptiveName() { return descriptiveName; } - public String getDescription() { return description; } - public int getWorkflowLength() { return workflowLength; } - public String getRunId() { return runId; } - public String getCwlName() { return cwlName; } - public String getFigureName() { return figureName; } - public String getBenchmarkFile() { return benchmarkFile; } - /** * Constructs a APEWorkflowMetadata instance from a given SolutionWorkflow and run configuration. * diff --git a/src/main/java/nl/esciencecenter/restape/RestApeUtils.java b/src/main/java/nl/esciencecenter/restape/RestApeUtils.java index 3d81125..69f7982 100644 --- a/src/main/java/nl/esciencecenter/restape/RestApeUtils.java +++ b/src/main/java/nl/esciencecenter/restape/RestApeUtils.java @@ -8,17 +8,17 @@ import org.json.JSONObject; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import lombok.NoArgsConstructor; +import lombok.extern.slf4j.Slf4j; +import lombok.AccessLevel; +import lombok.Getter; +@Slf4j +@NoArgsConstructor(access = AccessLevel.PRIVATE) public class RestApeUtils { - private static final Logger log = LoggerFactory.getLogger(RestApeUtils.class); + @Getter(lazy = true) private static final String solutionPath = getSolutionsDir(); - - private RestApeUtils() {} - - public static String getSolutionPath() { return solutionPath; } private static final String allSolutionsDirName = "apeOutputs"; private static final int hashLength = 10; private static final int currentTimestampLength = 13; From 0e262a00da270cb87d3fb803c89829b3e051a538 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 13:00:35 +0200 Subject: [PATCH 08/18] refactor: replace OWL-based taxonomy loading with static JSON lookup MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Remove EDAMTaxonomyService (OWL API, async loading, AtomicReference fallback). Bundle pre-built edam_labels.json (3471 entries, 227 KB) as classpath resource. EdamLabels loads it synchronously at startup via Jackson — no network access, no startup delay, no fallback labels. --- .../controller/AlternativesController.java | 6 +- .../restape/EDAMTaxonomyService.java | 94 - .../nl/esciencecenter/restape/EdamLabels.java | 52 + src/main/resources/edam_labels.json | 3473 +++++++++++++++++ 4 files changed, 3528 insertions(+), 97 deletions(-) delete mode 100644 src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java create mode 100644 src/main/java/nl/esciencecenter/restape/EdamLabels.java create mode 100644 src/main/resources/edam_labels.json diff --git a/src/main/java/nl/esciencecenter/controller/AlternativesController.java b/src/main/java/nl/esciencecenter/controller/AlternativesController.java index 9d39423..2ec7bc7 100644 --- a/src/main/java/nl/esciencecenter/controller/AlternativesController.java +++ b/src/main/java/nl/esciencecenter/controller/AlternativesController.java @@ -18,14 +18,14 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import nl.esciencecenter.controller.dto.ParseResponse; import nl.esciencecenter.restape.CwlParser; -import nl.esciencecenter.restape.EDAMTaxonomyService; +import nl.esciencecenter.restape.EdamLabels; @RestController @RequestMapping("/alternatives") public class AlternativesController { @Autowired - private EDAMTaxonomyService taxonomyService; + private EdamLabels edamLabels; /** * Parses a CWL v1.2 workflow and returns its DAG representation plus @@ -48,7 +48,7 @@ public class AlternativesController { }) public ResponseEntity parseCwl( @RequestParam("cwl_file") MultipartFile cwlFile) throws IOException { - ParseResponse response = CwlParser.parse(cwlFile.getInputStream(), taxonomyService::resolveLabel); + ParseResponse response = CwlParser.parse(cwlFile.getInputStream(), edamLabels::resolve); return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(response); } diff --git a/src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java b/src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java deleted file mode 100644 index ebcbf65..0000000 --- a/src/main/java/nl/esciencecenter/restape/EDAMTaxonomyService.java +++ /dev/null @@ -1,94 +0,0 @@ -package nl.esciencecenter.restape; - -import java.util.Collections; -import java.util.HashMap; -import java.util.Map; -import java.util.concurrent.CompletableFuture; -import java.util.concurrent.atomic.AtomicReference; - -import jakarta.annotation.PostConstruct; -import org.semanticweb.owlapi.apibinding.OWLManager; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.MissingImportHandlingStrategy; -import org.semanticweb.owlapi.model.OWLAnnotationValue; -import org.semanticweb.owlapi.model.OWLDataFactory; -import org.semanticweb.owlapi.model.OWLLiteral; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration; -import org.semanticweb.owlapi.model.OWLOntologyManager; -import org.semanticweb.owlapi.search.EntitySearcher; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.stereotype.Service; - -/** - * Loads the EDAM ontology once at startup and exposes O(1) URI → label resolution - * (concept §3.3: statisches Invertieren der Taxonomie). - * - * Label resolution falls back to the short-form EDAM ID while the ontology is - * still loading and whenever a URI is not found. - */ -@Service -public class EDAMTaxonomyService { - - private static final Logger log = LoggerFactory.getLogger(EDAMTaxonomyService.class); - - private static final String EDAM_OWL_IRI = - "https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/domains/edam.owl"; - - private final AtomicReference> labelMap = new AtomicReference<>(null); - - @PostConstruct - public void init() { - CompletableFuture.runAsync(this::loadOntology); - } - - public String resolveLabel(String uri) { - Map map = labelMap.get(); - if (map == null) return shortForm(uri); - return map.getOrDefault(uri, shortForm(uri)); - } - - public boolean isReady() { - return labelMap.get() != null; - } - - private void loadOntology() { - try { - log.info("Loading EDAM ontology for label resolution from {}", EDAM_OWL_IRI); - OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); - OWLOntologyLoaderConfiguration cfg = new OWLOntologyLoaderConfiguration() - .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); - manager.setOntologyLoaderConfiguration(cfg); - - OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(EDAM_OWL_IRI)); - OWLDataFactory factory = manager.getOWLDataFactory(); - - Map map = new HashMap<>(); - ontology.getClassesInSignature().forEach(cls -> { - String iri = cls.getIRI().toString(); - EntitySearcher.getAnnotations(cls, ontology, factory.getRDFSLabel()) - .findFirst() - .ifPresent(ann -> { - OWLAnnotationValue val = ann.getValue(); - if (val instanceof OWLLiteral lit) { - map.put(iri, lit.getLiteral()); - } - }); - }); - - labelMap.set(Collections.unmodifiableMap(map)); - log.info("EDAM ontology loaded: {} labels indexed.", map.size()); - } catch (Exception e) { - log.warn("Could not load EDAM ontology ({}). Falling back to short-form labels.", e.getMessage()); - labelMap.set(Collections.emptyMap()); - } - } - - static String shortForm(String uri) { - if (uri == null || uri.isBlank()) return ""; - int slash = uri.lastIndexOf('/'); - int hash = uri.lastIndexOf('#'); - return uri.substring(Math.max(slash, hash) + 1); - } -} diff --git a/src/main/java/nl/esciencecenter/restape/EdamLabels.java b/src/main/java/nl/esciencecenter/restape/EdamLabels.java new file mode 100644 index 0000000..fcbe180 --- /dev/null +++ b/src/main/java/nl/esciencecenter/restape/EdamLabels.java @@ -0,0 +1,52 @@ +package nl.esciencecenter.restape; + +import java.io.IOException; +import java.io.InputStream; +import java.util.Collections; +import java.util.Map; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Component; + +/** + * Resolves EDAM URIs to human-readable labels using a pre-built static mapping + * bundled as a classpath resource (edam_labels.json). + */ +@Component +public class EdamLabels { + + private static final Logger log = LoggerFactory.getLogger(EdamLabels.class); + private static final String RESOURCE = "/edam_labels.json"; + + private final Map labels; + + public EdamLabels() { + Map loaded = Collections.emptyMap(); + try (InputStream is = EdamLabels.class.getResourceAsStream(RESOURCE)) { + if (is == null) { + log.warn("edam_labels.json not found on classpath — URIs will be shown as short-form IDs"); + } else { + loaded = new ObjectMapper().readValue(is, new TypeReference<>() {}); + log.info("EDAM labels loaded: {} entries", loaded.size()); + } + } catch (IOException e) { + log.warn("Failed to load edam_labels.json: {}", e.getMessage()); + } + this.labels = Collections.unmodifiableMap(loaded); + } + + public String resolve(String uri) { + if (uri == null || uri.isBlank()) return ""; + return labels.getOrDefault(uri, shortForm(uri)); + } + + static String shortForm(String uri) { + if (uri == null || uri.isBlank()) return ""; + int slash = uri.lastIndexOf('/'); + int hash = uri.lastIndexOf('#'); + return uri.substring(Math.max(slash, hash) + 1); + } +} diff --git a/src/main/resources/edam_labels.json b/src/main/resources/edam_labels.json new file mode 100644 index 0000000..3ed0b2a --- /dev/null +++ b/src/main/resources/edam_labels.json @@ -0,0 +1,3473 @@ +{ + "http://edamontology.org/data_0005": "Resource type", + "http://edamontology.org/data_0006": "Data", + "http://edamontology.org/data_0007": "Tool", + "http://edamontology.org/data_0581": "Database", + "http://edamontology.org/data_0582": "Ontology", + "http://edamontology.org/data_0583": "Directory metadata", + "http://edamontology.org/data_0831": "MeSH vocabulary", + "http://edamontology.org/data_0832": "HGNC vocabulary", + "http://edamontology.org/data_0835": "UMLS vocabulary", + "http://edamontology.org/data_0842": "Identifier", + "http://edamontology.org/data_0843": "Database entry", + "http://edamontology.org/data_0844": "Molecular mass", + "http://edamontology.org/data_0845": "Molecular charge", + "http://edamontology.org/data_0846": "Chemical formula", + "http://edamontology.org/data_0847": "QSAR descriptor", + "http://edamontology.org/data_0848": "Raw sequence", + "http://edamontology.org/data_0849": "Sequence record", + "http://edamontology.org/data_0850": "Sequence set", + "http://edamontology.org/data_0851": "Sequence mask character", + "http://edamontology.org/data_0852": "Sequence mask type", + "http://edamontology.org/data_0853": "DNA sense specification", + "http://edamontology.org/data_0854": "Sequence length specification", + "http://edamontology.org/data_0855": "Sequence metadata", + "http://edamontology.org/data_0856": "Sequence feature source", + "http://edamontology.org/data_0857": "Sequence search results", + "http://edamontology.org/data_0858": "Sequence signature matches", + "http://edamontology.org/data_0859": "Sequence signature model", + "http://edamontology.org/data_0860": "Sequence signature data", + "http://edamontology.org/data_0861": "Sequence alignment (words)", + "http://edamontology.org/data_0862": "Dotplot", + "http://edamontology.org/data_0863": "Sequence alignment", + "http://edamontology.org/data_0864": "Sequence alignment parameter", + "http://edamontology.org/data_0865": "Sequence similarity score", + "http://edamontology.org/data_0866": "Sequence alignment metadata", + "http://edamontology.org/data_0867": "Sequence alignment report", + "http://edamontology.org/data_0868": "Profile-profile alignment", + "http://edamontology.org/data_0869": "Sequence-profile alignment", + "http://edamontology.org/data_0870": "Sequence distance matrix", + "http://edamontology.org/data_0871": "Phylogenetic character data", + "http://edamontology.org/data_0872": "Phylogenetic tree", + "http://edamontology.org/data_0874": "Comparison matrix", + "http://edamontology.org/data_0875": "Protein topology", + "http://edamontology.org/data_0876": "Protein features report (secondary structure)", + "http://edamontology.org/data_0877": "Protein features report (super-secondary)", + "http://edamontology.org/data_0878": "Protein secondary structure alignment", + "http://edamontology.org/data_0879": "Secondary structure alignment metadata (protein)", + "http://edamontology.org/data_0880": "RNA secondary structure", + "http://edamontology.org/data_0881": "RNA secondary structure alignment", + "http://edamontology.org/data_0882": "Secondary structure alignment metadata (RNA)", + "http://edamontology.org/data_0883": "Structure", + "http://edamontology.org/data_0884": "Tertiary structure record", + "http://edamontology.org/data_0885": "Structure database search results", + "http://edamontology.org/data_0886": "Structure alignment", + "http://edamontology.org/data_0887": "Structure alignment report", + "http://edamontology.org/data_0888": "Structure similarity score", + "http://edamontology.org/data_0889": "Structural profile", + "http://edamontology.org/data_0890": "Structural (3D) profile alignment", + "http://edamontology.org/data_0891": "Sequence-3D profile alignment", + "http://edamontology.org/data_0892": "Protein sequence-structure scoring matrix", + "http://edamontology.org/data_0893": "Sequence-structure alignment", + "http://edamontology.org/data_0894": "Amino acid annotation", + "http://edamontology.org/data_0895": "Peptide annotation", + "http://edamontology.org/data_0896": "Protein report", + "http://edamontology.org/data_0897": "Protein property", + "http://edamontology.org/data_0899": "Protein structural motifs and surfaces", + "http://edamontology.org/data_0900": "Protein domain classification", + "http://edamontology.org/data_0901": "Protein features report (domains)", + "http://edamontology.org/data_0902": "Protein architecture report", + "http://edamontology.org/data_0903": "Protein folding report", + "http://edamontology.org/data_0904": "Protein features (mutation)", + "http://edamontology.org/data_0905": "Protein interaction raw data", + "http://edamontology.org/data_0906": "Protein interaction data", + "http://edamontology.org/data_0907": "Protein family report", + "http://edamontology.org/data_0909": "Vmax", + "http://edamontology.org/data_0910": "Km", + "http://edamontology.org/data_0911": "Nucleotide base annotation", + "http://edamontology.org/data_0912": "Nucleic acid property", + "http://edamontology.org/data_0914": "Codon usage data", + "http://edamontology.org/data_0916": "Gene report", + "http://edamontology.org/data_0917": "Gene classification", + "http://edamontology.org/data_0918": "DNA variation", + "http://edamontology.org/data_0919": "Chromosome report", + "http://edamontology.org/data_0920": "Genotype/phenotype report", + "http://edamontology.org/data_0923": "PCR experiment report", + "http://edamontology.org/data_0924": "Sequence trace", + "http://edamontology.org/data_0925": "Sequence assembly", + "http://edamontology.org/data_0926": "RH scores", + "http://edamontology.org/data_0927": "Genetic linkage report", + "http://edamontology.org/data_0928": "Gene expression profile", + "http://edamontology.org/data_0931": "Microarray experiment report", + "http://edamontology.org/data_0932": "Oligonucleotide probe data", + "http://edamontology.org/data_0933": "SAGE experimental data", + "http://edamontology.org/data_0934": "MPSS experimental data", + "http://edamontology.org/data_0935": "SBS experimental data", + "http://edamontology.org/data_0936": "Sequence tag profile (with gene assignment)", + "http://edamontology.org/data_0937": "Electron density map", + "http://edamontology.org/data_0938": "Raw NMR data", + "http://edamontology.org/data_0939": "CD spectra", + "http://edamontology.org/data_0940": "Volume map", + "http://edamontology.org/data_0941": "Electron microscopy model", + "http://edamontology.org/data_0942": "2D PAGE image", + "http://edamontology.org/data_0943": "Mass spectrum", + "http://edamontology.org/data_0944": "Peptide mass fingerprint", + "http://edamontology.org/data_0945": "Peptide identification", + "http://edamontology.org/data_0946": "Pathway or network annotation", + "http://edamontology.org/data_0947": "Biological pathway map", + "http://edamontology.org/data_0948": "Data resource definition", + "http://edamontology.org/data_0949": "Workflow metadata", + "http://edamontology.org/data_0950": "Mathematical model", + "http://edamontology.org/data_0951": "Statistical estimate score", + "http://edamontology.org/data_0952": "EMBOSS database resource definition", + "http://edamontology.org/data_0953": "Version information", + "http://edamontology.org/data_0954": "Database cross-mapping", + "http://edamontology.org/data_0955": "Data index", + "http://edamontology.org/data_0956": "Data index report", + "http://edamontology.org/data_0957": "Database metadata", + "http://edamontology.org/data_0958": "Tool metadata", + "http://edamontology.org/data_0959": "Job metadata", + "http://edamontology.org/data_0960": "User metadata", + "http://edamontology.org/data_0962": "Small molecule report", + "http://edamontology.org/data_0963": "Cell line report", + "http://edamontology.org/data_0964": "Scent annotation", + "http://edamontology.org/data_0966": "Ontology term", + "http://edamontology.org/data_0967": "Ontology concept data", + "http://edamontology.org/data_0968": "Keyword", + "http://edamontology.org/data_0970": "Citation", + "http://edamontology.org/data_0971": "Article", + "http://edamontology.org/data_0972": "Text mining report", + "http://edamontology.org/data_0974": "Entity identifier", + "http://edamontology.org/data_0975": "Data resource identifier", + "http://edamontology.org/data_0976": "Identifier (by type of data)", + "http://edamontology.org/data_0977": "Tool identifier", + "http://edamontology.org/data_0978": "Discrete entity identifier", + "http://edamontology.org/data_0979": "Entity feature identifier", + "http://edamontology.org/data_0980": "Entity collection identifier", + "http://edamontology.org/data_0981": "Phenomenon identifier", + "http://edamontology.org/data_0982": "Molecule identifier", + "http://edamontology.org/data_0983": "Atom ID", + "http://edamontology.org/data_0984": "Molecule name", + "http://edamontology.org/data_0985": "Molecule type", + "http://edamontology.org/data_0986": "Chemical identifier", + "http://edamontology.org/data_0987": "Chromosome name", + "http://edamontology.org/data_0988": "Peptide identifier", + "http://edamontology.org/data_0989": "Protein identifier", + "http://edamontology.org/data_0990": "Compound name", + "http://edamontology.org/data_0991": "Chemical registry number", + "http://edamontology.org/data_0992": "Ligand identifier", + "http://edamontology.org/data_0993": "Drug identifier", + "http://edamontology.org/data_0994": "Amino acid identifier", + "http://edamontology.org/data_0995": "Nucleotide identifier", + "http://edamontology.org/data_0996": "Monosaccharide identifier", + "http://edamontology.org/data_0997": "Chemical name (ChEBI)", + "http://edamontology.org/data_0998": "Chemical name (IUPAC)", + "http://edamontology.org/data_0999": "Chemical name (INN)", + "http://edamontology.org/data_1000": "Chemical name (brand)", + "http://edamontology.org/data_1001": "Chemical name (synonymous)", + "http://edamontology.org/data_1002": "CAS number", + "http://edamontology.org/data_1003": "Chemical registry number (Beilstein)", + "http://edamontology.org/data_1004": "Chemical registry number (Gmelin)", + "http://edamontology.org/data_1005": "HET group name", + "http://edamontology.org/data_1006": "Amino acid name", + "http://edamontology.org/data_1007": "Nucleotide code", + "http://edamontology.org/data_1008": "Polypeptide chain ID", + "http://edamontology.org/data_1009": "Protein name", + "http://edamontology.org/data_1010": "Enzyme identifier", + "http://edamontology.org/data_1011": "EC number", + "http://edamontology.org/data_1012": "Enzyme name", + "http://edamontology.org/data_1013": "Restriction enzyme name", + "http://edamontology.org/data_1014": "Sequence position specification", + "http://edamontology.org/data_1015": "Sequence feature ID", + "http://edamontology.org/data_1016": "Sequence position", + "http://edamontology.org/data_1017": "Sequence range", + "http://edamontology.org/data_1018": "Nucleic acid feature identifier", + "http://edamontology.org/data_1019": "Protein feature identifier", + "http://edamontology.org/data_1020": "Sequence feature key", + "http://edamontology.org/data_1021": "Sequence feature qualifier", + "http://edamontology.org/data_1022": "Sequence feature label", + "http://edamontology.org/data_1023": "EMBOSS Uniform Feature Object", + "http://edamontology.org/data_1024": "Codon name", + "http://edamontology.org/data_1025": "Gene identifier", + "http://edamontology.org/data_1026": "Gene symbol", + "http://edamontology.org/data_1027": "Gene ID (NCBI)", + "http://edamontology.org/data_1028": "Gene identifier (NCBI RefSeq)", + "http://edamontology.org/data_1029": "Gene identifier (NCBI UniGene)", + "http://edamontology.org/data_1030": "Gene identifier (Entrez)", + "http://edamontology.org/data_1031": "Gene ID (CGD)", + "http://edamontology.org/data_1032": "Gene ID (DictyBase)", + "http://edamontology.org/data_1033": "Ensembl gene ID", + "http://edamontology.org/data_1034": "Gene ID (SGD)", + "http://edamontology.org/data_1035": "Gene ID (GeneDB)", + "http://edamontology.org/data_1036": "TIGR identifier", + "http://edamontology.org/data_1037": "TAIR accession (gene)", + "http://edamontology.org/data_1038": "Protein domain ID", + "http://edamontology.org/data_1039": "SCOP domain identifier", + "http://edamontology.org/data_1040": "CATH domain ID", + "http://edamontology.org/data_1041": "SCOP concise classification string (sccs)", + "http://edamontology.org/data_1042": "SCOP sunid", + "http://edamontology.org/data_1043": "CATH node ID", + "http://edamontology.org/data_1044": "Kingdom name", + "http://edamontology.org/data_1045": "Species name", + "http://edamontology.org/data_1046": "Strain name", + "http://edamontology.org/data_1047": "URI", + "http://edamontology.org/data_1048": "Database ID", + "http://edamontology.org/data_1049": "Directory name", + "http://edamontology.org/data_1050": "File name", + "http://edamontology.org/data_1051": "Ontology name", + "http://edamontology.org/data_1052": "URL", + "http://edamontology.org/data_1053": "URN", + "http://edamontology.org/data_1055": "LSID", + "http://edamontology.org/data_1056": "Database name", + "http://edamontology.org/data_1057": "Sequence database name", + "http://edamontology.org/data_1058": "Enumerated file name", + "http://edamontology.org/data_1059": "File name extension", + "http://edamontology.org/data_1060": "File base name", + "http://edamontology.org/data_1061": "QSAR descriptor name", + "http://edamontology.org/data_1062": "Database entry identifier", + "http://edamontology.org/data_1063": "Sequence identifier", + "http://edamontology.org/data_1064": "Sequence set ID", + "http://edamontology.org/data_1065": "Sequence signature identifier", + "http://edamontology.org/data_1066": "Sequence alignment ID", + "http://edamontology.org/data_1067": "Phylogenetic distance matrix identifier", + "http://edamontology.org/data_1068": "Phylogenetic tree ID", + "http://edamontology.org/data_1069": "Comparison matrix identifier", + "http://edamontology.org/data_1070": "Structure ID", + "http://edamontology.org/data_1071": "Structural (3D) profile ID", + "http://edamontology.org/data_1072": "Structure alignment ID", + "http://edamontology.org/data_1073": "Amino acid index ID", + "http://edamontology.org/data_1074": "Protein interaction ID", + "http://edamontology.org/data_1075": "Protein family identifier", + "http://edamontology.org/data_1076": "Codon usage table name", + "http://edamontology.org/data_1077": "Transcription factor identifier", + "http://edamontology.org/data_1078": "Experiment annotation ID", + "http://edamontology.org/data_1079": "Electron microscopy model ID", + "http://edamontology.org/data_1080": "Gene expression report ID", + "http://edamontology.org/data_1081": "Genotype and phenotype annotation ID", + "http://edamontology.org/data_1082": "Pathway or network identifier", + "http://edamontology.org/data_1083": "Workflow ID", + "http://edamontology.org/data_1084": "Data resource definition ID", + "http://edamontology.org/data_1085": "Biological model ID", + "http://edamontology.org/data_1086": "Compound identifier", + "http://edamontology.org/data_1087": "Ontology concept ID", + "http://edamontology.org/data_1088": "Article ID", + "http://edamontology.org/data_1089": "FlyBase ID", + "http://edamontology.org/data_1091": "WormBase name", + "http://edamontology.org/data_1092": "WormBase class", + "http://edamontology.org/data_1093": "Sequence accession", + "http://edamontology.org/data_1094": "Sequence type", + "http://edamontology.org/data_1095": "EMBOSS Uniform Sequence Address", + "http://edamontology.org/data_1096": "Sequence accession (protein)", + "http://edamontology.org/data_1097": "Sequence accession (nucleic acid)", + "http://edamontology.org/data_1098": "RefSeq accession", + "http://edamontology.org/data_1099": "UniProt accession (extended)", + "http://edamontology.org/data_1100": "PIR identifier", + "http://edamontology.org/data_1101": "TREMBL accession", + "http://edamontology.org/data_1102": "Gramene primary identifier", + "http://edamontology.org/data_1103": "EMBL/GenBank/DDBJ ID", + "http://edamontology.org/data_1104": "Sequence cluster ID (UniGene)", + "http://edamontology.org/data_1105": "dbEST accession", + "http://edamontology.org/data_1106": "dbSNP ID", + "http://edamontology.org/data_1110": "EMBOSS sequence type", + "http://edamontology.org/data_1111": "EMBOSS listfile", + "http://edamontology.org/data_1112": "Sequence cluster ID", + "http://edamontology.org/data_1113": "Sequence cluster ID (COG)", + "http://edamontology.org/data_1114": "Sequence motif identifier", + "http://edamontology.org/data_1115": "Sequence profile ID", + "http://edamontology.org/data_1116": "ELM ID", + "http://edamontology.org/data_1117": "Prosite accession number", + "http://edamontology.org/data_1118": "HMMER hidden Markov model ID", + "http://edamontology.org/data_1119": "JASPAR profile ID", + "http://edamontology.org/data_1120": "Sequence alignment type", + "http://edamontology.org/data_1121": "BLAST sequence alignment type", + "http://edamontology.org/data_1122": "Phylogenetic tree type", + "http://edamontology.org/data_1123": "TreeBASE study accession number", + "http://edamontology.org/data_1124": "TreeFam accession number", + "http://edamontology.org/data_1125": "Comparison matrix type", + "http://edamontology.org/data_1126": "Comparison matrix name", + "http://edamontology.org/data_1127": "PDB ID", + "http://edamontology.org/data_1128": "AAindex ID", + "http://edamontology.org/data_1129": "BIND accession number", + "http://edamontology.org/data_1130": "IntAct accession number", + "http://edamontology.org/data_1131": "Protein family name", + "http://edamontology.org/data_1132": "InterPro entry name", + "http://edamontology.org/data_1133": "InterPro accession", + "http://edamontology.org/data_1134": "InterPro secondary accession", + "http://edamontology.org/data_1135": "Gene3D ID", + "http://edamontology.org/data_1136": "PIRSF ID", + "http://edamontology.org/data_1137": "PRINTS code", + "http://edamontology.org/data_1138": "Pfam accession number", + "http://edamontology.org/data_1139": "SMART accession number", + "http://edamontology.org/data_1140": "Superfamily hidden Markov model number", + "http://edamontology.org/data_1141": "TIGRFam ID", + "http://edamontology.org/data_1142": "ProDom accession number", + "http://edamontology.org/data_1143": "TRANSFAC accession number", + "http://edamontology.org/data_1144": "ArrayExpress accession number", + "http://edamontology.org/data_1145": "PRIDE experiment accession number", + "http://edamontology.org/data_1146": "EMDB ID", + "http://edamontology.org/data_1147": "GEO accession number", + "http://edamontology.org/data_1148": "GermOnline ID", + "http://edamontology.org/data_1149": "EMAGE ID", + "http://edamontology.org/data_1150": "Disease ID", + "http://edamontology.org/data_1151": "HGVbase ID", + "http://edamontology.org/data_1152": "HIVDB identifier", + "http://edamontology.org/data_1153": "OMIM ID", + "http://edamontology.org/data_1154": "KEGG object identifier", + "http://edamontology.org/data_1155": "Pathway ID (reactome)", + "http://edamontology.org/data_1156": "Pathway ID (aMAZE)", + "http://edamontology.org/data_1157": "Pathway ID (BioCyc)", + "http://edamontology.org/data_1158": "Pathway ID (INOH)", + "http://edamontology.org/data_1159": "Pathway ID (PATIKA)", + "http://edamontology.org/data_1160": "Pathway ID (CPDB)", + "http://edamontology.org/data_1161": "Pathway ID (Panther)", + "http://edamontology.org/data_1162": "MIRIAM identifier", + "http://edamontology.org/data_1163": "MIRIAM data type name", + "http://edamontology.org/data_1164": "MIRIAM URI", + "http://edamontology.org/data_1165": "MIRIAM data type primary name", + "http://edamontology.org/data_1166": "MIRIAM data type synonymous name", + "http://edamontology.org/data_1167": "Taverna workflow ID", + "http://edamontology.org/data_1170": "Biological model name", + "http://edamontology.org/data_1171": "BioModel ID", + "http://edamontology.org/data_1172": "PubChem CID", + "http://edamontology.org/data_1173": "ChemSpider ID", + "http://edamontology.org/data_1174": "ChEBI ID", + "http://edamontology.org/data_1175": "BioPax concept ID", + "http://edamontology.org/data_1176": "GO concept ID", + "http://edamontology.org/data_1177": "MeSH concept ID", + "http://edamontology.org/data_1178": "HGNC concept ID", + "http://edamontology.org/data_1179": "NCBI taxonomy ID", + "http://edamontology.org/data_1180": "Plant Ontology concept ID", + "http://edamontology.org/data_1181": "UMLS concept ID", + "http://edamontology.org/data_1182": "FMA concept ID", + "http://edamontology.org/data_1183": "EMAP concept ID", + "http://edamontology.org/data_1184": "ChEBI concept ID", + "http://edamontology.org/data_1185": "MGED concept ID", + "http://edamontology.org/data_1186": "myGrid concept ID", + "http://edamontology.org/data_1187": "PubMed ID", + "http://edamontology.org/data_1188": "DOI", + "http://edamontology.org/data_1189": "Medline UI", + "http://edamontology.org/data_1190": "Tool name", + "http://edamontology.org/data_1191": "Tool name (signature)", + "http://edamontology.org/data_1192": "Tool name (BLAST)", + "http://edamontology.org/data_1193": "Tool name (FASTA)", + "http://edamontology.org/data_1194": "Tool name (EMBOSS)", + "http://edamontology.org/data_1195": "Tool name (EMBASSY package)", + "http://edamontology.org/data_1201": "QSAR descriptor (constitutional)", + "http://edamontology.org/data_1202": "QSAR descriptor (electronic)", + "http://edamontology.org/data_1203": "QSAR descriptor (geometrical)", + "http://edamontology.org/data_1204": "QSAR descriptor (topological)", + "http://edamontology.org/data_1205": "QSAR descriptor (molecular)", + "http://edamontology.org/data_1233": "Sequence set (protein)", + "http://edamontology.org/data_1234": "Sequence set (nucleic acid)", + "http://edamontology.org/data_1235": "Sequence cluster", + "http://edamontology.org/data_1236": "Psiblast checkpoint file", + "http://edamontology.org/data_1237": "HMMER synthetic sequences set", + "http://edamontology.org/data_1238": "Proteolytic digest", + "http://edamontology.org/data_1239": "Restriction digest", + "http://edamontology.org/data_1240": "PCR primers", + "http://edamontology.org/data_1241": "vectorstrip cloning vector definition file", + "http://edamontology.org/data_1242": "Primer3 internal oligo mishybridizing library", + "http://edamontology.org/data_1243": "Primer3 mispriming library file", + "http://edamontology.org/data_1244": "primersearch primer pairs sequence record", + "http://edamontology.org/data_1245": "Sequence cluster (protein)", + "http://edamontology.org/data_1246": "Sequence cluster (nucleic acid)", + "http://edamontology.org/data_1249": "Sequence length", + "http://edamontology.org/data_1250": "Word size", + "http://edamontology.org/data_1251": "Window size", + "http://edamontology.org/data_1252": "Sequence length range", + "http://edamontology.org/data_1253": "Sequence information report", + "http://edamontology.org/data_1254": "Sequence property", + "http://edamontology.org/data_1255": "Sequence features", + "http://edamontology.org/data_1256": "Sequence features (comparative)", + "http://edamontology.org/data_1257": "Sequence property (protein)", + "http://edamontology.org/data_1258": "Sequence property (nucleic acid)", + "http://edamontology.org/data_1259": "Sequence complexity report", + "http://edamontology.org/data_1260": "Sequence ambiguity report", + "http://edamontology.org/data_1261": "Sequence composition report", + "http://edamontology.org/data_1262": "Peptide molecular weight hits", + "http://edamontology.org/data_1263": "Base position variability plot", + "http://edamontology.org/data_1264": "Sequence composition table", + "http://edamontology.org/data_1265": "Base frequencies table", + "http://edamontology.org/data_1266": "Base word frequencies table", + "http://edamontology.org/data_1267": "Amino acid frequencies table", + "http://edamontology.org/data_1268": "Amino acid word frequencies table", + "http://edamontology.org/data_1269": "DAS sequence feature annotation", + "http://edamontology.org/data_1270": "Feature table", + "http://edamontology.org/data_1274": "Map", + "http://edamontology.org/data_1276": "Nucleic acid features", + "http://edamontology.org/data_1277": "Protein features", + "http://edamontology.org/data_1278": "Genetic map", + "http://edamontology.org/data_1279": "Sequence map", + "http://edamontology.org/data_1280": "Physical map", + "http://edamontology.org/data_1281": "Sequence signature map", + "http://edamontology.org/data_1283": "Cytogenetic map", + "http://edamontology.org/data_1284": "DNA transduction map", + "http://edamontology.org/data_1285": "Gene map", + "http://edamontology.org/data_1286": "Plasmid map", + "http://edamontology.org/data_1288": "Genome map", + "http://edamontology.org/data_1289": "Restriction map", + "http://edamontology.org/data_1290": "InterPro compact match image", + "http://edamontology.org/data_1291": "InterPro detailed match image", + "http://edamontology.org/data_1292": "InterPro architecture image", + "http://edamontology.org/data_1293": "SMART protein schematic", + "http://edamontology.org/data_1294": "GlobPlot domain image", + "http://edamontology.org/data_1298": "Sequence motif matches", + "http://edamontology.org/data_1299": "Sequence features (repeats)", + "http://edamontology.org/data_1300": "Gene and transcript structure (report)", + "http://edamontology.org/data_1301": "Mobile genetic elements", + "http://edamontology.org/data_1303": "Nucleic acid features (quadruplexes)", + "http://edamontology.org/data_1306": "Nucleosome exclusion sequences", + "http://edamontology.org/data_1309": "Gene features (exonic splicing enhancer)", + "http://edamontology.org/data_1310": "Nucleic acid features (microRNA)", + "http://edamontology.org/data_1313": "Coding region", + "http://edamontology.org/data_1314": "Gene features (SECIS element)", + "http://edamontology.org/data_1315": "Transcription factor binding sites", + "http://edamontology.org/data_1321": "Protein features (sites)", + "http://edamontology.org/data_1322": "Protein features report (signal peptides)", + "http://edamontology.org/data_1323": "Protein features report (cleavage sites)", + "http://edamontology.org/data_1324": "Protein features (post-translation modifications)", + "http://edamontology.org/data_1325": "Protein features report (active sites)", + "http://edamontology.org/data_1326": "Protein features report (binding sites)", + "http://edamontology.org/data_1327": "Protein features (epitopes)", + "http://edamontology.org/data_1328": "Protein features report (nucleic acid binding sites)", + "http://edamontology.org/data_1329": "MHC Class I epitopes report", + "http://edamontology.org/data_1330": "MHC Class II epitopes report", + "http://edamontology.org/data_1331": "Protein features (PEST sites)", + "http://edamontology.org/data_1338": "Sequence database hits scores list", + "http://edamontology.org/data_1339": "Sequence database hits alignments list", + "http://edamontology.org/data_1340": "Sequence database hits evaluation data", + "http://edamontology.org/data_1344": "MEME motif alphabet", + "http://edamontology.org/data_1345": "MEME background frequencies file", + "http://edamontology.org/data_1346": "MEME motifs directive file", + "http://edamontology.org/data_1347": "Dirichlet distribution", + "http://edamontology.org/data_1348": "HMM emission and transition counts", + "http://edamontology.org/data_1352": "Regular expression", + "http://edamontology.org/data_1353": "Sequence motif", + "http://edamontology.org/data_1354": "Sequence profile", + "http://edamontology.org/data_1355": "Protein signature", + "http://edamontology.org/data_1358": "Prosite nucleotide pattern", + "http://edamontology.org/data_1359": "Prosite protein pattern", + "http://edamontology.org/data_1361": "Position frequency matrix", + "http://edamontology.org/data_1362": "Position weight matrix", + "http://edamontology.org/data_1363": "Information content matrix", + "http://edamontology.org/data_1364": "Hidden Markov model", + "http://edamontology.org/data_1365": "Fingerprint", + "http://edamontology.org/data_1368": "Domainatrix signature", + "http://edamontology.org/data_1371": "HMMER NULL hidden Markov model", + "http://edamontology.org/data_1372": "Protein family signature", + "http://edamontology.org/data_1373": "Protein domain signature", + "http://edamontology.org/data_1374": "Protein region signature", + "http://edamontology.org/data_1375": "Protein repeat signature", + "http://edamontology.org/data_1376": "Protein site signature", + "http://edamontology.org/data_1377": "Protein conserved site signature", + "http://edamontology.org/data_1378": "Protein active site signature", + "http://edamontology.org/data_1379": "Protein binding site signature", + "http://edamontology.org/data_1380": "Protein post-translational modification signature", + "http://edamontology.org/data_1381": "Pair sequence alignment", + "http://edamontology.org/data_1382": "Sequence alignment (multiple)", + "http://edamontology.org/data_1383": "Nucleic acid sequence alignment", + "http://edamontology.org/data_1384": "Protein sequence alignment", + "http://edamontology.org/data_1385": "Hybrid sequence alignment", + "http://edamontology.org/data_1386": "Sequence alignment (nucleic acid pair)", + "http://edamontology.org/data_1387": "Sequence alignment (protein pair)", + "http://edamontology.org/data_1388": "Hybrid sequence alignment (pair)", + "http://edamontology.org/data_1389": "Multiple nucleotide sequence alignment", + "http://edamontology.org/data_1390": "Multiple protein sequence alignment", + "http://edamontology.org/data_1394": "Alignment score or penalty", + "http://edamontology.org/data_1395": "Score end gaps control", + "http://edamontology.org/data_1396": "Aligned sequence order", + "http://edamontology.org/data_1397": "Gap opening penalty", + "http://edamontology.org/data_1398": "Gap extension penalty", + "http://edamontology.org/data_1399": "Gap separation penalty", + "http://edamontology.org/data_1400": "Terminal gap penalty", + "http://edamontology.org/data_1401": "Match reward score", + "http://edamontology.org/data_1402": "Mismatch penalty score", + "http://edamontology.org/data_1403": "Drop off score", + "http://edamontology.org/data_1404": "Gap opening penalty (integer)", + "http://edamontology.org/data_1405": "Gap opening penalty (float)", + "http://edamontology.org/data_1406": "Gap extension penalty (integer)", + "http://edamontology.org/data_1407": "Gap extension penalty (float)", + "http://edamontology.org/data_1408": "Gap separation penalty (integer)", + "http://edamontology.org/data_1409": "Gap separation penalty (float)", + "http://edamontology.org/data_1410": "Terminal gap opening penalty", + "http://edamontology.org/data_1411": "Terminal gap extension penalty", + "http://edamontology.org/data_1412": "Sequence identity", + "http://edamontology.org/data_1413": "Sequence similarity", + "http://edamontology.org/data_1414": "Sequence alignment metadata (quality report)", + "http://edamontology.org/data_1415": "Sequence alignment report (site conservation)", + "http://edamontology.org/data_1416": "Sequence alignment report (site correlation)", + "http://edamontology.org/data_1417": "Sequence-profile alignment (Domainatrix signature)", + "http://edamontology.org/data_1418": "Sequence-profile alignment (HMM)", + "http://edamontology.org/data_1420": "Sequence-profile alignment (fingerprint)", + "http://edamontology.org/data_1426": "Phylogenetic continuous quantitative data", + "http://edamontology.org/data_1427": "Phylogenetic discrete data", + "http://edamontology.org/data_1428": "Phylogenetic character cliques", + "http://edamontology.org/data_1429": "Phylogenetic invariants", + "http://edamontology.org/data_1438": "Phylogenetic report", + "http://edamontology.org/data_1439": "DNA substitution model", + "http://edamontology.org/data_1440": "Phylogenetic tree report (tree shape)", + "http://edamontology.org/data_1441": "Phylogenetic tree report (tree evaluation)", + "http://edamontology.org/data_1442": "Phylogenetic tree distances", + "http://edamontology.org/data_1443": "Phylogenetic tree report (tree stratigraphic)", + "http://edamontology.org/data_1444": "Phylogenetic character contrasts", + "http://edamontology.org/data_1446": "Comparison matrix (integers)", + "http://edamontology.org/data_1447": "Comparison matrix (floats)", + "http://edamontology.org/data_1448": "Comparison matrix (nucleotide)", + "http://edamontology.org/data_1449": "Comparison matrix (amino acid)", + "http://edamontology.org/data_1450": "Nucleotide comparison matrix (integers)", + "http://edamontology.org/data_1451": "Nucleotide comparison matrix (floats)", + "http://edamontology.org/data_1452": "Amino acid comparison matrix (integers)", + "http://edamontology.org/data_1453": "Amino acid comparison matrix (floats)", + "http://edamontology.org/data_1459": "Nucleic acid structure", + "http://edamontology.org/data_1460": "Protein structure", + "http://edamontology.org/data_1461": "Protein-ligand complex", + "http://edamontology.org/data_1462": "Carbohydrate structure", + "http://edamontology.org/data_1463": "Small molecule structure", + "http://edamontology.org/data_1464": "DNA structure", + "http://edamontology.org/data_1465": "RNA structure", + "http://edamontology.org/data_1466": "tRNA structure", + "http://edamontology.org/data_1467": "Protein chain", + "http://edamontology.org/data_1468": "Protein domain", + "http://edamontology.org/data_1469": "Protein structure (all atoms)", + "http://edamontology.org/data_1470": "C-alpha trace", + "http://edamontology.org/data_1471": "Protein chain (all atoms)", + "http://edamontology.org/data_1472": "Protein chain (C-alpha atoms)", + "http://edamontology.org/data_1473": "Protein domain (all atoms)", + "http://edamontology.org/data_1474": "Protein domain (C-alpha atoms)", + "http://edamontology.org/data_1479": "Structure alignment (pair)", + "http://edamontology.org/data_1480": "Structure alignment (multiple)", + "http://edamontology.org/data_1481": "Protein structure alignment", + "http://edamontology.org/data_1482": "Nucleic acid structure alignment", + "http://edamontology.org/data_1483": "Structure alignment (protein pair)", + "http://edamontology.org/data_1484": "Multiple protein tertiary structure alignment", + "http://edamontology.org/data_1485": "Structure alignment (protein all atoms)", + "http://edamontology.org/data_1486": "Structure alignment (protein C-alpha atoms)", + "http://edamontology.org/data_1487": "Pairwise protein tertiary structure alignment (all atoms)", + "http://edamontology.org/data_1488": "Pairwise protein tertiary structure alignment (C-alpha atoms)", + "http://edamontology.org/data_1489": "Multiple protein tertiary structure alignment (all atoms)", + "http://edamontology.org/data_1490": "Multiple protein tertiary structure alignment (C-alpha atoms)", + "http://edamontology.org/data_1491": "Structure alignment (nucleic acid pair)", + "http://edamontology.org/data_1492": "Multiple nucleic acid tertiary structure alignment", + "http://edamontology.org/data_1493": "RNA structure alignment", + "http://edamontology.org/data_1494": "Structural transformation matrix", + "http://edamontology.org/data_1495": "DaliLite hit table", + "http://edamontology.org/data_1496": "Molecular similarity score", + "http://edamontology.org/data_1497": "Root-mean-square deviation", + "http://edamontology.org/data_1498": "Tanimoto similarity score", + "http://edamontology.org/data_1499": "3D-1D scoring matrix", + "http://edamontology.org/data_1501": "Amino acid index", + "http://edamontology.org/data_1502": "Amino acid index (chemical classes)", + "http://edamontology.org/data_1503": "Amino acid pair-wise contact potentials", + "http://edamontology.org/data_1505": "Amino acid index (molecular weight)", + "http://edamontology.org/data_1506": "Amino acid index (hydropathy)", + "http://edamontology.org/data_1507": "Amino acid index (White-Wimley data)", + "http://edamontology.org/data_1508": "Amino acid index (van der Waals radii)", + "http://edamontology.org/data_1509": "Enzyme report", + "http://edamontology.org/data_1517": "Restriction enzyme report", + "http://edamontology.org/data_1519": "Peptide molecular weights", + "http://edamontology.org/data_1520": "Peptide hydrophobic moment", + "http://edamontology.org/data_1521": "Protein aliphatic index", + "http://edamontology.org/data_1522": "Protein sequence hydropathy plot", + "http://edamontology.org/data_1523": "Protein charge plot", + "http://edamontology.org/data_1524": "Protein solubility", + "http://edamontology.org/data_1525": "Protein crystallizability", + "http://edamontology.org/data_1526": "Protein globularity", + "http://edamontology.org/data_1527": "Protein titration curve", + "http://edamontology.org/data_1528": "Protein isoelectric point", + "http://edamontology.org/data_1529": "Protein pKa value", + "http://edamontology.org/data_1530": "Protein hydrogen exchange rate", + "http://edamontology.org/data_1531": "Protein extinction coefficient", + "http://edamontology.org/data_1532": "Protein optical density", + "http://edamontology.org/data_1533": "Protein subcellular localisation", + "http://edamontology.org/data_1534": "Peptide immunogenicity data", + "http://edamontology.org/data_1536": "MHC peptide immunogenicity report", + "http://edamontology.org/data_1537": "Protein structure report", + "http://edamontology.org/data_1539": "Protein structural quality report", + "http://edamontology.org/data_1540": "Protein non-covalent interactions report", + "http://edamontology.org/data_1541": "Protein flexibility or motion report", + "http://edamontology.org/data_1542": "Protein solvent accessibility", + "http://edamontology.org/data_1543": "Protein surface report", + "http://edamontology.org/data_1544": "Ramachandran plot", + "http://edamontology.org/data_1545": "Protein dipole moment", + "http://edamontology.org/data_1546": "Protein distance matrix", + "http://edamontology.org/data_1547": "Protein contact map", + "http://edamontology.org/data_1548": "Protein residue 3D cluster", + "http://edamontology.org/data_1549": "Protein hydrogen bonds", + "http://edamontology.org/data_1550": "Protein non-canonical interactions", + "http://edamontology.org/data_1553": "CATH node", + "http://edamontology.org/data_1554": "SCOP node", + "http://edamontology.org/data_1555": "EMBASSY domain classification", + "http://edamontology.org/data_1556": "CATH class", + "http://edamontology.org/data_1557": "CATH architecture", + "http://edamontology.org/data_1558": "CATH topology", + "http://edamontology.org/data_1559": "CATH homologous superfamily", + "http://edamontology.org/data_1560": "CATH structurally similar group", + "http://edamontology.org/data_1561": "CATH functional category", + "http://edamontology.org/data_1564": "Protein fold recognition report", + "http://edamontology.org/data_1565": "Protein-protein interaction report", + "http://edamontology.org/data_1566": "Protein-ligand interaction report", + "http://edamontology.org/data_1567": "Protein-nucleic acid interactions report", + "http://edamontology.org/data_1583": "Nucleic acid melting profile", + "http://edamontology.org/data_1584": "Nucleic acid enthalpy", + "http://edamontology.org/data_1585": "Nucleic acid entropy", + "http://edamontology.org/data_1586": "Nucleic acid melting temperature", + "http://edamontology.org/data_1587": "Nucleic acid stitch profile", + "http://edamontology.org/data_1588": "DNA base pair stacking energies data", + "http://edamontology.org/data_1589": "DNA base pair twist angle data", + "http://edamontology.org/data_1590": "DNA base trimer roll angles data", + "http://edamontology.org/data_1591": "Vienna RNA parameters", + "http://edamontology.org/data_1592": "Vienna RNA structure constraints", + "http://edamontology.org/data_1593": "Vienna RNA concentration data", + "http://edamontology.org/data_1594": "Vienna RNA calculated energy", + "http://edamontology.org/data_1595": "Base pairing probability matrix dotplot", + "http://edamontology.org/data_1596": "Nucleic acid folding report", + "http://edamontology.org/data_1597": "Codon usage table", + "http://edamontology.org/data_1598": "Genetic code", + "http://edamontology.org/data_1599": "Codon adaptation index", + "http://edamontology.org/data_1600": "Codon usage bias plot", + "http://edamontology.org/data_1601": "Nc statistic", + "http://edamontology.org/data_1602": "Codon usage fraction difference", + "http://edamontology.org/data_1621": "Pharmacogenomic test report", + "http://edamontology.org/data_1622": "Disease report", + "http://edamontology.org/data_1634": "Linkage disequilibrium (report)", + "http://edamontology.org/data_1636": "Heat map", + "http://edamontology.org/data_1642": "Affymetrix probe sets library file", + "http://edamontology.org/data_1643": "Affymetrix probe sets information library file", + "http://edamontology.org/data_1646": "Molecular weights standard fingerprint", + "http://edamontology.org/data_1656": "Metabolic pathway report", + "http://edamontology.org/data_1657": "Genetic information processing pathway report", + "http://edamontology.org/data_1658": "Environmental information processing pathway report", + "http://edamontology.org/data_1659": "Signal transduction pathway report", + "http://edamontology.org/data_1660": "Cellular process pathways report", + "http://edamontology.org/data_1661": "Disease pathway or network report", + "http://edamontology.org/data_1662": "Drug structure relationship map", + "http://edamontology.org/data_1663": "Protein interaction networks", + "http://edamontology.org/data_1664": "MIRIAM datatype", + "http://edamontology.org/data_1667": "E-value", + "http://edamontology.org/data_1668": "Z-value", + "http://edamontology.org/data_1669": "P-value", + "http://edamontology.org/data_1670": "Database version information", + "http://edamontology.org/data_1671": "Tool version information", + "http://edamontology.org/data_1672": "CATH version information", + "http://edamontology.org/data_1673": "Swiss-Prot to PDB mapping", + "http://edamontology.org/data_1674": "Sequence database cross-references", + "http://edamontology.org/data_1675": "Job status", + "http://edamontology.org/data_1676": "Job ID", + "http://edamontology.org/data_1677": "Job type", + "http://edamontology.org/data_1678": "Tool log", + "http://edamontology.org/data_1679": "DaliLite log file", + "http://edamontology.org/data_1680": "STRIDE log file", + "http://edamontology.org/data_1681": "NACCESS log file", + "http://edamontology.org/data_1682": "EMBOSS wordfinder log file", + "http://edamontology.org/data_1683": "EMBOSS domainatrix log file", + "http://edamontology.org/data_1684": "EMBOSS sites log file", + "http://edamontology.org/data_1685": "EMBOSS supermatcher error file", + "http://edamontology.org/data_1686": "EMBOSS megamerger log file", + "http://edamontology.org/data_1687": "EMBOSS whichdb log file", + "http://edamontology.org/data_1688": "EMBOSS vectorstrip log file", + "http://edamontology.org/data_1689": "Username", + "http://edamontology.org/data_1690": "Password", + "http://edamontology.org/data_1691": "Email address", + "http://edamontology.org/data_1692": "Person name", + "http://edamontology.org/data_1693": "Number of iterations", + "http://edamontology.org/data_1694": "Number of output entities", + "http://edamontology.org/data_1695": "Hit sort order", + "http://edamontology.org/data_1696": "Drug report", + "http://edamontology.org/data_1707": "Phylogenetic tree image", + "http://edamontology.org/data_1708": "RNA secondary structure image", + "http://edamontology.org/data_1709": "Protein secondary structure image", + "http://edamontology.org/data_1710": "Structure image", + "http://edamontology.org/data_1711": "Sequence alignment image", + "http://edamontology.org/data_1712": "Chemical structure image", + "http://edamontology.org/data_1713": "Fate map", + "http://edamontology.org/data_1714": "Microarray spots image", + "http://edamontology.org/data_1715": "BioPax term", + "http://edamontology.org/data_1716": "GO", + "http://edamontology.org/data_1717": "MeSH", + "http://edamontology.org/data_1718": "HGNC", + "http://edamontology.org/data_1719": "NCBI taxonomy vocabulary", + "http://edamontology.org/data_1720": "Plant ontology term", + "http://edamontology.org/data_1721": "UMLS", + "http://edamontology.org/data_1722": "FMA", + "http://edamontology.org/data_1723": "EMAP", + "http://edamontology.org/data_1724": "ChEBI", + "http://edamontology.org/data_1725": "MGED", + "http://edamontology.org/data_1726": "myGrid", + "http://edamontology.org/data_1727": "GO (biological process)", + "http://edamontology.org/data_1728": "GO (molecular function)", + "http://edamontology.org/data_1729": "GO (cellular component)", + "http://edamontology.org/data_1730": "Ontology relation type", + "http://edamontology.org/data_1731": "Ontology concept definition", + "http://edamontology.org/data_1732": "Ontology concept comment", + "http://edamontology.org/data_1733": "Ontology concept reference", + "http://edamontology.org/data_1738": "doc2loc document information", + "http://edamontology.org/data_1742": "PDB residue number", + "http://edamontology.org/data_1743": "Atomic coordinate", + "http://edamontology.org/data_1744": "Atomic x coordinate", + "http://edamontology.org/data_1745": "Atomic y coordinate", + "http://edamontology.org/data_1746": "Atomic z coordinate", + "http://edamontology.org/data_1748": "PDB atom name", + "http://edamontology.org/data_1755": "Protein atom", + "http://edamontology.org/data_1756": "Protein residue", + "http://edamontology.org/data_1757": "Atom name", + "http://edamontology.org/data_1758": "PDB residue name", + "http://edamontology.org/data_1759": "PDB model number", + "http://edamontology.org/data_1762": "CATH domain report", + "http://edamontology.org/data_1764": "CATH representative domain sequences (ATOM)", + "http://edamontology.org/data_1765": "CATH representative domain sequences (COMBS)", + "http://edamontology.org/data_1766": "CATH domain sequences (ATOM)", + "http://edamontology.org/data_1767": "CATH domain sequences (COMBS)", + "http://edamontology.org/data_1771": "Sequence version", + "http://edamontology.org/data_1772": "Score", + "http://edamontology.org/data_1776": "Protein report (function)", + "http://edamontology.org/data_1783": "Gene name (ASPGD)", + "http://edamontology.org/data_1784": "Gene name (CGD)", + "http://edamontology.org/data_1785": "Gene name (dictyBase)", + "http://edamontology.org/data_1786": "Gene name (EcoGene primary)", + "http://edamontology.org/data_1787": "Gene name (MaizeGDB)", + "http://edamontology.org/data_1788": "Gene name (SGD)", + "http://edamontology.org/data_1789": "Gene name (TGD)", + "http://edamontology.org/data_1790": "Gene name (CGSC)", + "http://edamontology.org/data_1791": "Gene name (HGNC)", + "http://edamontology.org/data_1792": "Gene name (MGD)", + "http://edamontology.org/data_1793": "Gene name (Bacillus subtilis)", + "http://edamontology.org/data_1794": "Gene ID (PlasmoDB)", + "http://edamontology.org/data_1795": "Gene ID (EcoGene)", + "http://edamontology.org/data_1796": "Gene ID (FlyBase)", + "http://edamontology.org/data_1797": "Gene ID (GeneDB Glossina morsitans)", + "http://edamontology.org/data_1798": "Gene ID (GeneDB Leishmania major)", + "http://edamontology.org/data_1799": "Gene ID (GeneDB Plasmodium falciparum)", + "http://edamontology.org/data_1800": "Gene ID (GeneDB Schizosaccharomyces pombe)", + "http://edamontology.org/data_1801": "Gene ID (GeneDB Trypanosoma brucei)", + "http://edamontology.org/data_1802": "Gene ID (Gramene)", + "http://edamontology.org/data_1803": "Gene ID (Virginia microbial)", + "http://edamontology.org/data_1804": "Gene ID (SGN)", + "http://edamontology.org/data_1805": "Gene ID (WormBase)", + "http://edamontology.org/data_1806": "Gene synonym", + "http://edamontology.org/data_1807": "ORF name", + "http://edamontology.org/data_1852": "Sequence assembly component", + "http://edamontology.org/data_1853": "Chromosome annotation (aberration)", + "http://edamontology.org/data_1855": "Clone ID", + "http://edamontology.org/data_1856": "PDB insertion code", + "http://edamontology.org/data_1857": "Atomic occupancy", + "http://edamontology.org/data_1858": "Isotropic B factor", + "http://edamontology.org/data_1859": "Deletion map", + "http://edamontology.org/data_1860": "QTL map", + "http://edamontology.org/data_1863": "Haplotype map", + "http://edamontology.org/data_1864": "Map set data", + "http://edamontology.org/data_1865": "Map feature", + "http://edamontology.org/data_1866": "Map type", + "http://edamontology.org/data_1867": "Protein fold name", + "http://edamontology.org/data_1868": "Taxon", + "http://edamontology.org/data_1869": "Organism identifier", + "http://edamontology.org/data_1870": "Genus name", + "http://edamontology.org/data_1872": "Taxonomic classification", + "http://edamontology.org/data_1873": "iHOP organism ID", + "http://edamontology.org/data_1874": "Genbank common name", + "http://edamontology.org/data_1875": "NCBI taxon", + "http://edamontology.org/data_1877": "Synonym", + "http://edamontology.org/data_1878": "Misspelling", + "http://edamontology.org/data_1879": "Acronym", + "http://edamontology.org/data_1880": "Misnomer", + "http://edamontology.org/data_1881": "Author ID", + "http://edamontology.org/data_1882": "DragonDB author identifier", + "http://edamontology.org/data_1883": "Annotated URI", + "http://edamontology.org/data_1884": "UniProt keywords", + "http://edamontology.org/data_1885": "Gene ID (GeneFarm)", + "http://edamontology.org/data_1886": "Blattner number", + "http://edamontology.org/data_1887": "Gene ID (MIPS Maize)", + "http://edamontology.org/data_1888": "Gene ID (MIPS Medicago)", + "http://edamontology.org/data_1889": "Gene name (DragonDB)", + "http://edamontology.org/data_1890": "Gene name (Arabidopsis)", + "http://edamontology.org/data_1891": "iHOP symbol", + "http://edamontology.org/data_1892": "Gene name (GeneFarm)", + "http://edamontology.org/data_1893": "Locus ID", + "http://edamontology.org/data_1895": "Locus ID (AGI)", + "http://edamontology.org/data_1896": "Locus ID (ASPGD)", + "http://edamontology.org/data_1897": "Locus ID (MGG)", + "http://edamontology.org/data_1898": "Locus ID (CGD)", + "http://edamontology.org/data_1899": "Locus ID (CMR)", + "http://edamontology.org/data_1900": "NCBI locus tag", + "http://edamontology.org/data_1901": "Locus ID (SGD)", + "http://edamontology.org/data_1902": "Locus ID (MMP)", + "http://edamontology.org/data_1903": "Locus ID (DictyBase)", + "http://edamontology.org/data_1904": "Locus ID (EntrezGene)", + "http://edamontology.org/data_1905": "Locus ID (MaizeGDB)", + "http://edamontology.org/data_1906": "Quantitative trait locus", + "http://edamontology.org/data_1907": "Gene ID (KOME)", + "http://edamontology.org/data_1908": "Locus ID (Tropgene)", + "http://edamontology.org/data_1916": "Alignment", + "http://edamontology.org/data_1917": "Atomic property", + "http://edamontology.org/data_2007": "UniProt keyword", + "http://edamontology.org/data_2009": "Ordered locus name", + "http://edamontology.org/data_2012": "Sequence coordinates", + "http://edamontology.org/data_2016": "Amino acid property", + "http://edamontology.org/data_2018": "Annotation", + "http://edamontology.org/data_2019": "Map data", + "http://edamontology.org/data_2022": "Vienna RNA structural data", + "http://edamontology.org/data_2023": "Sequence mask parameter", + "http://edamontology.org/data_2024": "Enzyme kinetics data", + "http://edamontology.org/data_2025": "Michaelis Menten plot", + "http://edamontology.org/data_2026": "Hanes Woolf plot", + "http://edamontology.org/data_2028": "Experimental data", + "http://edamontology.org/data_2041": "Genome version information", + "http://edamontology.org/data_2042": "Evidence", + "http://edamontology.org/data_2043": "Sequence record lite", + "http://edamontology.org/data_2044": "Sequence", + "http://edamontology.org/data_2046": "Nucleic acid sequence record (lite)", + "http://edamontology.org/data_2047": "Protein sequence record (lite)", + "http://edamontology.org/data_2048": "Report", + "http://edamontology.org/data_2050": "Molecular property (general)", + "http://edamontology.org/data_2053": "Structural data", + "http://edamontology.org/data_2070": "Sequence motif (nucleic acid)", + "http://edamontology.org/data_2071": "Sequence motif (protein)", + "http://edamontology.org/data_2079": "Search parameter", + "http://edamontology.org/data_2080": "Database search results", + "http://edamontology.org/data_2081": "Secondary structure", + "http://edamontology.org/data_2082": "Matrix", + "http://edamontology.org/data_2083": "Alignment data", + "http://edamontology.org/data_2084": "Nucleic acid report", + "http://edamontology.org/data_2085": "Structure report", + "http://edamontology.org/data_2086": "Nucleic acid structure data", + "http://edamontology.org/data_2087": "Molecular property", + "http://edamontology.org/data_2088": "DNA base structural data", + "http://edamontology.org/data_2090": "Database entry version information", + "http://edamontology.org/data_2091": "Accession", + "http://edamontology.org/data_2092": "SNP", + "http://edamontology.org/data_2093": "Data reference", + "http://edamontology.org/data_2098": "Job identifier", + "http://edamontology.org/data_2099": "Name", + "http://edamontology.org/data_2100": "Type", + "http://edamontology.org/data_2101": "User ID", + "http://edamontology.org/data_2102": "KEGG organism code", + "http://edamontology.org/data_2103": "Gene name (KEGG GENES)", + "http://edamontology.org/data_2104": "BioCyc ID", + "http://edamontology.org/data_2105": "Compound ID (BioCyc)", + "http://edamontology.org/data_2106": "Reaction ID (BioCyc)", + "http://edamontology.org/data_2107": "Enzyme ID (BioCyc)", + "http://edamontology.org/data_2108": "Reaction ID", + "http://edamontology.org/data_2109": "Identifier (hybrid)", + "http://edamontology.org/data_2110": "Molecular property identifier", + "http://edamontology.org/data_2111": "Codon usage table ID", + "http://edamontology.org/data_2112": "FlyBase primary identifier", + "http://edamontology.org/data_2113": "WormBase identifier", + "http://edamontology.org/data_2114": "WormBase wormpep ID", + "http://edamontology.org/data_2116": "Nucleic acid features (codon)", + "http://edamontology.org/data_2117": "Map identifier", + "http://edamontology.org/data_2118": "Person identifier", + "http://edamontology.org/data_2119": "Nucleic acid identifier", + "http://edamontology.org/data_2126": "Translation frame specification", + "http://edamontology.org/data_2127": "Genetic code identifier", + "http://edamontology.org/data_2128": "Genetic code name", + "http://edamontology.org/data_2129": "File format name", + "http://edamontology.org/data_2130": "Sequence profile type", + "http://edamontology.org/data_2131": "Operating system name", + "http://edamontology.org/data_2132": "Mutation type", + "http://edamontology.org/data_2133": "Logical operator", + "http://edamontology.org/data_2134": "Results sort order", + "http://edamontology.org/data_2135": "Toggle", + "http://edamontology.org/data_2136": "Sequence width", + "http://edamontology.org/data_2137": "Gap penalty", + "http://edamontology.org/data_2139": "Nucleic acid melting temperature", + "http://edamontology.org/data_2140": "Concentration", + "http://edamontology.org/data_2141": "Window step size", + "http://edamontology.org/data_2142": "EMBOSS graph", + "http://edamontology.org/data_2143": "EMBOSS report", + "http://edamontology.org/data_2145": "Sequence offset", + "http://edamontology.org/data_2146": "Threshold", + "http://edamontology.org/data_2147": "Protein report (transcription factor)", + "http://edamontology.org/data_2149": "Database category name", + "http://edamontology.org/data_2150": "Sequence profile name", + "http://edamontology.org/data_2151": "Color", + "http://edamontology.org/data_2152": "Rendering parameter", + "http://edamontology.org/data_2154": "Sequence name", + "http://edamontology.org/data_2156": "Date", + "http://edamontology.org/data_2157": "Word composition", + "http://edamontology.org/data_2160": "Fickett testcode plot", + "http://edamontology.org/data_2161": "Sequence similarity plot", + "http://edamontology.org/data_2162": "Helical wheel", + "http://edamontology.org/data_2163": "Helical net", + "http://edamontology.org/data_2164": "Protein sequence properties plot", + "http://edamontology.org/data_2165": "Protein ionisation curve", + "http://edamontology.org/data_2166": "Sequence composition plot", + "http://edamontology.org/data_2167": "Nucleic acid density plot", + "http://edamontology.org/data_2168": "Sequence trace image", + "http://edamontology.org/data_2169": "Nucleic acid features (siRNA)", + "http://edamontology.org/data_2173": "Sequence set (stream)", + "http://edamontology.org/data_2174": "FlyBase secondary identifier", + "http://edamontology.org/data_2176": "Cardinality", + "http://edamontology.org/data_2177": "Exactly 1", + "http://edamontology.org/data_2178": "1 or more", + "http://edamontology.org/data_2179": "Exactly 2", + "http://edamontology.org/data_2180": "2 or more", + "http://edamontology.org/data_2190": "Sequence checksum", + "http://edamontology.org/data_2191": "Protein features report (chemical modifications)", + "http://edamontology.org/data_2192": "Error", + "http://edamontology.org/data_2193": "Database entry metadata", + "http://edamontology.org/data_2198": "Gene cluster", + "http://edamontology.org/data_2201": "Sequence record full", + "http://edamontology.org/data_2208": "Plasmid identifier", + "http://edamontology.org/data_2209": "Mutation ID", + "http://edamontology.org/data_2212": "Mutation annotation (basic)", + "http://edamontology.org/data_2213": "Mutation annotation (prevalence)", + "http://edamontology.org/data_2214": "Mutation annotation (prognostic)", + "http://edamontology.org/data_2215": "Mutation annotation (functional)", + "http://edamontology.org/data_2216": "Codon number", + "http://edamontology.org/data_2217": "Tumor annotation", + "http://edamontology.org/data_2218": "Server metadata", + "http://edamontology.org/data_2219": "Database field name", + "http://edamontology.org/data_2220": "Sequence cluster ID (SYSTERS)", + "http://edamontology.org/data_2223": "Ontology metadata", + "http://edamontology.org/data_2235": "Raw SCOP domain classification", + "http://edamontology.org/data_2236": "Raw CATH domain classification", + "http://edamontology.org/data_2240": "Heterogen annotation", + "http://edamontology.org/data_2242": "Phylogenetic property values", + "http://edamontology.org/data_2245": "Sequence set (bootstrapped)", + "http://edamontology.org/data_2247": "Phylogenetic consensus tree", + "http://edamontology.org/data_2248": "Schema", + "http://edamontology.org/data_2249": "DTD", + "http://edamontology.org/data_2250": "XML Schema", + "http://edamontology.org/data_2251": "Relax-NG schema", + "http://edamontology.org/data_2252": "XSLT stylesheet", + "http://edamontology.org/data_2253": "Data resource definition name", + "http://edamontology.org/data_2254": "OBO file format name", + "http://edamontology.org/data_2285": "Gene ID (MIPS)", + "http://edamontology.org/data_2288": "Sequence identifier (protein)", + "http://edamontology.org/data_2289": "Sequence identifier (nucleic acid)", + "http://edamontology.org/data_2290": "EMBL accession", + "http://edamontology.org/data_2291": "UniProt ID", + "http://edamontology.org/data_2292": "GenBank accession", + "http://edamontology.org/data_2293": "Gramene secondary identifier", + "http://edamontology.org/data_2294": "Sequence variation ID", + "http://edamontology.org/data_2295": "Gene ID", + "http://edamontology.org/data_2296": "Gene name (AceView)", + "http://edamontology.org/data_2297": "Gene ID (ECK)", + "http://edamontology.org/data_2298": "Gene ID (HGNC)", + "http://edamontology.org/data_2299": "Gene name", + "http://edamontology.org/data_2300": "Gene name (NCBI)", + "http://edamontology.org/data_2301": "SMILES string", + "http://edamontology.org/data_2302": "STRING ID", + "http://edamontology.org/data_2307": "Virus annotation", + "http://edamontology.org/data_2308": "Virus annotation (taxonomy)", + "http://edamontology.org/data_2309": "Reaction ID (SABIO-RK)", + "http://edamontology.org/data_2313": "Carbohydrate report", + "http://edamontology.org/data_2314": "GI number", + "http://edamontology.org/data_2315": "NCBI version", + "http://edamontology.org/data_2316": "Cell line name", + "http://edamontology.org/data_2317": "Cell line name (exact)", + "http://edamontology.org/data_2318": "Cell line name (truncated)", + "http://edamontology.org/data_2319": "Cell line name (no punctuation)", + "http://edamontology.org/data_2320": "Cell line name (assonant)", + "http://edamontology.org/data_2321": "Enzyme ID", + "http://edamontology.org/data_2325": "REBASE enzyme number", + "http://edamontology.org/data_2326": "DrugBank ID", + "http://edamontology.org/data_2327": "GI number (protein)", + "http://edamontology.org/data_2335": "Bit score", + "http://edamontology.org/data_2336": "Translation phase specification", + "http://edamontology.org/data_2337": "Resource metadata", + "http://edamontology.org/data_2338": "Ontology identifier", + "http://edamontology.org/data_2339": "Ontology concept name", + "http://edamontology.org/data_2340": "Genome build identifier", + "http://edamontology.org/data_2342": "Pathway or network name", + "http://edamontology.org/data_2343": "Pathway ID (KEGG)", + "http://edamontology.org/data_2344": "Pathway ID (NCI-Nature)", + "http://edamontology.org/data_2345": "Pathway ID (ConsensusPathDB)", + "http://edamontology.org/data_2346": "Sequence cluster ID (UniRef)", + "http://edamontology.org/data_2347": "Sequence cluster ID (UniRef100)", + "http://edamontology.org/data_2348": "Sequence cluster ID (UniRef90)", + "http://edamontology.org/data_2349": "Sequence cluster ID (UniRef50)", + "http://edamontology.org/data_2353": "Ontology data", + "http://edamontology.org/data_2354": "RNA family report", + "http://edamontology.org/data_2355": "RNA family identifier", + "http://edamontology.org/data_2356": "RFAM accession", + "http://edamontology.org/data_2357": "Protein signature type", + "http://edamontology.org/data_2358": "Domain-nucleic acid interaction report", + "http://edamontology.org/data_2359": "Domain-domain interactions", + "http://edamontology.org/data_2360": "Domain-domain interaction (indirect)", + "http://edamontology.org/data_2362": "Sequence accession (hybrid)", + "http://edamontology.org/data_2363": "2D PAGE data", + "http://edamontology.org/data_2364": "2D PAGE report", + "http://edamontology.org/data_2365": "Pathway or network accession", + "http://edamontology.org/data_2366": "Secondary structure alignment", + "http://edamontology.org/data_2367": "ASTD ID", + "http://edamontology.org/data_2368": "ASTD ID (exon)", + "http://edamontology.org/data_2369": "ASTD ID (intron)", + "http://edamontology.org/data_2370": "ASTD ID (polya)", + "http://edamontology.org/data_2371": "ASTD ID (tss)", + "http://edamontology.org/data_2372": "2D PAGE spot report", + "http://edamontology.org/data_2373": "Spot ID", + "http://edamontology.org/data_2374": "Spot serial number", + "http://edamontology.org/data_2375": "Spot ID (HSC-2DPAGE)", + "http://edamontology.org/data_2378": "Protein-motif interaction", + "http://edamontology.org/data_2379": "Strain identifier", + "http://edamontology.org/data_2380": "CABRI accession", + "http://edamontology.org/data_2381": "Experiment report (genotyping)", + "http://edamontology.org/data_2382": "Genotype experiment ID", + "http://edamontology.org/data_2383": "EGA accession", + "http://edamontology.org/data_2384": "IPI protein ID", + "http://edamontology.org/data_2385": "RefSeq accession (protein)", + "http://edamontology.org/data_2386": "EPD ID", + "http://edamontology.org/data_2387": "TAIR accession", + "http://edamontology.org/data_2388": "TAIR accession (At gene)", + "http://edamontology.org/data_2389": "UniSTS accession", + "http://edamontology.org/data_2390": "UNITE accession", + "http://edamontology.org/data_2391": "UTR accession", + "http://edamontology.org/data_2392": "UniParc accession", + "http://edamontology.org/data_2393": "mFLJ/mKIAA number", + "http://edamontology.org/data_2395": "Fungi annotation", + "http://edamontology.org/data_2396": "Fungi annotation (anamorph)", + "http://edamontology.org/data_2398": "Ensembl protein ID", + "http://edamontology.org/data_2400": "Toxin annotation", + "http://edamontology.org/data_2401": "Protein report (membrane protein)", + "http://edamontology.org/data_2402": "Protein-drug interaction report", + "http://edamontology.org/data_2522": "Map data", + "http://edamontology.org/data_2523": "Phylogenetic data", + "http://edamontology.org/data_2524": "Protein data", + "http://edamontology.org/data_2525": "Nucleic acid data", + "http://edamontology.org/data_2526": "Text data", + "http://edamontology.org/data_2527": "Parameter", + "http://edamontology.org/data_2528": "Molecular data", + "http://edamontology.org/data_2529": "Molecule report", + "http://edamontology.org/data_2530": "Organism report", + "http://edamontology.org/data_2531": "Protocol", + "http://edamontology.org/data_2534": "Sequence attribute", + "http://edamontology.org/data_2535": "Sequence tag profile", + "http://edamontology.org/data_2536": "Mass spectrometry data", + "http://edamontology.org/data_2537": "Protein structure raw data", + "http://edamontology.org/data_2538": "Mutation identifier", + "http://edamontology.org/data_2539": "Alignment data", + "http://edamontology.org/data_2540": "Data index data", + "http://edamontology.org/data_2563": "Amino acid name (single letter)", + "http://edamontology.org/data_2564": "Amino acid name (three letter)", + "http://edamontology.org/data_2565": "Amino acid name (full name)", + "http://edamontology.org/data_2576": "Toxin identifier", + "http://edamontology.org/data_2578": "ArachnoServer ID", + "http://edamontology.org/data_2579": "Expressed gene list", + "http://edamontology.org/data_2580": "BindingDB Monomer ID", + "http://edamontology.org/data_2581": "GO concept name", + "http://edamontology.org/data_2582": "GO concept ID (biological process)", + "http://edamontology.org/data_2583": "GO concept ID (molecular function)", + "http://edamontology.org/data_2584": "GO concept name (cellular component)", + "http://edamontology.org/data_2586": "Northern blot image", + "http://edamontology.org/data_2587": "Blot ID", + "http://edamontology.org/data_2588": "BlotBase blot ID", + "http://edamontology.org/data_2589": "Hierarchy", + "http://edamontology.org/data_2590": "Hierarchy identifier", + "http://edamontology.org/data_2591": "Brite hierarchy ID", + "http://edamontology.org/data_2592": "Cancer type", + "http://edamontology.org/data_2593": "BRENDA organism ID", + "http://edamontology.org/data_2594": "UniGene taxon", + "http://edamontology.org/data_2595": "UTRdb taxon", + "http://edamontology.org/data_2596": "Catalogue ID", + "http://edamontology.org/data_2597": "CABRI catalogue name", + "http://edamontology.org/data_2598": "Secondary structure alignment metadata", + "http://edamontology.org/data_2599": "Molecule interaction report", + "http://edamontology.org/data_2600": "Pathway or network", + "http://edamontology.org/data_2601": "Small molecule data", + "http://edamontology.org/data_2602": "Genotype and phenotype data", + "http://edamontology.org/data_2603": "Expression data", + "http://edamontology.org/data_2605": "Compound ID (KEGG)", + "http://edamontology.org/data_2606": "RFAM name", + "http://edamontology.org/data_2608": "Reaction ID (KEGG)", + "http://edamontology.org/data_2609": "Drug ID (KEGG)", + "http://edamontology.org/data_2610": "Ensembl ID", + "http://edamontology.org/data_2611": "ICD identifier", + "http://edamontology.org/data_2612": "Sequence cluster ID (CluSTr)", + "http://edamontology.org/data_2613": "KEGG Glycan ID", + "http://edamontology.org/data_2614": "TCDB ID", + "http://edamontology.org/data_2615": "MINT ID", + "http://edamontology.org/data_2616": "DIP ID", + "http://edamontology.org/data_2617": "Signaling Gateway protein ID", + "http://edamontology.org/data_2618": "Protein modification ID", + "http://edamontology.org/data_2619": "RESID ID", + "http://edamontology.org/data_2620": "RGD ID", + "http://edamontology.org/data_2621": "TAIR accession (protein)", + "http://edamontology.org/data_2622": "Compound ID (HMDB)", + "http://edamontology.org/data_2625": "LIPID MAPS ID", + "http://edamontology.org/data_2626": "PeptideAtlas ID", + "http://edamontology.org/data_2627": "Molecular interaction ID", + "http://edamontology.org/data_2628": "BioGRID interaction ID", + "http://edamontology.org/data_2629": "Enzyme ID (MEROPS)", + "http://edamontology.org/data_2630": "Mobile genetic element ID", + "http://edamontology.org/data_2631": "ACLAME ID", + "http://edamontology.org/data_2632": "SGD ID", + "http://edamontology.org/data_2633": "Book ID", + "http://edamontology.org/data_2634": "ISBN", + "http://edamontology.org/data_2635": "Compound ID (3DMET)", + "http://edamontology.org/data_2636": "MatrixDB interaction ID", + "http://edamontology.org/data_2637": "cPath ID", + "http://edamontology.org/data_2638": "PubChem bioassay ID", + "http://edamontology.org/data_2639": "PubChem ID", + "http://edamontology.org/data_2641": "Reaction ID (MACie)", + "http://edamontology.org/data_2642": "Gene ID (miRBase)", + "http://edamontology.org/data_2643": "Gene ID (ZFIN)", + "http://edamontology.org/data_2644": "Reaction ID (Rhea)", + "http://edamontology.org/data_2645": "Pathway ID (Unipathway)", + "http://edamontology.org/data_2646": "Compound ID (ChEMBL)", + "http://edamontology.org/data_2647": "LGICdb identifier", + "http://edamontology.org/data_2648": "Reaction kinetics ID (SABIO-RK)", + "http://edamontology.org/data_2649": "PharmGKB ID", + "http://edamontology.org/data_2650": "Pathway ID (PharmGKB)", + "http://edamontology.org/data_2651": "Disease ID (PharmGKB)", + "http://edamontology.org/data_2652": "Drug ID (PharmGKB)", + "http://edamontology.org/data_2653": "Drug ID (TTD)", + "http://edamontology.org/data_2654": "Target ID (TTD)", + "http://edamontology.org/data_2655": "Cell type identifier", + "http://edamontology.org/data_2656": "NeuronDB ID", + "http://edamontology.org/data_2657": "NeuroMorpho ID", + "http://edamontology.org/data_2658": "Compound ID (ChemIDplus)", + "http://edamontology.org/data_2659": "Pathway ID (SMPDB)", + "http://edamontology.org/data_2660": "BioNumbers ID", + "http://edamontology.org/data_2662": "T3DB ID", + "http://edamontology.org/data_2663": "Carbohydrate identifier", + "http://edamontology.org/data_2664": "GlycomeDB ID", + "http://edamontology.org/data_2665": "LipidBank ID", + "http://edamontology.org/data_2666": "CDD ID", + "http://edamontology.org/data_2667": "MMDB ID", + "http://edamontology.org/data_2668": "iRefIndex ID", + "http://edamontology.org/data_2669": "ModelDB ID", + "http://edamontology.org/data_2670": "Pathway ID (DQCS)", + "http://edamontology.org/data_2671": "Ensembl ID (Homo sapiens)", + "http://edamontology.org/data_2672": "Ensembl ID ('Bos taurus')", + "http://edamontology.org/data_2673": "Ensembl ID ('Canis familiaris')", + "http://edamontology.org/data_2674": "Ensembl ID ('Cavia porcellus')", + "http://edamontology.org/data_2675": "Ensembl ID ('Ciona intestinalis')", + "http://edamontology.org/data_2676": "Ensembl ID ('Ciona savignyi')", + "http://edamontology.org/data_2677": "Ensembl ID ('Danio rerio')", + "http://edamontology.org/data_2678": "Ensembl ID ('Dasypus novemcinctus')", + "http://edamontology.org/data_2679": "Ensembl ID ('Echinops telfairi')", + "http://edamontology.org/data_2680": "Ensembl ID ('Erinaceus europaeus')", + "http://edamontology.org/data_2681": "Ensembl ID ('Felis catus')", + "http://edamontology.org/data_2682": "Ensembl ID ('Gallus gallus')", + "http://edamontology.org/data_2683": "Ensembl ID ('Gasterosteus aculeatus')", + "http://edamontology.org/data_2684": "Ensembl ID ('Homo sapiens')", + "http://edamontology.org/data_2685": "Ensembl ID ('Loxodonta africana')", + "http://edamontology.org/data_2686": "Ensembl ID ('Macaca mulatta')", + "http://edamontology.org/data_2687": "Ensembl ID ('Monodelphis domestica')", + "http://edamontology.org/data_2688": "Ensembl ID ('Mus musculus')", + "http://edamontology.org/data_2689": "Ensembl ID ('Myotis lucifugus')", + "http://edamontology.org/data_2690": "Ensembl ID (\"Ornithorhynchus anatinus\")", + "http://edamontology.org/data_2691": "Ensembl ID ('Oryctolagus cuniculus')", + "http://edamontology.org/data_2692": "Ensembl ID ('Oryzias latipes')", + "http://edamontology.org/data_2693": "Ensembl ID ('Otolemur garnettii')", + "http://edamontology.org/data_2694": "Ensembl ID ('Pan troglodytes')", + "http://edamontology.org/data_2695": "Ensembl ID ('Rattus norvegicus')", + "http://edamontology.org/data_2696": "Ensembl ID ('Spermophilus tridecemlineatus')", + "http://edamontology.org/data_2697": "Ensembl ID ('Takifugu rubripes')", + "http://edamontology.org/data_2698": "Ensembl ID ('Tupaia belangeri')", + "http://edamontology.org/data_2699": "Ensembl ID ('Xenopus tropicalis')", + "http://edamontology.org/data_2700": "CATH identifier", + "http://edamontology.org/data_2701": "CATH node ID (family)", + "http://edamontology.org/data_2702": "Enzyme ID (CAZy)", + "http://edamontology.org/data_2704": "Clone ID (IMAGE)", + "http://edamontology.org/data_2705": "GO concept ID (cellular component)", + "http://edamontology.org/data_2706": "Chromosome name (BioCyc)", + "http://edamontology.org/data_2709": "CleanEx entry name", + "http://edamontology.org/data_2710": "CleanEx dataset code", + "http://edamontology.org/data_2711": "Genome report", + "http://edamontology.org/data_2713": "Protein ID (CORUM)", + "http://edamontology.org/data_2714": "CDD PSSM-ID", + "http://edamontology.org/data_2715": "Protein ID (CuticleDB)", + "http://edamontology.org/data_2716": "DBD ID", + "http://edamontology.org/data_2717": "Oligonucleotide probe annotation", + "http://edamontology.org/data_2718": "Oligonucleotide ID", + "http://edamontology.org/data_2719": "dbProbe ID", + "http://edamontology.org/data_2720": "Dinucleotide property", + "http://edamontology.org/data_2721": "DiProDB ID", + "http://edamontology.org/data_2722": "Protein features report (disordered structure)", + "http://edamontology.org/data_2723": "Protein ID (DisProt)", + "http://edamontology.org/data_2724": "Embryo report", + "http://edamontology.org/data_2725": "Ensembl transcript ID", + "http://edamontology.org/data_2726": "Inhibitor annotation", + "http://edamontology.org/data_2727": "Promoter ID", + "http://edamontology.org/data_2728": "EST accession", + "http://edamontology.org/data_2729": "COGEME EST ID", + "http://edamontology.org/data_2730": "COGEME unisequence ID", + "http://edamontology.org/data_2731": "Protein family ID (GeneFarm)", + "http://edamontology.org/data_2732": "Family name", + "http://edamontology.org/data_2733": "Genus name (virus)", + "http://edamontology.org/data_2734": "Family name (virus)", + "http://edamontology.org/data_2735": "Database name (SwissRegulon)", + "http://edamontology.org/data_2736": "Sequence feature ID (SwissRegulon)", + "http://edamontology.org/data_2737": "FIG ID", + "http://edamontology.org/data_2738": "Gene ID (Xenbase)", + "http://edamontology.org/data_2739": "Gene ID (Genolist)", + "http://edamontology.org/data_2740": "Gene name (Genolist)", + "http://edamontology.org/data_2741": "ABS ID", + "http://edamontology.org/data_2742": "AraC-XylS ID", + "http://edamontology.org/data_2743": "Gene name (HUGO)", + "http://edamontology.org/data_2744": "Locus ID (PseudoCAP)", + "http://edamontology.org/data_2745": "Locus ID (UTR)", + "http://edamontology.org/data_2746": "MonosaccharideDB ID", + "http://edamontology.org/data_2747": "Database name (CMD)", + "http://edamontology.org/data_2748": "Database name (Osteogenesis)", + "http://edamontology.org/data_2749": "Genome identifier", + "http://edamontology.org/data_2751": "GenomeReviews ID", + "http://edamontology.org/data_2752": "GlycoMap ID", + "http://edamontology.org/data_2753": "Carbohydrate conformational map", + "http://edamontology.org/data_2755": "Transcription factor name", + "http://edamontology.org/data_2756": "TCID", + "http://edamontology.org/data_2757": "Pfam domain name", + "http://edamontology.org/data_2758": "Pfam clan ID", + "http://edamontology.org/data_2759": "Gene ID (VectorBase)", + "http://edamontology.org/data_2761": "UTRSite ID", + "http://edamontology.org/data_2762": "Sequence signature report", + "http://edamontology.org/data_2763": "Locus annotation", + "http://edamontology.org/data_2764": "Protein name (UniProt)", + "http://edamontology.org/data_2765": "Term ID list", + "http://edamontology.org/data_2766": "HAMAP ID", + "http://edamontology.org/data_2767": "Identifier with metadata", + "http://edamontology.org/data_2768": "Gene symbol annotation", + "http://edamontology.org/data_2769": "Transcript ID", + "http://edamontology.org/data_2770": "HIT ID", + "http://edamontology.org/data_2771": "HIX ID", + "http://edamontology.org/data_2772": "HPA antibody id", + "http://edamontology.org/data_2773": "IMGT/HLA ID", + "http://edamontology.org/data_2774": "Gene ID (JCVI)", + "http://edamontology.org/data_2775": "Kinase name", + "http://edamontology.org/data_2776": "ConsensusPathDB entity ID", + "http://edamontology.org/data_2777": "ConsensusPathDB entity name", + "http://edamontology.org/data_2778": "CCAP strain number", + "http://edamontology.org/data_2779": "Stock number", + "http://edamontology.org/data_2780": "Stock number (TAIR)", + "http://edamontology.org/data_2781": "REDIdb ID", + "http://edamontology.org/data_2782": "SMART domain name", + "http://edamontology.org/data_2783": "Protein family ID (PANTHER)", + "http://edamontology.org/data_2784": "RNAVirusDB ID", + "http://edamontology.org/data_2785": "Virus ID", + "http://edamontology.org/data_2786": "NCBI Genome Project ID", + "http://edamontology.org/data_2787": "NCBI genome accession", + "http://edamontology.org/data_2788": "Sequence profile data", + "http://edamontology.org/data_2789": "Protein ID (TopDB)", + "http://edamontology.org/data_2790": "Gel ID", + "http://edamontology.org/data_2791": "Reference map name (SWISS-2DPAGE)", + "http://edamontology.org/data_2792": "Protein ID (PeroxiBase)", + "http://edamontology.org/data_2793": "SISYPHUS ID", + "http://edamontology.org/data_2794": "ORF ID", + "http://edamontology.org/data_2795": "ORF identifier", + "http://edamontology.org/data_2796": "Linucs ID", + "http://edamontology.org/data_2797": "Protein ID (LGICdb)", + "http://edamontology.org/data_2798": "MaizeDB ID", + "http://edamontology.org/data_2799": "Gene ID (MfunGD)", + "http://edamontology.org/data_2800": "Orpha number", + "http://edamontology.org/data_2802": "Protein ID (EcID)", + "http://edamontology.org/data_2803": "Clone ID (RefSeq)", + "http://edamontology.org/data_2804": "Protein ID (ConoServer)", + "http://edamontology.org/data_2805": "GeneSNP ID", + "http://edamontology.org/data_2812": "Lipid identifier", + "http://edamontology.org/data_2831": "Databank", + "http://edamontology.org/data_2832": "Web portal", + "http://edamontology.org/data_2835": "Gene ID (VBASE2)", + "http://edamontology.org/data_2836": "DPVweb ID", + "http://edamontology.org/data_2837": "Pathway ID (BioSystems)", + "http://edamontology.org/data_2838": "Experimental data (proteomics)", + "http://edamontology.org/data_2849": "Abstract", + "http://edamontology.org/data_2850": "Lipid structure", + "http://edamontology.org/data_2851": "Drug structure", + "http://edamontology.org/data_2852": "Toxin structure", + "http://edamontology.org/data_2854": "Position-specific scoring matrix", + "http://edamontology.org/data_2855": "Distance matrix", + "http://edamontology.org/data_2856": "Structural distance matrix", + "http://edamontology.org/data_2857": "Article metadata", + "http://edamontology.org/data_2858": "Ontology concept", + "http://edamontology.org/data_2865": "Codon usage bias", + "http://edamontology.org/data_2866": "Northern blot report", + "http://edamontology.org/data_2870": "Radiation hybrid map", + "http://edamontology.org/data_2872": "ID list", + "http://edamontology.org/data_2873": "Phylogenetic gene frequencies data", + "http://edamontology.org/data_2874": "Sequence set (polymorphic)", + "http://edamontology.org/data_2875": "DRCAT resource", + "http://edamontology.org/data_2877": "Protein complex", + "http://edamontology.org/data_2878": "Protein structural motif", + "http://edamontology.org/data_2879": "Lipid report", + "http://edamontology.org/data_2880": "Secondary structure image", + "http://edamontology.org/data_2881": "Secondary structure report", + "http://edamontology.org/data_2882": "DNA features", + "http://edamontology.org/data_2883": "RNA features report", + "http://edamontology.org/data_2884": "Plot", + "http://edamontology.org/data_2886": "Protein sequence record", + "http://edamontology.org/data_2887": "Nucleic acid sequence record", + "http://edamontology.org/data_2888": "Protein sequence record 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binning", + "http://edamontology.org/operation_3799": "Quantification", + "http://edamontology.org/operation_3800": "RNA-Seq quantification", + "http://edamontology.org/operation_3801": "Spectral library search", + "http://edamontology.org/operation_3802": "Sorting", + "http://edamontology.org/operation_3803": "Natural product identification", + "http://edamontology.org/operation_3809": "DMR identification", + "http://edamontology.org/operation_3840": "Multilocus sequence typing", + "http://edamontology.org/operation_3860": "Spectrum calculation", + "http://edamontology.org/operation_3890": "Trajectory visualization", + "http://edamontology.org/operation_3891": "Essential dynamics", + "http://edamontology.org/operation_3893": "Forcefield parameterisation", + "http://edamontology.org/operation_3894": "DNA profiling", + "http://edamontology.org/operation_3896": "Active site prediction", + "http://edamontology.org/operation_3897": "Ligand-binding site prediction", + "http://edamontology.org/operation_3898": "Metal-binding site prediction", + "http://edamontology.org/operation_3899": "Protein-protein docking", + "http://edamontology.org/operation_3900": "DNA-binding protein prediction", + "http://edamontology.org/operation_3901": "RNA-binding protein prediction", + "http://edamontology.org/operation_3902": "RNA binding site prediction", + "http://edamontology.org/operation_3903": "DNA binding site prediction", + "http://edamontology.org/operation_3904": "Protein disorder prediction", + "http://edamontology.org/operation_3907": "Information extraction", + "http://edamontology.org/operation_3908": "Information retrieval", + "http://edamontology.org/operation_3918": "Genome analysis", + "http://edamontology.org/operation_3919": "Methylation calling", + "http://edamontology.org/operation_3920": "DNA testing", + "http://edamontology.org/operation_3921": "Sequence read processing", + "http://edamontology.org/operation_3923": "Genome resequencing", + "http://edamontology.org/operation_3925": "Network visualisation", + "http://edamontology.org/operation_3926": "Pathway visualisation", + "http://edamontology.org/operation_3927": "Network analysis", + "http://edamontology.org/operation_3928": "Pathway analysis", + "http://edamontology.org/operation_3929": "Metabolic pathway prediction", + "http://edamontology.org/operation_3931": "Chemometrics", + "http://edamontology.org/operation_3933": "Demultiplexing", + "http://edamontology.org/operation_3935": "Dimensionality reduction", + "http://edamontology.org/operation_3936": "Feature selection", + "http://edamontology.org/operation_3937": "Feature extraction", + "http://edamontology.org/operation_3938": "Virtual screening", + "http://edamontology.org/operation_3939": "Metabolic engineering", + "http://edamontology.org/operation_3942": "Tree dating", + "http://edamontology.org/operation_3946": "Ecological modelling", + "http://edamontology.org/operation_3947": "Phylogenetic tree reconciliation", + "http://edamontology.org/operation_3950": "Selection detection", + "http://edamontology.org/operation_3960": "Principal component analysis", + "http://edamontology.org/operation_3961": "Copy number variation detection", + "http://edamontology.org/operation_3962": "Deletion detection", + "http://edamontology.org/operation_3963": "Duplication detection", + "http://edamontology.org/operation_3964": "Complex CNV detection", + "http://edamontology.org/operation_3965": "Amplification detection", + "http://edamontology.org/operation_3968": "Adhesin prediction", + "http://edamontology.org/operation_4008": "Protein design", + "http://edamontology.org/operation_4009": "Small molecule design", + "http://edamontology.org/topic_0003": "Topic", + "http://edamontology.org/topic_0077": "Nucleic acids", + "http://edamontology.org/topic_0078": "Proteins", + "http://edamontology.org/topic_0079": "Metabolites", + "http://edamontology.org/topic_0080": "Sequence analysis", + "http://edamontology.org/topic_0081": "Structure analysis", + "http://edamontology.org/topic_0082": "Structure prediction", + "http://edamontology.org/topic_0083": "Alignment", + "http://edamontology.org/topic_0084": "Phylogeny", + "http://edamontology.org/topic_0085": "Functional genomics", + "http://edamontology.org/topic_0089": "Ontology and terminology", + "http://edamontology.org/topic_0090": "Information retrieval", + "http://edamontology.org/topic_0091": "Bioinformatics", + "http://edamontology.org/topic_0092": "Data visualisation", + "http://edamontology.org/topic_0094": "Nucleic acid thermodynamics", + "http://edamontology.org/topic_0097": "Nucleic acid structure analysis", + "http://edamontology.org/topic_0099": "RNA", + "http://edamontology.org/topic_0100": "Nucleic acid restriction", + "http://edamontology.org/topic_0102": "Mapping", + "http://edamontology.org/topic_0107": "Genetic codes and codon usage", + "http://edamontology.org/topic_0108": "Protein expression", + "http://edamontology.org/topic_0109": "Gene finding", + "http://edamontology.org/topic_0110": "Transcription", + "http://edamontology.org/topic_0111": "Promoters", + "http://edamontology.org/topic_0112": "Nucleic acid folding", + "http://edamontology.org/topic_0114": "Gene structure", + "http://edamontology.org/topic_0121": "Proteomics", + "http://edamontology.org/topic_0122": "Structural genomics", + "http://edamontology.org/topic_0123": "Protein properties", + "http://edamontology.org/topic_0128": "Protein interactions", + "http://edamontology.org/topic_0130": "Protein folding, stability and design", + "http://edamontology.org/topic_0133": "Two-dimensional gel electrophoresis", + "http://edamontology.org/topic_0134": "Mass spectrometry", + "http://edamontology.org/topic_0135": "Protein microarrays", + "http://edamontology.org/topic_0137": "Protein hydropathy", + "http://edamontology.org/topic_0140": "Protein targeting and localisation", + "http://edamontology.org/topic_0141": "Protein cleavage sites and proteolysis", + "http://edamontology.org/topic_0143": "Protein structure comparison", + "http://edamontology.org/topic_0144": "Protein residue interactions", + "http://edamontology.org/topic_0147": "Protein-protein interactions", + "http://edamontology.org/topic_0148": "Protein-ligand interactions", + "http://edamontology.org/topic_0149": "Protein-nucleic acid interactions", + "http://edamontology.org/topic_0150": "Protein design", + "http://edamontology.org/topic_0151": "G protein-coupled receptors (GPCR)", + "http://edamontology.org/topic_0152": "Carbohydrates", + "http://edamontology.org/topic_0153": "Lipids", + "http://edamontology.org/topic_0154": "Small molecules", + "http://edamontology.org/topic_0156": "Sequence editing", + "http://edamontology.org/topic_0157": "Sequence composition, complexity and repeats", + "http://edamontology.org/topic_0158": "Sequence motifs", + "http://edamontology.org/topic_0159": "Sequence comparison", + "http://edamontology.org/topic_0160": "Sequence sites, features and motifs", + "http://edamontology.org/topic_0163": "Sequence database search", + "http://edamontology.org/topic_0164": "Sequence clustering", + "http://edamontology.org/topic_0166": "Protein structural motifs and surfaces", + "http://edamontology.org/topic_0167": "Structural (3D) profiles", + "http://edamontology.org/topic_0172": "Protein structure prediction", + "http://edamontology.org/topic_0173": "Nucleic acid structure prediction", + "http://edamontology.org/topic_0174": "Ab initio structure prediction", + "http://edamontology.org/topic_0175": "Homology modelling", + "http://edamontology.org/topic_0176": "Molecular dynamics", + "http://edamontology.org/topic_0177": "Molecular docking", + "http://edamontology.org/topic_0178": "Protein secondary structure prediction", + "http://edamontology.org/topic_0179": "Protein tertiary structure prediction", + "http://edamontology.org/topic_0180": "Protein fold recognition", + "http://edamontology.org/topic_0182": "Sequence alignment", + "http://edamontology.org/topic_0183": "Structure alignment", + "http://edamontology.org/topic_0184": "Threading", + "http://edamontology.org/topic_0188": "Sequence profiles and HMMs", + "http://edamontology.org/topic_0191": "Phylogeny reconstruction", + "http://edamontology.org/topic_0194": "Phylogenomics", + "http://edamontology.org/topic_0195": "Virtual PCR", + "http://edamontology.org/topic_0196": "Sequence assembly", + "http://edamontology.org/topic_0199": "Genetic variation", + "http://edamontology.org/topic_0200": "Microarrays", + "http://edamontology.org/topic_0202": "Pharmacology", + "http://edamontology.org/topic_0203": "Gene expression", + "http://edamontology.org/topic_0204": "Gene regulation", + "http://edamontology.org/topic_0208": "Pharmacogenomics", + "http://edamontology.org/topic_0209": "Medicinal chemistry", + "http://edamontology.org/topic_0210": "Fish", + "http://edamontology.org/topic_0211": "Flies", + "http://edamontology.org/topic_0213": "Mice or rats", + "http://edamontology.org/topic_0215": "Worms", + "http://edamontology.org/topic_0217": "Literature analysis", + "http://edamontology.org/topic_0218": "Natural language processing", + "http://edamontology.org/topic_0219": "Data submission, annotation and curation", + "http://edamontology.org/topic_0220": "Document, record and content management", + "http://edamontology.org/topic_0221": "Sequence annotation", + "http://edamontology.org/topic_0222": "Genome annotation", + "http://edamontology.org/topic_0593": "NMR", + "http://edamontology.org/topic_0594": "Sequence classification", + "http://edamontology.org/topic_0595": "Protein classification", + "http://edamontology.org/topic_0598": "Sequence motif or profile", + "http://edamontology.org/topic_0601": "Protein modifications", + "http://edamontology.org/topic_0602": "Molecular interactions, pathways and networks", + "http://edamontology.org/topic_0605": "Informatics", + "http://edamontology.org/topic_0606": "Literature data resources", + "http://edamontology.org/topic_0607": "Laboratory information management", + "http://edamontology.org/topic_0608": "Cell and tissue culture", + "http://edamontology.org/topic_0610": "Ecology", + "http://edamontology.org/topic_0611": "Electron microscopy", + "http://edamontology.org/topic_0612": "Cell cycle", + "http://edamontology.org/topic_0613": "Peptides and amino acids", + "http://edamontology.org/topic_0616": "Organelles", + "http://edamontology.org/topic_0617": "Ribosomes", + "http://edamontology.org/topic_0618": "Scents", + "http://edamontology.org/topic_0620": "Drugs and target structures", + "http://edamontology.org/topic_0621": "Model organisms", + "http://edamontology.org/topic_0622": "Genomics", + "http://edamontology.org/topic_0623": "Gene and protein families", + "http://edamontology.org/topic_0624": "Chromosomes", + "http://edamontology.org/topic_0625": "Genotype and phenotype", + "http://edamontology.org/topic_0629": "Gene expression and microarray", + "http://edamontology.org/topic_0632": "Probes and primers", + "http://edamontology.org/topic_0634": "Pathology", + "http://edamontology.org/topic_0635": "Specific protein resources", + "http://edamontology.org/topic_0637": "Taxonomy", + "http://edamontology.org/topic_0639": "Protein sequence analysis", + "http://edamontology.org/topic_0640": "Nucleic acid sequence analysis", + "http://edamontology.org/topic_0641": "Repeat sequences", + "http://edamontology.org/topic_0642": "Low complexity sequences", + "http://edamontology.org/topic_0644": "Proteome", + "http://edamontology.org/topic_0654": "DNA", + "http://edamontology.org/topic_0655": "Coding RNA", + "http://edamontology.org/topic_0659": "Functional, regulatory and non-coding RNA", + "http://edamontology.org/topic_0660": "rRNA", + "http://edamontology.org/topic_0663": "tRNA", + "http://edamontology.org/topic_0694": "Protein secondary structure", + "http://edamontology.org/topic_0697": "RNA structure", + "http://edamontology.org/topic_0698": "Protein tertiary structure", + "http://edamontology.org/topic_0722": "Nucleic acid classification", + "http://edamontology.org/topic_0724": "Protein families", + "http://edamontology.org/topic_0736": "Protein folds and structural domains", + "http://edamontology.org/topic_0740": "Nucleic acid sequence alignment", + "http://edamontology.org/topic_0741": "Protein sequence alignment", + "http://edamontology.org/topic_0747": "Nucleic acid sites and features", + "http://edamontology.org/topic_0748": "Protein sites and features", + "http://edamontology.org/topic_0749": "Transcription factors and regulatory sites", + "http://edamontology.org/topic_0751": "Phosphorylation sites", + "http://edamontology.org/topic_0753": "Metabolic pathways", + "http://edamontology.org/topic_0754": "Signaling pathways", + "http://edamontology.org/topic_0767": "Protein and peptide identification", + "http://edamontology.org/topic_0769": "Workflows", + "http://edamontology.org/topic_0770": "Data types and objects", + "http://edamontology.org/topic_0771": "Theoretical biology", + "http://edamontology.org/topic_0779": "Mitochondria", + "http://edamontology.org/topic_0780": "Plant biology", + "http://edamontology.org/topic_0781": "Virology", + "http://edamontology.org/topic_0782": "Fungi", + "http://edamontology.org/topic_0783": "Pathogens", + "http://edamontology.org/topic_0786": "Arabidopsis", + "http://edamontology.org/topic_0787": "Rice", + "http://edamontology.org/topic_0796": "Genetic mapping and linkage", + "http://edamontology.org/topic_0797": "Comparative genomics", + "http://edamontology.org/topic_0798": "Mobile genetic elements", + "http://edamontology.org/topic_0803": "Human disease", + "http://edamontology.org/topic_0804": "Immunology", + "http://edamontology.org/topic_0820": "Membrane and lipoproteins", + "http://edamontology.org/topic_0821": "Enzymes", + "http://edamontology.org/topic_0922": "Primers", + "http://edamontology.org/topic_1302": "PolyA signal or sites", + "http://edamontology.org/topic_1304": "CpG island and isochores", + "http://edamontology.org/topic_1305": "Restriction sites", + "http://edamontology.org/topic_1307": "Splice sites", + "http://edamontology.org/topic_1308": "Matrix/scaffold attachment sites", + "http://edamontology.org/topic_1311": "Operon", + "http://edamontology.org/topic_1312": "Promoters", + "http://edamontology.org/topic_1317": "Structural biology", + "http://edamontology.org/topic_1456": "Protein membrane regions", + "http://edamontology.org/topic_1770": "Structure comparison", + "http://edamontology.org/topic_1775": "Function analysis", + "http://edamontology.org/topic_1811": "Prokaryotes and Archaea", + "http://edamontology.org/topic_2225": "Protein databases", + "http://edamontology.org/topic_2226": "Structure determination", + "http://edamontology.org/topic_2229": "Cell biology", + "http://edamontology.org/topic_2230": "Classification", + "http://edamontology.org/topic_2232": "Lipoproteins", + "http://edamontology.org/topic_2257": "Phylogeny visualisation", + "http://edamontology.org/topic_2258": "Cheminformatics", + "http://edamontology.org/topic_2259": "Systems biology", + "http://edamontology.org/topic_2269": "Statistics and probability", + "http://edamontology.org/topic_2271": "Structure database search", + "http://edamontology.org/topic_2275": "Molecular modelling", + "http://edamontology.org/topic_2276": "Protein function prediction", + "http://edamontology.org/topic_2277": "SNP", + "http://edamontology.org/topic_2278": "Transmembrane protein prediction", + "http://edamontology.org/topic_2280": "Nucleic acid structure comparison", + "http://edamontology.org/topic_2397": "Exons", + "http://edamontology.org/topic_2399": "Gene transcription", + "http://edamontology.org/topic_2533": "DNA mutation", + "http://edamontology.org/topic_2640": "Oncology", + "http://edamontology.org/topic_2661": "Toxins and targets", + "http://edamontology.org/topic_2754": "Introns", + "http://edamontology.org/topic_2807": "Tool topic", + "http://edamontology.org/topic_2809": "Study topic", + "http://edamontology.org/topic_2811": "Nomenclature", + "http://edamontology.org/topic_2813": "Disease genes and proteins", + "http://edamontology.org/topic_2814": "Protein structure analysis", + "http://edamontology.org/topic_2815": "Human biology", + "http://edamontology.org/topic_2816": "Gene resources", + "http://edamontology.org/topic_2817": "Yeast", + "http://edamontology.org/topic_2818": "Eukaryotes", + "http://edamontology.org/topic_2819": "Invertebrates", + "http://edamontology.org/topic_2820": "Vertebrates", + "http://edamontology.org/topic_2821": "Unicellular eukaryotes", + "http://edamontology.org/topic_2826": "Protein structure alignment", + "http://edamontology.org/topic_2828": "X-ray diffraction", + "http://edamontology.org/topic_2829": "Ontologies, nomenclature and classification", + "http://edamontology.org/topic_2830": "Immunoproteins and antigens", + "http://edamontology.org/topic_2839": "Molecules", + "http://edamontology.org/topic_2840": "Toxicology", + "http://edamontology.org/topic_2842": "High-throughput sequencing", + "http://edamontology.org/topic_2846": "Gene regulatory networks", + "http://edamontology.org/topic_2847": "Disease (specific)", + "http://edamontology.org/topic_2867": "VNTR", + "http://edamontology.org/topic_2868": "Microsatellites", + "http://edamontology.org/topic_2869": "RFLP", + "http://edamontology.org/topic_2885": "DNA polymorphism", + "http://edamontology.org/topic_2953": "Nucleic acid design", + "http://edamontology.org/topic_3032": "Primer or probe design", + "http://edamontology.org/topic_3038": "Structure databases", + "http://edamontology.org/topic_3039": "Nucleic acid structure", + "http://edamontology.org/topic_3041": "Sequence databases", + "http://edamontology.org/topic_3042": "Nucleic acid sequences", + "http://edamontology.org/topic_3043": "Protein sequences", + "http://edamontology.org/topic_3044": "Protein interaction networks", + "http://edamontology.org/topic_3047": "Molecular biology", + "http://edamontology.org/topic_3048": "Mammals", + "http://edamontology.org/topic_3050": "Biodiversity", + "http://edamontology.org/topic_3052": "Sequence clusters and classification", + "http://edamontology.org/topic_3053": "Genetics", + "http://edamontology.org/topic_3055": "Quantitative genetics", + "http://edamontology.org/topic_3056": "Population genetics", + "http://edamontology.org/topic_3060": "Regulatory RNA", + "http://edamontology.org/topic_3061": "Documentation and help", + "http://edamontology.org/topic_3062": "Genetic organisation", + "http://edamontology.org/topic_3063": "Medical informatics", + "http://edamontology.org/topic_3064": "Developmental biology", + "http://edamontology.org/topic_3065": "Embryology", + "http://edamontology.org/topic_3067": "Anatomy", + "http://edamontology.org/topic_3068": "Literature and language", + "http://edamontology.org/topic_3070": "Biology", + "http://edamontology.org/topic_3071": "Biological databases", + "http://edamontology.org/topic_3072": "Sequence feature detection", + "http://edamontology.org/topic_3073": "Nucleic acid feature detection", + "http://edamontology.org/topic_3074": "Protein feature detection", + "http://edamontology.org/topic_3075": "Biological system modelling", + "http://edamontology.org/topic_3077": "Data acquisition", + "http://edamontology.org/topic_3078": "Genes and proteins resources", + "http://edamontology.org/topic_3118": "Protein topological domains", + "http://edamontology.org/topic_3120": "Protein variants", + "http://edamontology.org/topic_3123": "Expression signals", + "http://edamontology.org/topic_3125": "DNA binding sites", + "http://edamontology.org/topic_3126": "Nucleic acid repeats", + "http://edamontology.org/topic_3127": "DNA replication and recombination", + "http://edamontology.org/topic_3135": "Signal or transit peptide", + "http://edamontology.org/topic_3139": "Sequence tagged sites", + "http://edamontology.org/topic_3168": "Sequencing", + "http://edamontology.org/topic_3169": "ChIP-seq", + "http://edamontology.org/topic_3170": "RNA-Seq", + "http://edamontology.org/topic_3171": "DNA methylation", + "http://edamontology.org/topic_3172": "Metabolomics", + "http://edamontology.org/topic_3173": "Epigenomics", + "http://edamontology.org/topic_3174": "Metagenomics", + "http://edamontology.org/topic_3175": "Structural variation", + "http://edamontology.org/topic_3176": "DNA packaging", + "http://edamontology.org/topic_3177": "DNA-Seq", + "http://edamontology.org/topic_3178": "RNA-Seq alignment", + "http://edamontology.org/topic_3179": "ChIP-on-chip", + "http://edamontology.org/topic_3263": "Data security", + "http://edamontology.org/topic_3277": "Sample collections", + "http://edamontology.org/topic_3292": "Biochemistry", + "http://edamontology.org/topic_3293": "Phylogenetics", + "http://edamontology.org/topic_3295": "Epigenetics", + "http://edamontology.org/topic_3297": "Biotechnology", + "http://edamontology.org/topic_3298": "Phenomics", + "http://edamontology.org/topic_3299": "Evolutionary biology", + "http://edamontology.org/topic_3300": "Physiology", + "http://edamontology.org/topic_3301": "Microbiology", + "http://edamontology.org/topic_3302": "Parasitology", + "http://edamontology.org/topic_3303": "Medicine", + "http://edamontology.org/topic_3304": "Neurobiology", + "http://edamontology.org/topic_3305": "Public health and epidemiology", + "http://edamontology.org/topic_3306": "Biophysics", + "http://edamontology.org/topic_3307": "Computational biology", + "http://edamontology.org/topic_3308": "Transcriptomics", + "http://edamontology.org/topic_3314": "Chemistry", + "http://edamontology.org/topic_3315": "Mathematics", + "http://edamontology.org/topic_3316": "Computer science", + "http://edamontology.org/topic_3318": "Physics", + "http://edamontology.org/topic_3320": "RNA splicing", + "http://edamontology.org/topic_3321": "Molecular genetics", + "http://edamontology.org/topic_3322": "Respiratory medicine", + "http://edamontology.org/topic_3323": "Metabolic disease", + "http://edamontology.org/topic_3324": "Infectious disease", + "http://edamontology.org/topic_3325": "Rare diseases", + "http://edamontology.org/topic_3332": "Computational chemistry", + "http://edamontology.org/topic_3334": "Neurology", + "http://edamontology.org/topic_3335": "Cardiology", + "http://edamontology.org/topic_3336": "Drug discovery", + "http://edamontology.org/topic_3337": "Biobank", + "http://edamontology.org/topic_3338": "Mouse clinic", + "http://edamontology.org/topic_3339": "Microbial collection", + "http://edamontology.org/topic_3340": "Cell culture collection", + "http://edamontology.org/topic_3341": "Clone library", + "http://edamontology.org/topic_3342": "Translational medicine", + "http://edamontology.org/topic_3343": "Compound libraries and screening", + "http://edamontology.org/topic_3344": "Biomedical science", + "http://edamontology.org/topic_3345": "Data identity and mapping", + "http://edamontology.org/topic_3346": "Sequence search", + "http://edamontology.org/topic_3360": "Biomarkers", + "http://edamontology.org/topic_3361": "Laboratory techniques", + "http://edamontology.org/topic_3365": "Data architecture, analysis and design", + "http://edamontology.org/topic_3366": "Data integration and warehousing", + "http://edamontology.org/topic_3368": "Biomaterials", + "http://edamontology.org/topic_3369": "Chemical biology", + "http://edamontology.org/topic_3370": "Analytical chemistry", + "http://edamontology.org/topic_3371": "Synthetic chemistry", + "http://edamontology.org/topic_3372": "Software engineering", + "http://edamontology.org/topic_3373": "Drug development", + "http://edamontology.org/topic_3374": "Biotherapeutics", + "http://edamontology.org/topic_3375": "Drug metabolism", + "http://edamontology.org/topic_3376": "Medicines research and development", + "http://edamontology.org/topic_3377": "Safety sciences", + "http://edamontology.org/topic_3378": "Pharmacovigilance", + "http://edamontology.org/topic_3379": "Preclinical and clinical studies", + "http://edamontology.org/topic_3382": "Imaging", + "http://edamontology.org/topic_3383": "Bioimaging", + "http://edamontology.org/topic_3384": "Medical imaging", + "http://edamontology.org/topic_3385": "Light microscopy", + "http://edamontology.org/topic_3386": "Laboratory animal science", + "http://edamontology.org/topic_3387": "Marine biology", + "http://edamontology.org/topic_3388": "Molecular medicine", + "http://edamontology.org/topic_3390": "Nutritional science", + "http://edamontology.org/topic_3391": "Omics", + "http://edamontology.org/topic_3393": "Quality affairs", + "http://edamontology.org/topic_3394": "Regulatory affairs", + "http://edamontology.org/topic_3395": "Regenerative medicine", + "http://edamontology.org/topic_3396": "Systems medicine", + "http://edamontology.org/topic_3397": "Veterinary medicine", + "http://edamontology.org/topic_3398": "Bioengineering", + "http://edamontology.org/topic_3399": "Geriatric medicine", + "http://edamontology.org/topic_3400": "Allergy, clinical immunology and immunotherapeutics", + "http://edamontology.org/topic_3401": "Pain medicine", + "http://edamontology.org/topic_3402": "Anaesthesiology", + "http://edamontology.org/topic_3403": "Critical care medicine", + "http://edamontology.org/topic_3404": "Dermatology", + "http://edamontology.org/topic_3405": "Dentistry", + "http://edamontology.org/topic_3406": "Ear, nose and throat medicine", + "http://edamontology.org/topic_3407": "Endocrinology and metabolism", + "http://edamontology.org/topic_3408": "Haematology", + "http://edamontology.org/topic_3409": "Gastroenterology", + "http://edamontology.org/topic_3410": "Gender medicine", + "http://edamontology.org/topic_3411": "Gynaecology and obstetrics", + "http://edamontology.org/topic_3412": "Hepatic and biliary medicine", + "http://edamontology.org/topic_3413": "Infectious tropical disease", + "http://edamontology.org/topic_3414": "Trauma medicine", + "http://edamontology.org/topic_3415": "Medical toxicology", + "http://edamontology.org/topic_3416": "Musculoskeletal medicine", + "http://edamontology.org/topic_3417": "Opthalmology", + "http://edamontology.org/topic_3418": "Paediatrics", + "http://edamontology.org/topic_3419": "Psychiatry", + "http://edamontology.org/topic_3420": "Reproductive health", + "http://edamontology.org/topic_3421": "Surgery", + "http://edamontology.org/topic_3422": "Urology and nephrology", + "http://edamontology.org/topic_3423": "Complementary medicine", + "http://edamontology.org/topic_3444": "MRI", + "http://edamontology.org/topic_3448": "Neutron diffraction", + "http://edamontology.org/topic_3452": "Tomography", + "http://edamontology.org/topic_3473": "Data mining", + "http://edamontology.org/topic_3474": "Machine learning", + "http://edamontology.org/topic_3489": "Database management", + "http://edamontology.org/topic_3500": "Zoology", + "http://edamontology.org/topic_3510": "Protein sites, features and motifs", + "http://edamontology.org/topic_3511": "Nucleic acid sites, features and motifs", + "http://edamontology.org/topic_3512": "Gene transcripts", + "http://edamontology.org/topic_3514": "Protein-ligand interactions", + "http://edamontology.org/topic_3515": "Protein-drug interactions", + "http://edamontology.org/topic_3516": "Genotyping experiment", + "http://edamontology.org/topic_3517": "GWAS study", + "http://edamontology.org/topic_3518": "Microarray experiment", + "http://edamontology.org/topic_3519": "PCR experiment", + "http://edamontology.org/topic_3520": "Proteomics experiment", + "http://edamontology.org/topic_3521": "2D PAGE experiment", + "http://edamontology.org/topic_3522": "Northern blot experiment", + "http://edamontology.org/topic_3523": "RNAi experiment", + "http://edamontology.org/topic_3524": "Simulation experiment", + "http://edamontology.org/topic_3525": "Protein-nucleic acid interactions", + "http://edamontology.org/topic_3526": "Protein-protein interactions", + "http://edamontology.org/topic_3527": "Cellular process pathways", + "http://edamontology.org/topic_3528": "Disease pathways", + "http://edamontology.org/topic_3529": "Environmental information processing pathways", + "http://edamontology.org/topic_3530": "Genetic information processing pathways", + "http://edamontology.org/topic_3531": "Protein super-secondary structure", + "http://edamontology.org/topic_3533": "Protein active sites", + "http://edamontology.org/topic_3534": "Protein binding sites", + "http://edamontology.org/topic_3535": "Protein-nucleic acid binding sites", + "http://edamontology.org/topic_3536": "Protein cleavage sites", + "http://edamontology.org/topic_3537": "Protein chemical modifications", + "http://edamontology.org/topic_3538": "Protein disordered structure", + "http://edamontology.org/topic_3539": "Protein domains", + "http://edamontology.org/topic_3540": "Protein key folding sites", + "http://edamontology.org/topic_3541": "Protein post-translational modifications", + "http://edamontology.org/topic_3542": "Protein secondary structure", + "http://edamontology.org/topic_3543": "Protein sequence repeats", + "http://edamontology.org/topic_3544": "Protein signal peptides", + "http://edamontology.org/topic_3569": "Applied mathematics", + "http://edamontology.org/topic_3570": "Pure mathematics", + "http://edamontology.org/topic_3571": "Data governance", + "http://edamontology.org/topic_3572": "Data quality management", + "http://edamontology.org/topic_3573": "Freshwater biology", + "http://edamontology.org/topic_3574": "Human genetics", + "http://edamontology.org/topic_3575": "Tropical medicine", + "http://edamontology.org/topic_3576": "Medical biotechnology", + "http://edamontology.org/topic_3577": "Personalised medicine", + "http://edamontology.org/topic_3656": "Immunoprecipitation experiment", + "http://edamontology.org/topic_3673": "Whole genome sequencing", + "http://edamontology.org/topic_3674": "Methylated DNA immunoprecipitation", + "http://edamontology.org/topic_3676": "Exome sequencing", + "http://edamontology.org/topic_3678": "Experimental design and studies", + "http://edamontology.org/topic_3679": "Animal study", + "http://edamontology.org/topic_3697": "Microbial ecology", + "http://edamontology.org/topic_3794": "RNA immunoprecipitation", + "http://edamontology.org/topic_3796": "Population genomics", + "http://edamontology.org/topic_3810": "Agricultural science", + "http://edamontology.org/topic_3837": "Metagenomic sequencing", + "http://edamontology.org/topic_3855": "Environmental science", + "http://edamontology.org/topic_3892": "Biomolecular simulation", + "http://edamontology.org/topic_3895": "Synthetic biology", + "http://edamontology.org/topic_3912": "Genetic engineering", + "http://edamontology.org/topic_3922": "Proteogenomics", + "http://edamontology.org/topic_3930": "Immunogenetics", + "http://edamontology.org/topic_3934": "Cytometry", + "http://edamontology.org/topic_3940": "Chromosome conformation capture", + "http://edamontology.org/topic_3941": "Metatranscriptomics", + "http://edamontology.org/topic_3943": "Paleogenomics", + "http://edamontology.org/topic_3944": "Cladistics", + "http://edamontology.org/topic_3945": "Molecular evolution", + "http://edamontology.org/topic_3948": "Immunoinformatics", + "http://edamontology.org/topic_3954": "Echography", + "http://edamontology.org/topic_3955": "Fluxomics", + "http://edamontology.org/topic_3957": "Protein interaction experiment", + "http://edamontology.org/topic_3958": "Copy number variation", + "http://edamontology.org/topic_3959": "Cytogenetics", + "http://edamontology.org/topic_3966": "Vaccinology", + "http://edamontology.org/topic_3967": "Immunomics", + "http://edamontology.org/topic_3974": "Epistasis" +} \ No newline at end of file From 12233256580601955d87a19900366e5f0d38f8ec Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 13:05:17 +0200 Subject: [PATCH 09/18] refactor: load EDAM OWL lazily on demand instead of static JSON Replace bundled edam_labels.json with live OWL fetch via EdamLabels. ensureLoaded() blocks synchronously on first call (double-checked lock), subsequent calls return immediately. Add GET /alternatives/warm so the frontend can trigger loading on page mount before the first upload. --- .../controller/AlternativesController.java | 12 + .../nl/esciencecenter/restape/EdamLabels.java | 80 +- src/main/resources/edam_labels.json | 3473 ----------------- 3 files changed, 69 insertions(+), 3496 deletions(-) delete mode 100644 src/main/resources/edam_labels.json diff --git a/src/main/java/nl/esciencecenter/controller/AlternativesController.java b/src/main/java/nl/esciencecenter/controller/AlternativesController.java index 2ec7bc7..33b04e3 100644 --- a/src/main/java/nl/esciencecenter/controller/AlternativesController.java +++ b/src/main/java/nl/esciencecenter/controller/AlternativesController.java @@ -6,6 +6,7 @@ import org.springframework.http.MediaType; import org.springframework.http.ResponseEntity; import org.springframework.web.bind.annotation.ExceptionHandler; +import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.PostMapping; import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.RequestParam; @@ -27,6 +28,16 @@ public class AlternativesController { @Autowired private EdamLabels edamLabels; + /** + * Ensures the EDAM label index is ready. Blocks until loading completes. + * The frontend calls this on page mount to trigger loading before the first upload. + */ + @GetMapping("/warm") + public ResponseEntity warm() { + edamLabels.ensureLoaded(); + return ResponseEntity.ok().build(); + } + /** * Parses a CWL v1.2 workflow and returns its DAG representation plus * workflow-level I/O terms for use as APE synthesis constraints (concept §2.3, §3.2). @@ -48,6 +59,7 @@ public class AlternativesController { }) public ResponseEntity parseCwl( @RequestParam("cwl_file") MultipartFile cwlFile) throws IOException { + edamLabels.ensureLoaded(); ParseResponse response = CwlParser.parse(cwlFile.getInputStream(), edamLabels::resolve); return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(response); } diff --git a/src/main/java/nl/esciencecenter/restape/EdamLabels.java b/src/main/java/nl/esciencecenter/restape/EdamLabels.java index fcbe180..abb9e97 100644 --- a/src/main/java/nl/esciencecenter/restape/EdamLabels.java +++ b/src/main/java/nl/esciencecenter/restape/EdamLabels.java @@ -1,46 +1,80 @@ package nl.esciencecenter.restape; -import java.io.IOException; -import java.io.InputStream; import java.util.Collections; +import java.util.HashMap; import java.util.Map; -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.ObjectMapper; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.MissingImportHandlingStrategy; +import org.semanticweb.owlapi.model.OWLAnnotationValue; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.search.EntitySearcher; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.stereotype.Component; /** - * Resolves EDAM URIs to human-readable labels using a pre-built static mapping - * bundled as a classpath resource (edam_labels.json). + * Resolves EDAM URIs to human-readable labels. + * The EDAM ontology is fetched and indexed on the first call to {@link #ensureLoaded()}, + * which blocks until loading completes. Subsequent calls return immediately. */ @Component public class EdamLabels { private static final Logger log = LoggerFactory.getLogger(EdamLabels.class); - private static final String RESOURCE = "/edam_labels.json"; - - private final Map labels; - - public EdamLabels() { - Map loaded = Collections.emptyMap(); - try (InputStream is = EdamLabels.class.getResourceAsStream(RESOURCE)) { - if (is == null) { - log.warn("edam_labels.json not found on classpath — URIs will be shown as short-form IDs"); - } else { - loaded = new ObjectMapper().readValue(is, new TypeReference<>() {}); - log.info("EDAM labels loaded: {} entries", loaded.size()); - } - } catch (IOException e) { - log.warn("Failed to load edam_labels.json: {}", e.getMessage()); + + static final String EDAM_OWL_IRI = + "https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/domains/edam.owl"; + + private volatile Map labels = null; + + /** + * Triggers loading if not already done and blocks until the index is ready. + * Safe to call concurrently — only one thread performs the actual load. + */ + public synchronized void ensureLoaded() { + if (labels != null) return; + log.info("Loading EDAM ontology from {}", EDAM_OWL_IRI); + try { + OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); + OWLOntologyLoaderConfiguration cfg = new OWLOntologyLoaderConfiguration() + .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); + manager.setOntologyLoaderConfiguration(cfg); + + OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(EDAM_OWL_IRI)); + OWLDataFactory factory = manager.getOWLDataFactory(); + + Map map = new HashMap<>(); + ontology.getClassesInSignature().forEach(cls -> { + String iri = cls.getIRI().toString(); + EntitySearcher.getAnnotations(cls, ontology, factory.getRDFSLabel()) + .findFirst() + .ifPresent(ann -> { + OWLAnnotationValue val = ann.getValue(); + if (val instanceof OWLLiteral lit) { + map.put(iri, lit.getLiteral()); + } + }); + }); + + labels = Collections.unmodifiableMap(map); + log.info("EDAM ontology loaded: {} labels indexed.", labels.size()); + } catch (Exception e) { + log.error("Failed to load EDAM ontology: {}", e.getMessage()); + throw new IllegalStateException("EDAM ontology could not be loaded: " + e.getMessage(), e); } - this.labels = Collections.unmodifiableMap(loaded); } public String resolve(String uri) { if (uri == null || uri.isBlank()) return ""; - return labels.getOrDefault(uri, shortForm(uri)); + Map map = labels; + if (map == null) return shortForm(uri); + return map.getOrDefault(uri, shortForm(uri)); } static String shortForm(String uri) { diff --git a/src/main/resources/edam_labels.json b/src/main/resources/edam_labels.json deleted file mode 100644 index 3ed0b2a..0000000 --- a/src/main/resources/edam_labels.json +++ /dev/null @@ -1,3473 +0,0 @@ -{ - "http://edamontology.org/data_0005": "Resource type", - "http://edamontology.org/data_0006": "Data", - "http://edamontology.org/data_0007": "Tool", - "http://edamontology.org/data_0581": "Database", - "http://edamontology.org/data_0582": "Ontology", - "http://edamontology.org/data_0583": "Directory metadata", - "http://edamontology.org/data_0831": "MeSH vocabulary", - "http://edamontology.org/data_0832": "HGNC vocabulary", - "http://edamontology.org/data_0835": "UMLS vocabulary", - "http://edamontology.org/data_0842": "Identifier", - "http://edamontology.org/data_0843": "Database entry", - "http://edamontology.org/data_0844": "Molecular mass", - "http://edamontology.org/data_0845": "Molecular charge", - "http://edamontology.org/data_0846": "Chemical formula", - "http://edamontology.org/data_0847": "QSAR descriptor", - "http://edamontology.org/data_0848": "Raw sequence", - "http://edamontology.org/data_0849": "Sequence record", - "http://edamontology.org/data_0850": "Sequence set", - "http://edamontology.org/data_0851": "Sequence mask character", - "http://edamontology.org/data_0852": "Sequence mask type", - "http://edamontology.org/data_0853": "DNA sense specification", - "http://edamontology.org/data_0854": "Sequence length specification", - "http://edamontology.org/data_0855": "Sequence metadata", - "http://edamontology.org/data_0856": "Sequence feature source", - "http://edamontology.org/data_0857": "Sequence search results", - "http://edamontology.org/data_0858": "Sequence signature matches", - "http://edamontology.org/data_0859": "Sequence signature model", - "http://edamontology.org/data_0860": "Sequence signature data", - "http://edamontology.org/data_0861": "Sequence alignment (words)", - "http://edamontology.org/data_0862": "Dotplot", - "http://edamontology.org/data_0863": "Sequence alignment", - "http://edamontology.org/data_0864": "Sequence alignment parameter", - "http://edamontology.org/data_0865": "Sequence similarity score", - "http://edamontology.org/data_0866": "Sequence alignment metadata", - "http://edamontology.org/data_0867": "Sequence alignment report", - "http://edamontology.org/data_0868": "Profile-profile alignment", - "http://edamontology.org/data_0869": "Sequence-profile alignment", - "http://edamontology.org/data_0870": "Sequence distance matrix", - "http://edamontology.org/data_0871": "Phylogenetic character data", - "http://edamontology.org/data_0872": "Phylogenetic tree", - "http://edamontology.org/data_0874": "Comparison matrix", - "http://edamontology.org/data_0875": "Protein topology", - "http://edamontology.org/data_0876": "Protein features report (secondary structure)", - "http://edamontology.org/data_0877": "Protein features report (super-secondary)", - "http://edamontology.org/data_0878": "Protein secondary structure alignment", - "http://edamontology.org/data_0879": "Secondary structure alignment metadata (protein)", - "http://edamontology.org/data_0880": "RNA secondary structure", - "http://edamontology.org/data_0881": "RNA secondary structure alignment", - "http://edamontology.org/data_0882": "Secondary structure alignment metadata (RNA)", - "http://edamontology.org/data_0883": "Structure", - "http://edamontology.org/data_0884": "Tertiary structure record", - "http://edamontology.org/data_0885": "Structure database search results", - "http://edamontology.org/data_0886": "Structure alignment", - "http://edamontology.org/data_0887": "Structure alignment report", - "http://edamontology.org/data_0888": "Structure similarity score", - "http://edamontology.org/data_0889": "Structural profile", - "http://edamontology.org/data_0890": "Structural (3D) profile alignment", - "http://edamontology.org/data_0891": "Sequence-3D profile alignment", - "http://edamontology.org/data_0892": "Protein sequence-structure scoring matrix", - "http://edamontology.org/data_0893": "Sequence-structure alignment", - "http://edamontology.org/data_0894": "Amino acid annotation", - "http://edamontology.org/data_0895": "Peptide annotation", - "http://edamontology.org/data_0896": "Protein report", - "http://edamontology.org/data_0897": "Protein property", - "http://edamontology.org/data_0899": "Protein structural motifs and surfaces", - "http://edamontology.org/data_0900": "Protein domain classification", - "http://edamontology.org/data_0901": "Protein features report (domains)", - "http://edamontology.org/data_0902": "Protein architecture report", - "http://edamontology.org/data_0903": "Protein folding report", - "http://edamontology.org/data_0904": "Protein features (mutation)", - "http://edamontology.org/data_0905": "Protein interaction raw data", - "http://edamontology.org/data_0906": "Protein interaction data", - "http://edamontology.org/data_0907": "Protein family report", - "http://edamontology.org/data_0909": "Vmax", - "http://edamontology.org/data_0910": "Km", - "http://edamontology.org/data_0911": "Nucleotide base annotation", - "http://edamontology.org/data_0912": "Nucleic acid property", - "http://edamontology.org/data_0914": "Codon usage data", - "http://edamontology.org/data_0916": "Gene report", - "http://edamontology.org/data_0917": "Gene classification", - "http://edamontology.org/data_0918": "DNA variation", - "http://edamontology.org/data_0919": "Chromosome report", - "http://edamontology.org/data_0920": "Genotype/phenotype report", - "http://edamontology.org/data_0923": "PCR experiment report", - "http://edamontology.org/data_0924": "Sequence trace", - "http://edamontology.org/data_0925": "Sequence assembly", - "http://edamontology.org/data_0926": "RH scores", - "http://edamontology.org/data_0927": "Genetic linkage report", - "http://edamontology.org/data_0928": "Gene expression profile", - "http://edamontology.org/data_0931": "Microarray experiment report", - "http://edamontology.org/data_0932": "Oligonucleotide probe data", - "http://edamontology.org/data_0933": "SAGE experimental data", - "http://edamontology.org/data_0934": "MPSS experimental data", - "http://edamontology.org/data_0935": "SBS experimental data", - "http://edamontology.org/data_0936": "Sequence tag profile (with gene assignment)", - "http://edamontology.org/data_0937": "Electron density map", - "http://edamontology.org/data_0938": "Raw NMR data", - "http://edamontology.org/data_0939": "CD spectra", - "http://edamontology.org/data_0940": "Volume map", - "http://edamontology.org/data_0941": "Electron microscopy model", - "http://edamontology.org/data_0942": "2D PAGE image", - "http://edamontology.org/data_0943": "Mass spectrum", - "http://edamontology.org/data_0944": "Peptide mass fingerprint", - "http://edamontology.org/data_0945": "Peptide identification", - "http://edamontology.org/data_0946": "Pathway or network annotation", - "http://edamontology.org/data_0947": "Biological pathway map", - "http://edamontology.org/data_0948": "Data resource definition", - "http://edamontology.org/data_0949": "Workflow metadata", - "http://edamontology.org/data_0950": "Mathematical model", - "http://edamontology.org/data_0951": "Statistical estimate score", - "http://edamontology.org/data_0952": "EMBOSS database resource definition", - "http://edamontology.org/data_0953": "Version information", - "http://edamontology.org/data_0954": "Database cross-mapping", - "http://edamontology.org/data_0955": "Data index", - "http://edamontology.org/data_0956": "Data index report", - "http://edamontology.org/data_0957": "Database metadata", - "http://edamontology.org/data_0958": "Tool metadata", - "http://edamontology.org/data_0959": "Job metadata", - "http://edamontology.org/data_0960": "User metadata", - "http://edamontology.org/data_0962": "Small molecule report", - "http://edamontology.org/data_0963": "Cell line report", - "http://edamontology.org/data_0964": "Scent annotation", - "http://edamontology.org/data_0966": "Ontology term", - "http://edamontology.org/data_0967": "Ontology concept data", - "http://edamontology.org/data_0968": "Keyword", - "http://edamontology.org/data_0970": "Citation", - "http://edamontology.org/data_0971": "Article", - "http://edamontology.org/data_0972": "Text mining report", - "http://edamontology.org/data_0974": "Entity identifier", - "http://edamontology.org/data_0975": "Data resource identifier", - "http://edamontology.org/data_0976": "Identifier (by type of data)", - "http://edamontology.org/data_0977": "Tool identifier", - "http://edamontology.org/data_0978": "Discrete entity identifier", - "http://edamontology.org/data_0979": "Entity feature identifier", - "http://edamontology.org/data_0980": "Entity collection identifier", - "http://edamontology.org/data_0981": "Phenomenon identifier", - "http://edamontology.org/data_0982": "Molecule identifier", - "http://edamontology.org/data_0983": "Atom ID", - "http://edamontology.org/data_0984": "Molecule name", - "http://edamontology.org/data_0985": "Molecule type", - "http://edamontology.org/data_0986": "Chemical identifier", - "http://edamontology.org/data_0987": "Chromosome name", - "http://edamontology.org/data_0988": "Peptide identifier", - "http://edamontology.org/data_0989": "Protein identifier", - "http://edamontology.org/data_0990": "Compound name", - "http://edamontology.org/data_0991": "Chemical registry number", - "http://edamontology.org/data_0992": "Ligand identifier", - "http://edamontology.org/data_0993": "Drug identifier", - "http://edamontology.org/data_0994": "Amino acid identifier", - "http://edamontology.org/data_0995": "Nucleotide identifier", - "http://edamontology.org/data_0996": "Monosaccharide identifier", - "http://edamontology.org/data_0997": "Chemical name (ChEBI)", - "http://edamontology.org/data_0998": "Chemical name (IUPAC)", - "http://edamontology.org/data_0999": "Chemical name (INN)", - "http://edamontology.org/data_1000": "Chemical name (brand)", - "http://edamontology.org/data_1001": "Chemical name (synonymous)", - "http://edamontology.org/data_1002": "CAS number", - "http://edamontology.org/data_1003": "Chemical registry number (Beilstein)", - "http://edamontology.org/data_1004": "Chemical registry number (Gmelin)", - "http://edamontology.org/data_1005": "HET group name", - "http://edamontology.org/data_1006": "Amino acid name", - "http://edamontology.org/data_1007": "Nucleotide code", - "http://edamontology.org/data_1008": "Polypeptide chain ID", - "http://edamontology.org/data_1009": "Protein name", - "http://edamontology.org/data_1010": "Enzyme identifier", - "http://edamontology.org/data_1011": "EC number", - "http://edamontology.org/data_1012": "Enzyme name", - "http://edamontology.org/data_1013": "Restriction enzyme name", - "http://edamontology.org/data_1014": "Sequence position specification", - "http://edamontology.org/data_1015": "Sequence feature ID", - "http://edamontology.org/data_1016": "Sequence position", - "http://edamontology.org/data_1017": "Sequence range", - "http://edamontology.org/data_1018": "Nucleic acid feature identifier", - "http://edamontology.org/data_1019": "Protein feature identifier", - "http://edamontology.org/data_1020": "Sequence feature key", - "http://edamontology.org/data_1021": "Sequence feature qualifier", - "http://edamontology.org/data_1022": "Sequence feature label", - "http://edamontology.org/data_1023": "EMBOSS Uniform Feature Object", - "http://edamontology.org/data_1024": "Codon name", - "http://edamontology.org/data_1025": "Gene identifier", - "http://edamontology.org/data_1026": "Gene symbol", - "http://edamontology.org/data_1027": "Gene ID (NCBI)", - "http://edamontology.org/data_1028": "Gene identifier (NCBI RefSeq)", - "http://edamontology.org/data_1029": "Gene identifier (NCBI UniGene)", - "http://edamontology.org/data_1030": "Gene identifier (Entrez)", - "http://edamontology.org/data_1031": "Gene ID (CGD)", - "http://edamontology.org/data_1032": "Gene ID (DictyBase)", - "http://edamontology.org/data_1033": "Ensembl gene ID", - "http://edamontology.org/data_1034": "Gene ID (SGD)", - "http://edamontology.org/data_1035": "Gene ID (GeneDB)", - "http://edamontology.org/data_1036": "TIGR identifier", - "http://edamontology.org/data_1037": "TAIR accession (gene)", - "http://edamontology.org/data_1038": "Protein domain ID", - "http://edamontology.org/data_1039": "SCOP domain identifier", - "http://edamontology.org/data_1040": "CATH domain ID", - "http://edamontology.org/data_1041": "SCOP concise classification string (sccs)", - "http://edamontology.org/data_1042": "SCOP sunid", - "http://edamontology.org/data_1043": "CATH node ID", - "http://edamontology.org/data_1044": "Kingdom name", - "http://edamontology.org/data_1045": "Species name", - "http://edamontology.org/data_1046": "Strain name", - "http://edamontology.org/data_1047": "URI", - "http://edamontology.org/data_1048": "Database ID", - "http://edamontology.org/data_1049": "Directory name", - "http://edamontology.org/data_1050": "File name", - "http://edamontology.org/data_1051": "Ontology name", - "http://edamontology.org/data_1052": "URL", - "http://edamontology.org/data_1053": "URN", - "http://edamontology.org/data_1055": "LSID", - "http://edamontology.org/data_1056": "Database name", - "http://edamontology.org/data_1057": "Sequence database name", - "http://edamontology.org/data_1058": "Enumerated file name", - "http://edamontology.org/data_1059": "File name extension", - "http://edamontology.org/data_1060": "File base name", - "http://edamontology.org/data_1061": "QSAR descriptor name", - "http://edamontology.org/data_1062": "Database entry identifier", - "http://edamontology.org/data_1063": "Sequence identifier", - "http://edamontology.org/data_1064": "Sequence set ID", - "http://edamontology.org/data_1065": "Sequence signature identifier", - "http://edamontology.org/data_1066": "Sequence alignment ID", - "http://edamontology.org/data_1067": "Phylogenetic distance matrix identifier", - "http://edamontology.org/data_1068": "Phylogenetic tree ID", - "http://edamontology.org/data_1069": "Comparison matrix identifier", - "http://edamontology.org/data_1070": "Structure ID", - "http://edamontology.org/data_1071": "Structural (3D) profile ID", - "http://edamontology.org/data_1072": "Structure alignment ID", - "http://edamontology.org/data_1073": "Amino acid index ID", - "http://edamontology.org/data_1074": "Protein interaction ID", - "http://edamontology.org/data_1075": "Protein family identifier", - "http://edamontology.org/data_1076": "Codon usage table name", - "http://edamontology.org/data_1077": "Transcription factor identifier", - "http://edamontology.org/data_1078": "Experiment annotation ID", - "http://edamontology.org/data_1079": "Electron microscopy model ID", - "http://edamontology.org/data_1080": "Gene expression report ID", - "http://edamontology.org/data_1081": "Genotype and phenotype annotation ID", - "http://edamontology.org/data_1082": "Pathway or network identifier", - "http://edamontology.org/data_1083": "Workflow ID", - "http://edamontology.org/data_1084": "Data resource definition ID", - "http://edamontology.org/data_1085": "Biological model ID", - "http://edamontology.org/data_1086": "Compound identifier", - "http://edamontology.org/data_1087": "Ontology concept ID", - "http://edamontology.org/data_1088": "Article ID", - "http://edamontology.org/data_1089": "FlyBase ID", - "http://edamontology.org/data_1091": "WormBase name", - "http://edamontology.org/data_1092": "WormBase class", - "http://edamontology.org/data_1093": "Sequence accession", - "http://edamontology.org/data_1094": "Sequence type", - "http://edamontology.org/data_1095": "EMBOSS Uniform Sequence Address", - "http://edamontology.org/data_1096": "Sequence accession (protein)", - "http://edamontology.org/data_1097": "Sequence accession (nucleic acid)", - "http://edamontology.org/data_1098": "RefSeq accession", - "http://edamontology.org/data_1099": "UniProt accession (extended)", - "http://edamontology.org/data_1100": "PIR identifier", - "http://edamontology.org/data_1101": "TREMBL accession", - "http://edamontology.org/data_1102": "Gramene primary identifier", - "http://edamontology.org/data_1103": "EMBL/GenBank/DDBJ ID", - "http://edamontology.org/data_1104": "Sequence cluster ID (UniGene)", - "http://edamontology.org/data_1105": "dbEST accession", - "http://edamontology.org/data_1106": "dbSNP ID", - "http://edamontology.org/data_1110": "EMBOSS sequence type", - "http://edamontology.org/data_1111": "EMBOSS listfile", - "http://edamontology.org/data_1112": "Sequence cluster ID", - "http://edamontology.org/data_1113": "Sequence cluster ID (COG)", - "http://edamontology.org/data_1114": "Sequence motif identifier", - "http://edamontology.org/data_1115": "Sequence profile ID", - "http://edamontology.org/data_1116": "ELM ID", - "http://edamontology.org/data_1117": "Prosite accession number", - "http://edamontology.org/data_1118": "HMMER hidden Markov model ID", - "http://edamontology.org/data_1119": "JASPAR profile ID", - "http://edamontology.org/data_1120": "Sequence alignment type", - "http://edamontology.org/data_1121": "BLAST sequence alignment type", - "http://edamontology.org/data_1122": "Phylogenetic tree type", - "http://edamontology.org/data_1123": "TreeBASE study accession number", - "http://edamontology.org/data_1124": "TreeFam accession number", - "http://edamontology.org/data_1125": "Comparison matrix type", - "http://edamontology.org/data_1126": "Comparison matrix name", - "http://edamontology.org/data_1127": "PDB ID", - "http://edamontology.org/data_1128": "AAindex ID", - "http://edamontology.org/data_1129": "BIND accession number", - "http://edamontology.org/data_1130": "IntAct accession number", - "http://edamontology.org/data_1131": "Protein family name", - "http://edamontology.org/data_1132": "InterPro entry name", - "http://edamontology.org/data_1133": "InterPro accession", - "http://edamontology.org/data_1134": "InterPro secondary accession", - "http://edamontology.org/data_1135": "Gene3D ID", - "http://edamontology.org/data_1136": "PIRSF ID", - "http://edamontology.org/data_1137": "PRINTS code", - "http://edamontology.org/data_1138": "Pfam accession number", - "http://edamontology.org/data_1139": "SMART accession number", - "http://edamontology.org/data_1140": "Superfamily hidden Markov model number", - "http://edamontology.org/data_1141": "TIGRFam ID", - "http://edamontology.org/data_1142": "ProDom accession number", - "http://edamontology.org/data_1143": "TRANSFAC accession number", - "http://edamontology.org/data_1144": "ArrayExpress accession number", - "http://edamontology.org/data_1145": "PRIDE experiment accession number", - "http://edamontology.org/data_1146": "EMDB ID", - "http://edamontology.org/data_1147": "GEO accession number", - "http://edamontology.org/data_1148": "GermOnline ID", - "http://edamontology.org/data_1149": "EMAGE ID", - "http://edamontology.org/data_1150": "Disease ID", - "http://edamontology.org/data_1151": "HGVbase ID", - "http://edamontology.org/data_1152": "HIVDB identifier", - "http://edamontology.org/data_1153": "OMIM ID", - "http://edamontology.org/data_1154": "KEGG object identifier", - "http://edamontology.org/data_1155": "Pathway ID (reactome)", - "http://edamontology.org/data_1156": "Pathway ID (aMAZE)", - "http://edamontology.org/data_1157": "Pathway ID (BioCyc)", - "http://edamontology.org/data_1158": "Pathway ID (INOH)", - "http://edamontology.org/data_1159": "Pathway ID (PATIKA)", - "http://edamontology.org/data_1160": "Pathway ID (CPDB)", - "http://edamontology.org/data_1161": "Pathway ID (Panther)", - "http://edamontology.org/data_1162": "MIRIAM identifier", - "http://edamontology.org/data_1163": "MIRIAM data type name", - "http://edamontology.org/data_1164": "MIRIAM URI", - "http://edamontology.org/data_1165": "MIRIAM data type primary name", - "http://edamontology.org/data_1166": "MIRIAM data type synonymous name", - "http://edamontology.org/data_1167": "Taverna workflow ID", - "http://edamontology.org/data_1170": "Biological model name", - "http://edamontology.org/data_1171": "BioModel ID", - "http://edamontology.org/data_1172": "PubChem CID", - "http://edamontology.org/data_1173": "ChemSpider ID", - "http://edamontology.org/data_1174": "ChEBI ID", - "http://edamontology.org/data_1175": "BioPax concept ID", - "http://edamontology.org/data_1176": "GO concept ID", - "http://edamontology.org/data_1177": "MeSH concept ID", - "http://edamontology.org/data_1178": "HGNC concept ID", - "http://edamontology.org/data_1179": "NCBI taxonomy ID", - "http://edamontology.org/data_1180": "Plant Ontology concept ID", - "http://edamontology.org/data_1181": "UMLS concept ID", - "http://edamontology.org/data_1182": "FMA concept ID", - "http://edamontology.org/data_1183": "EMAP concept ID", - "http://edamontology.org/data_1184": "ChEBI concept ID", - "http://edamontology.org/data_1185": "MGED concept ID", - "http://edamontology.org/data_1186": "myGrid concept ID", - "http://edamontology.org/data_1187": "PubMed ID", - "http://edamontology.org/data_1188": "DOI", - "http://edamontology.org/data_1189": "Medline UI", - "http://edamontology.org/data_1190": "Tool name", - "http://edamontology.org/data_1191": "Tool name (signature)", - "http://edamontology.org/data_1192": "Tool name (BLAST)", - "http://edamontology.org/data_1193": "Tool name (FASTA)", - "http://edamontology.org/data_1194": "Tool name (EMBOSS)", - "http://edamontology.org/data_1195": "Tool name (EMBASSY package)", - "http://edamontology.org/data_1201": "QSAR descriptor (constitutional)", - "http://edamontology.org/data_1202": "QSAR descriptor (electronic)", - "http://edamontology.org/data_1203": "QSAR descriptor (geometrical)", - "http://edamontology.org/data_1204": "QSAR descriptor (topological)", - "http://edamontology.org/data_1205": "QSAR descriptor (molecular)", - "http://edamontology.org/data_1233": "Sequence set (protein)", - "http://edamontology.org/data_1234": "Sequence set (nucleic acid)", - "http://edamontology.org/data_1235": "Sequence cluster", - "http://edamontology.org/data_1236": "Psiblast checkpoint file", - "http://edamontology.org/data_1237": "HMMER synthetic sequences set", - "http://edamontology.org/data_1238": "Proteolytic digest", - "http://edamontology.org/data_1239": "Restriction digest", - "http://edamontology.org/data_1240": "PCR primers", - "http://edamontology.org/data_1241": "vectorstrip cloning vector definition file", - "http://edamontology.org/data_1242": "Primer3 internal oligo mishybridizing library", - "http://edamontology.org/data_1243": "Primer3 mispriming library file", - "http://edamontology.org/data_1244": "primersearch primer pairs sequence record", - "http://edamontology.org/data_1245": "Sequence cluster (protein)", - "http://edamontology.org/data_1246": "Sequence cluster (nucleic acid)", - "http://edamontology.org/data_1249": "Sequence length", - "http://edamontology.org/data_1250": "Word size", - "http://edamontology.org/data_1251": "Window size", - "http://edamontology.org/data_1252": "Sequence length range", - "http://edamontology.org/data_1253": "Sequence information report", - "http://edamontology.org/data_1254": "Sequence property", - "http://edamontology.org/data_1255": "Sequence features", - "http://edamontology.org/data_1256": "Sequence features (comparative)", - "http://edamontology.org/data_1257": "Sequence property (protein)", - "http://edamontology.org/data_1258": "Sequence property (nucleic acid)", - "http://edamontology.org/data_1259": "Sequence complexity report", - "http://edamontology.org/data_1260": "Sequence ambiguity report", - "http://edamontology.org/data_1261": "Sequence composition report", - "http://edamontology.org/data_1262": "Peptide molecular weight hits", - "http://edamontology.org/data_1263": "Base position variability plot", - "http://edamontology.org/data_1264": "Sequence composition table", - "http://edamontology.org/data_1265": "Base frequencies table", - "http://edamontology.org/data_1266": "Base word frequencies table", - "http://edamontology.org/data_1267": "Amino acid frequencies table", - "http://edamontology.org/data_1268": "Amino acid word frequencies table", - "http://edamontology.org/data_1269": "DAS sequence feature annotation", - "http://edamontology.org/data_1270": "Feature table", - "http://edamontology.org/data_1274": "Map", - "http://edamontology.org/data_1276": "Nucleic acid features", - "http://edamontology.org/data_1277": "Protein features", - "http://edamontology.org/data_1278": "Genetic map", - "http://edamontology.org/data_1279": "Sequence map", - "http://edamontology.org/data_1280": "Physical map", - "http://edamontology.org/data_1281": "Sequence signature map", - "http://edamontology.org/data_1283": "Cytogenetic map", - "http://edamontology.org/data_1284": "DNA transduction map", - "http://edamontology.org/data_1285": "Gene map", - "http://edamontology.org/data_1286": "Plasmid map", - "http://edamontology.org/data_1288": "Genome map", - "http://edamontology.org/data_1289": "Restriction map", - "http://edamontology.org/data_1290": "InterPro compact match image", - "http://edamontology.org/data_1291": "InterPro detailed match image", - "http://edamontology.org/data_1292": "InterPro architecture image", - "http://edamontology.org/data_1293": "SMART protein schematic", - "http://edamontology.org/data_1294": "GlobPlot domain image", - "http://edamontology.org/data_1298": "Sequence motif matches", - "http://edamontology.org/data_1299": "Sequence features (repeats)", - "http://edamontology.org/data_1300": "Gene and transcript structure (report)", - "http://edamontology.org/data_1301": "Mobile genetic elements", - "http://edamontology.org/data_1303": "Nucleic acid features (quadruplexes)", - "http://edamontology.org/data_1306": "Nucleosome exclusion sequences", - "http://edamontology.org/data_1309": "Gene features (exonic splicing enhancer)", - "http://edamontology.org/data_1310": "Nucleic acid features (microRNA)", - "http://edamontology.org/data_1313": "Coding region", - "http://edamontology.org/data_1314": "Gene features (SECIS element)", - "http://edamontology.org/data_1315": "Transcription factor binding sites", - "http://edamontology.org/data_1321": "Protein features (sites)", - "http://edamontology.org/data_1322": "Protein features report (signal peptides)", - "http://edamontology.org/data_1323": "Protein features report (cleavage sites)", - "http://edamontology.org/data_1324": "Protein features (post-translation modifications)", - "http://edamontology.org/data_1325": "Protein features report (active sites)", - "http://edamontology.org/data_1326": "Protein features report (binding sites)", - "http://edamontology.org/data_1327": "Protein features (epitopes)", - "http://edamontology.org/data_1328": "Protein features report (nucleic acid binding sites)", - "http://edamontology.org/data_1329": "MHC Class I epitopes report", - "http://edamontology.org/data_1330": "MHC Class II epitopes report", - "http://edamontology.org/data_1331": "Protein features (PEST sites)", - "http://edamontology.org/data_1338": "Sequence database hits scores list", - "http://edamontology.org/data_1339": "Sequence database hits alignments list", - "http://edamontology.org/data_1340": "Sequence database hits evaluation data", - "http://edamontology.org/data_1344": "MEME motif alphabet", - "http://edamontology.org/data_1345": "MEME background frequencies file", - "http://edamontology.org/data_1346": "MEME motifs directive file", - "http://edamontology.org/data_1347": "Dirichlet distribution", - "http://edamontology.org/data_1348": "HMM emission and transition counts", - "http://edamontology.org/data_1352": "Regular expression", - "http://edamontology.org/data_1353": "Sequence motif", - "http://edamontology.org/data_1354": "Sequence profile", - "http://edamontology.org/data_1355": "Protein signature", - "http://edamontology.org/data_1358": "Prosite nucleotide pattern", - "http://edamontology.org/data_1359": "Prosite protein pattern", - "http://edamontology.org/data_1361": "Position frequency matrix", - "http://edamontology.org/data_1362": "Position weight matrix", - "http://edamontology.org/data_1363": "Information content matrix", - "http://edamontology.org/data_1364": "Hidden Markov model", - "http://edamontology.org/data_1365": "Fingerprint", - "http://edamontology.org/data_1368": "Domainatrix signature", - "http://edamontology.org/data_1371": "HMMER NULL hidden Markov model", - "http://edamontology.org/data_1372": "Protein family signature", - "http://edamontology.org/data_1373": "Protein domain signature", - "http://edamontology.org/data_1374": "Protein region signature", - "http://edamontology.org/data_1375": "Protein repeat signature", - "http://edamontology.org/data_1376": "Protein site signature", - "http://edamontology.org/data_1377": "Protein conserved site signature", - "http://edamontology.org/data_1378": "Protein active site signature", - "http://edamontology.org/data_1379": "Protein binding site signature", - "http://edamontology.org/data_1380": "Protein post-translational modification signature", - "http://edamontology.org/data_1381": "Pair sequence alignment", - "http://edamontology.org/data_1382": "Sequence alignment (multiple)", - "http://edamontology.org/data_1383": "Nucleic acid sequence alignment", - "http://edamontology.org/data_1384": "Protein sequence alignment", - "http://edamontology.org/data_1385": "Hybrid sequence alignment", - "http://edamontology.org/data_1386": "Sequence alignment (nucleic acid pair)", - "http://edamontology.org/data_1387": "Sequence alignment (protein pair)", - "http://edamontology.org/data_1388": "Hybrid sequence alignment (pair)", - "http://edamontology.org/data_1389": "Multiple nucleotide sequence alignment", - "http://edamontology.org/data_1390": "Multiple protein sequence alignment", - "http://edamontology.org/data_1394": "Alignment score or penalty", - "http://edamontology.org/data_1395": "Score end gaps control", - "http://edamontology.org/data_1396": "Aligned sequence order", - "http://edamontology.org/data_1397": "Gap opening penalty", - "http://edamontology.org/data_1398": "Gap extension penalty", - "http://edamontology.org/data_1399": "Gap separation penalty", - "http://edamontology.org/data_1400": "Terminal gap penalty", - "http://edamontology.org/data_1401": "Match reward score", - "http://edamontology.org/data_1402": "Mismatch penalty score", - "http://edamontology.org/data_1403": "Drop off score", - "http://edamontology.org/data_1404": "Gap opening penalty (integer)", - "http://edamontology.org/data_1405": "Gap opening penalty (float)", - "http://edamontology.org/data_1406": "Gap extension penalty (integer)", - "http://edamontology.org/data_1407": "Gap extension penalty (float)", - "http://edamontology.org/data_1408": "Gap separation penalty (integer)", - "http://edamontology.org/data_1409": "Gap separation penalty (float)", - "http://edamontology.org/data_1410": "Terminal gap opening penalty", - "http://edamontology.org/data_1411": "Terminal gap extension penalty", - "http://edamontology.org/data_1412": "Sequence identity", - "http://edamontology.org/data_1413": "Sequence similarity", - "http://edamontology.org/data_1414": "Sequence alignment metadata (quality report)", - "http://edamontology.org/data_1415": "Sequence alignment report (site conservation)", - "http://edamontology.org/data_1416": "Sequence alignment report (site correlation)", - "http://edamontology.org/data_1417": "Sequence-profile alignment (Domainatrix signature)", - "http://edamontology.org/data_1418": "Sequence-profile alignment (HMM)", - "http://edamontology.org/data_1420": "Sequence-profile alignment (fingerprint)", - "http://edamontology.org/data_1426": "Phylogenetic continuous quantitative data", - "http://edamontology.org/data_1427": "Phylogenetic discrete data", - "http://edamontology.org/data_1428": "Phylogenetic character cliques", - "http://edamontology.org/data_1429": "Phylogenetic invariants", - "http://edamontology.org/data_1438": "Phylogenetic report", - "http://edamontology.org/data_1439": "DNA substitution model", - "http://edamontology.org/data_1440": "Phylogenetic tree report (tree shape)", - "http://edamontology.org/data_1441": "Phylogenetic tree report (tree evaluation)", - "http://edamontology.org/data_1442": "Phylogenetic tree distances", - "http://edamontology.org/data_1443": "Phylogenetic tree report (tree stratigraphic)", - "http://edamontology.org/data_1444": "Phylogenetic character contrasts", - "http://edamontology.org/data_1446": "Comparison matrix (integers)", - "http://edamontology.org/data_1447": "Comparison matrix (floats)", - "http://edamontology.org/data_1448": "Comparison matrix (nucleotide)", - "http://edamontology.org/data_1449": "Comparison matrix (amino acid)", - "http://edamontology.org/data_1450": "Nucleotide comparison matrix (integers)", - "http://edamontology.org/data_1451": "Nucleotide comparison matrix (floats)", - "http://edamontology.org/data_1452": "Amino acid comparison matrix (integers)", - "http://edamontology.org/data_1453": "Amino acid comparison matrix (floats)", - "http://edamontology.org/data_1459": "Nucleic acid structure", - "http://edamontology.org/data_1460": "Protein structure", - "http://edamontology.org/data_1461": "Protein-ligand complex", - "http://edamontology.org/data_1462": "Carbohydrate structure", - "http://edamontology.org/data_1463": "Small molecule structure", - "http://edamontology.org/data_1464": "DNA structure", - "http://edamontology.org/data_1465": "RNA structure", - "http://edamontology.org/data_1466": "tRNA structure", - "http://edamontology.org/data_1467": "Protein chain", - "http://edamontology.org/data_1468": "Protein domain", - "http://edamontology.org/data_1469": "Protein structure (all atoms)", - "http://edamontology.org/data_1470": "C-alpha trace", - "http://edamontology.org/data_1471": "Protein chain (all atoms)", - "http://edamontology.org/data_1472": "Protein chain (C-alpha atoms)", - "http://edamontology.org/data_1473": "Protein domain (all atoms)", - "http://edamontology.org/data_1474": "Protein domain (C-alpha atoms)", - "http://edamontology.org/data_1479": "Structure alignment (pair)", - "http://edamontology.org/data_1480": "Structure alignment (multiple)", - "http://edamontology.org/data_1481": "Protein structure alignment", - "http://edamontology.org/data_1482": "Nucleic acid structure alignment", - "http://edamontology.org/data_1483": "Structure alignment (protein pair)", - "http://edamontology.org/data_1484": "Multiple protein tertiary structure alignment", - "http://edamontology.org/data_1485": "Structure alignment (protein all atoms)", - "http://edamontology.org/data_1486": "Structure alignment (protein C-alpha atoms)", - "http://edamontology.org/data_1487": "Pairwise protein tertiary structure alignment (all atoms)", - "http://edamontology.org/data_1488": "Pairwise protein tertiary structure alignment (C-alpha atoms)", - "http://edamontology.org/data_1489": "Multiple protein tertiary structure alignment (all atoms)", - "http://edamontology.org/data_1490": "Multiple protein tertiary structure alignment (C-alpha atoms)", - "http://edamontology.org/data_1491": "Structure alignment (nucleic acid pair)", - "http://edamontology.org/data_1492": "Multiple nucleic acid tertiary structure alignment", - "http://edamontology.org/data_1493": "RNA structure alignment", - "http://edamontology.org/data_1494": "Structural transformation matrix", - "http://edamontology.org/data_1495": "DaliLite hit table", - "http://edamontology.org/data_1496": "Molecular similarity score", - "http://edamontology.org/data_1497": "Root-mean-square deviation", - "http://edamontology.org/data_1498": "Tanimoto similarity score", - "http://edamontology.org/data_1499": "3D-1D scoring matrix", - "http://edamontology.org/data_1501": "Amino acid index", - "http://edamontology.org/data_1502": "Amino acid index (chemical classes)", - "http://edamontology.org/data_1503": "Amino acid pair-wise contact potentials", - "http://edamontology.org/data_1505": "Amino acid index (molecular weight)", - "http://edamontology.org/data_1506": "Amino acid index (hydropathy)", - "http://edamontology.org/data_1507": "Amino acid index (White-Wimley data)", - "http://edamontology.org/data_1508": "Amino acid index (van der Waals radii)", - "http://edamontology.org/data_1509": "Enzyme report", - "http://edamontology.org/data_1517": "Restriction enzyme report", - "http://edamontology.org/data_1519": "Peptide molecular weights", - "http://edamontology.org/data_1520": "Peptide hydrophobic moment", - "http://edamontology.org/data_1521": "Protein aliphatic index", - "http://edamontology.org/data_1522": "Protein sequence hydropathy plot", - "http://edamontology.org/data_1523": "Protein charge plot", - "http://edamontology.org/data_1524": "Protein solubility", - "http://edamontology.org/data_1525": "Protein crystallizability", - "http://edamontology.org/data_1526": "Protein globularity", - "http://edamontology.org/data_1527": "Protein titration curve", - "http://edamontology.org/data_1528": "Protein isoelectric point", - "http://edamontology.org/data_1529": "Protein pKa value", - "http://edamontology.org/data_1530": "Protein hydrogen exchange rate", - "http://edamontology.org/data_1531": "Protein extinction coefficient", - "http://edamontology.org/data_1532": "Protein optical density", - "http://edamontology.org/data_1533": "Protein subcellular localisation", - "http://edamontology.org/data_1534": "Peptide immunogenicity data", - "http://edamontology.org/data_1536": "MHC peptide immunogenicity report", - "http://edamontology.org/data_1537": "Protein structure report", - "http://edamontology.org/data_1539": "Protein structural quality report", - "http://edamontology.org/data_1540": "Protein non-covalent interactions report", - "http://edamontology.org/data_1541": "Protein flexibility or motion report", - "http://edamontology.org/data_1542": "Protein solvent accessibility", - "http://edamontology.org/data_1543": "Protein surface report", - "http://edamontology.org/data_1544": "Ramachandran plot", - "http://edamontology.org/data_1545": "Protein dipole moment", - "http://edamontology.org/data_1546": "Protein distance matrix", - "http://edamontology.org/data_1547": "Protein contact map", - "http://edamontology.org/data_1548": "Protein residue 3D cluster", - "http://edamontology.org/data_1549": "Protein hydrogen bonds", - "http://edamontology.org/data_1550": "Protein non-canonical interactions", - "http://edamontology.org/data_1553": "CATH node", - "http://edamontology.org/data_1554": "SCOP node", - "http://edamontology.org/data_1555": "EMBASSY domain classification", - "http://edamontology.org/data_1556": "CATH class", - "http://edamontology.org/data_1557": "CATH architecture", - "http://edamontology.org/data_1558": "CATH topology", - "http://edamontology.org/data_1559": "CATH homologous superfamily", - "http://edamontology.org/data_1560": "CATH structurally similar group", - "http://edamontology.org/data_1561": "CATH functional category", - "http://edamontology.org/data_1564": "Protein fold recognition report", - "http://edamontology.org/data_1565": "Protein-protein interaction report", - "http://edamontology.org/data_1566": "Protein-ligand interaction report", - "http://edamontology.org/data_1567": "Protein-nucleic acid interactions report", - "http://edamontology.org/data_1583": "Nucleic acid melting profile", - "http://edamontology.org/data_1584": "Nucleic acid enthalpy", - "http://edamontology.org/data_1585": "Nucleic acid entropy", - "http://edamontology.org/data_1586": "Nucleic acid melting temperature", - "http://edamontology.org/data_1587": "Nucleic acid stitch profile", - "http://edamontology.org/data_1588": "DNA base pair stacking energies data", - "http://edamontology.org/data_1589": "DNA base pair twist angle data", - "http://edamontology.org/data_1590": "DNA base trimer roll angles data", - "http://edamontology.org/data_1591": "Vienna RNA parameters", - "http://edamontology.org/data_1592": "Vienna RNA structure constraints", - "http://edamontology.org/data_1593": "Vienna RNA concentration data", - "http://edamontology.org/data_1594": "Vienna RNA calculated energy", - "http://edamontology.org/data_1595": "Base pairing probability matrix dotplot", - "http://edamontology.org/data_1596": "Nucleic acid folding report", - "http://edamontology.org/data_1597": "Codon usage table", - "http://edamontology.org/data_1598": "Genetic code", - "http://edamontology.org/data_1599": "Codon adaptation index", - "http://edamontology.org/data_1600": "Codon usage bias plot", - "http://edamontology.org/data_1601": "Nc statistic", - "http://edamontology.org/data_1602": "Codon usage fraction difference", - "http://edamontology.org/data_1621": "Pharmacogenomic test report", - "http://edamontology.org/data_1622": "Disease report", - "http://edamontology.org/data_1634": "Linkage disequilibrium (report)", - "http://edamontology.org/data_1636": "Heat map", - "http://edamontology.org/data_1642": "Affymetrix probe sets library file", - "http://edamontology.org/data_1643": "Affymetrix probe sets information library file", - "http://edamontology.org/data_1646": "Molecular weights standard fingerprint", - "http://edamontology.org/data_1656": "Metabolic pathway report", - "http://edamontology.org/data_1657": "Genetic information processing pathway report", - "http://edamontology.org/data_1658": "Environmental information processing pathway report", - "http://edamontology.org/data_1659": "Signal transduction pathway report", - "http://edamontology.org/data_1660": "Cellular process pathways report", - "http://edamontology.org/data_1661": "Disease pathway or network report", - "http://edamontology.org/data_1662": "Drug structure relationship map", - "http://edamontology.org/data_1663": "Protein interaction networks", - "http://edamontology.org/data_1664": "MIRIAM datatype", - "http://edamontology.org/data_1667": "E-value", - "http://edamontology.org/data_1668": "Z-value", - "http://edamontology.org/data_1669": "P-value", - "http://edamontology.org/data_1670": "Database version information", - "http://edamontology.org/data_1671": "Tool version information", - "http://edamontology.org/data_1672": "CATH version information", - "http://edamontology.org/data_1673": "Swiss-Prot to PDB mapping", - "http://edamontology.org/data_1674": "Sequence database cross-references", - "http://edamontology.org/data_1675": "Job status", - "http://edamontology.org/data_1676": "Job ID", - "http://edamontology.org/data_1677": "Job type", - "http://edamontology.org/data_1678": "Tool log", - "http://edamontology.org/data_1679": "DaliLite log file", - "http://edamontology.org/data_1680": "STRIDE log file", - "http://edamontology.org/data_1681": "NACCESS log file", - "http://edamontology.org/data_1682": "EMBOSS wordfinder log file", - "http://edamontology.org/data_1683": "EMBOSS domainatrix log file", - "http://edamontology.org/data_1684": "EMBOSS sites log file", - "http://edamontology.org/data_1685": "EMBOSS supermatcher error file", - "http://edamontology.org/data_1686": "EMBOSS megamerger log file", - "http://edamontology.org/data_1687": "EMBOSS whichdb log file", - "http://edamontology.org/data_1688": "EMBOSS vectorstrip log file", - "http://edamontology.org/data_1689": "Username", - "http://edamontology.org/data_1690": "Password", - "http://edamontology.org/data_1691": "Email address", - "http://edamontology.org/data_1692": "Person name", - "http://edamontology.org/data_1693": "Number of iterations", - "http://edamontology.org/data_1694": "Number of output entities", - "http://edamontology.org/data_1695": "Hit sort order", - "http://edamontology.org/data_1696": "Drug report", - "http://edamontology.org/data_1707": "Phylogenetic tree image", - "http://edamontology.org/data_1708": "RNA secondary structure image", - "http://edamontology.org/data_1709": "Protein secondary structure image", - "http://edamontology.org/data_1710": "Structure image", - "http://edamontology.org/data_1711": "Sequence alignment image", - "http://edamontology.org/data_1712": "Chemical structure image", - "http://edamontology.org/data_1713": "Fate map", - "http://edamontology.org/data_1714": "Microarray spots image", - "http://edamontology.org/data_1715": "BioPax term", - "http://edamontology.org/data_1716": "GO", - "http://edamontology.org/data_1717": "MeSH", - "http://edamontology.org/data_1718": "HGNC", - "http://edamontology.org/data_1719": "NCBI taxonomy vocabulary", - "http://edamontology.org/data_1720": "Plant ontology term", - "http://edamontology.org/data_1721": "UMLS", - "http://edamontology.org/data_1722": "FMA", - "http://edamontology.org/data_1723": "EMAP", - "http://edamontology.org/data_1724": "ChEBI", - "http://edamontology.org/data_1725": "MGED", - "http://edamontology.org/data_1726": "myGrid", - "http://edamontology.org/data_1727": "GO (biological process)", - "http://edamontology.org/data_1728": "GO (molecular function)", - "http://edamontology.org/data_1729": "GO (cellular component)", - "http://edamontology.org/data_1730": "Ontology relation type", - "http://edamontology.org/data_1731": "Ontology concept definition", - "http://edamontology.org/data_1732": "Ontology concept comment", - "http://edamontology.org/data_1733": "Ontology concept reference", - "http://edamontology.org/data_1738": "doc2loc document information", - "http://edamontology.org/data_1742": "PDB residue number", - "http://edamontology.org/data_1743": "Atomic coordinate", - "http://edamontology.org/data_1744": "Atomic x coordinate", - "http://edamontology.org/data_1745": "Atomic y coordinate", - "http://edamontology.org/data_1746": "Atomic z coordinate", - "http://edamontology.org/data_1748": "PDB atom name", - "http://edamontology.org/data_1755": "Protein atom", - "http://edamontology.org/data_1756": "Protein residue", - "http://edamontology.org/data_1757": "Atom name", - "http://edamontology.org/data_1758": "PDB residue name", - "http://edamontology.org/data_1759": "PDB model number", - "http://edamontology.org/data_1762": "CATH domain report", - "http://edamontology.org/data_1764": "CATH representative domain sequences (ATOM)", - "http://edamontology.org/data_1765": "CATH representative domain sequences (COMBS)", - "http://edamontology.org/data_1766": "CATH domain sequences (ATOM)", - "http://edamontology.org/data_1767": "CATH domain sequences (COMBS)", - "http://edamontology.org/data_1771": "Sequence version", - "http://edamontology.org/data_1772": "Score", - "http://edamontology.org/data_1776": "Protein report (function)", - "http://edamontology.org/data_1783": "Gene name (ASPGD)", - "http://edamontology.org/data_1784": "Gene name (CGD)", - "http://edamontology.org/data_1785": "Gene name (dictyBase)", - "http://edamontology.org/data_1786": "Gene name (EcoGene primary)", - "http://edamontology.org/data_1787": "Gene name (MaizeGDB)", - "http://edamontology.org/data_1788": "Gene name (SGD)", - "http://edamontology.org/data_1789": "Gene name (TGD)", - "http://edamontology.org/data_1790": "Gene name (CGSC)", - "http://edamontology.org/data_1791": "Gene name (HGNC)", - "http://edamontology.org/data_1792": "Gene name (MGD)", - "http://edamontology.org/data_1793": "Gene name (Bacillus subtilis)", - "http://edamontology.org/data_1794": "Gene ID (PlasmoDB)", - "http://edamontology.org/data_1795": "Gene ID (EcoGene)", - "http://edamontology.org/data_1796": "Gene ID (FlyBase)", - "http://edamontology.org/data_1797": "Gene ID (GeneDB Glossina morsitans)", - "http://edamontology.org/data_1798": "Gene ID (GeneDB Leishmania major)", - "http://edamontology.org/data_1799": "Gene ID (GeneDB Plasmodium falciparum)", - "http://edamontology.org/data_1800": "Gene ID (GeneDB Schizosaccharomyces pombe)", - "http://edamontology.org/data_1801": "Gene ID (GeneDB Trypanosoma brucei)", - "http://edamontology.org/data_1802": "Gene ID (Gramene)", - "http://edamontology.org/data_1803": "Gene ID (Virginia microbial)", - "http://edamontology.org/data_1804": "Gene ID (SGN)", - "http://edamontology.org/data_1805": "Gene ID (WormBase)", - "http://edamontology.org/data_1806": "Gene synonym", - "http://edamontology.org/data_1807": "ORF name", - "http://edamontology.org/data_1852": "Sequence assembly component", - "http://edamontology.org/data_1853": "Chromosome annotation (aberration)", - "http://edamontology.org/data_1855": "Clone ID", - "http://edamontology.org/data_1856": "PDB insertion code", - "http://edamontology.org/data_1857": "Atomic occupancy", - "http://edamontology.org/data_1858": "Isotropic B factor", - "http://edamontology.org/data_1859": "Deletion map", - "http://edamontology.org/data_1860": "QTL map", - "http://edamontology.org/data_1863": "Haplotype map", - "http://edamontology.org/data_1864": "Map set data", - "http://edamontology.org/data_1865": "Map feature", - "http://edamontology.org/data_1866": "Map type", - "http://edamontology.org/data_1867": "Protein fold name", - "http://edamontology.org/data_1868": "Taxon", - "http://edamontology.org/data_1869": "Organism identifier", - "http://edamontology.org/data_1870": "Genus name", - "http://edamontology.org/data_1872": "Taxonomic classification", - "http://edamontology.org/data_1873": "iHOP organism ID", - "http://edamontology.org/data_1874": "Genbank common name", - "http://edamontology.org/data_1875": "NCBI taxon", - "http://edamontology.org/data_1877": "Synonym", - "http://edamontology.org/data_1878": "Misspelling", - "http://edamontology.org/data_1879": "Acronym", - "http://edamontology.org/data_1880": "Misnomer", - "http://edamontology.org/data_1881": "Author ID", - "http://edamontology.org/data_1882": "DragonDB author identifier", - "http://edamontology.org/data_1883": "Annotated URI", - "http://edamontology.org/data_1884": "UniProt keywords", - "http://edamontology.org/data_1885": "Gene ID (GeneFarm)", - "http://edamontology.org/data_1886": "Blattner number", - "http://edamontology.org/data_1887": "Gene ID (MIPS Maize)", - "http://edamontology.org/data_1888": "Gene ID (MIPS Medicago)", - "http://edamontology.org/data_1889": "Gene name (DragonDB)", - "http://edamontology.org/data_1890": "Gene name (Arabidopsis)", - "http://edamontology.org/data_1891": "iHOP symbol", - "http://edamontology.org/data_1892": "Gene name (GeneFarm)", - "http://edamontology.org/data_1893": "Locus ID", - "http://edamontology.org/data_1895": "Locus ID (AGI)", - "http://edamontology.org/data_1896": "Locus ID (ASPGD)", - "http://edamontology.org/data_1897": "Locus ID (MGG)", - "http://edamontology.org/data_1898": "Locus ID (CGD)", - "http://edamontology.org/data_1899": "Locus ID (CMR)", - "http://edamontology.org/data_1900": "NCBI locus tag", - "http://edamontology.org/data_1901": "Locus ID (SGD)", - "http://edamontology.org/data_1902": "Locus ID (MMP)", - "http://edamontology.org/data_1903": "Locus ID (DictyBase)", - "http://edamontology.org/data_1904": "Locus ID (EntrezGene)", - "http://edamontology.org/data_1905": "Locus ID (MaizeGDB)", - "http://edamontology.org/data_1906": "Quantitative trait locus", - "http://edamontology.org/data_1907": "Gene ID (KOME)", - "http://edamontology.org/data_1908": "Locus ID (Tropgene)", - "http://edamontology.org/data_1916": "Alignment", - "http://edamontology.org/data_1917": "Atomic property", - "http://edamontology.org/data_2007": "UniProt keyword", - "http://edamontology.org/data_2009": "Ordered locus name", - "http://edamontology.org/data_2012": "Sequence coordinates", - "http://edamontology.org/data_2016": "Amino acid property", - "http://edamontology.org/data_2018": "Annotation", - "http://edamontology.org/data_2019": "Map data", - "http://edamontology.org/data_2022": "Vienna RNA structural data", - "http://edamontology.org/data_2023": "Sequence mask parameter", - "http://edamontology.org/data_2024": "Enzyme kinetics data", - "http://edamontology.org/data_2025": "Michaelis Menten plot", - "http://edamontology.org/data_2026": "Hanes Woolf plot", - "http://edamontology.org/data_2028": "Experimental data", - "http://edamontology.org/data_2041": "Genome version information", - "http://edamontology.org/data_2042": "Evidence", - "http://edamontology.org/data_2043": "Sequence record lite", - "http://edamontology.org/data_2044": "Sequence", - "http://edamontology.org/data_2046": "Nucleic acid sequence record (lite)", - "http://edamontology.org/data_2047": "Protein sequence record (lite)", - "http://edamontology.org/data_2048": "Report", - "http://edamontology.org/data_2050": "Molecular property (general)", - "http://edamontology.org/data_2053": "Structural data", - "http://edamontology.org/data_2070": "Sequence motif (nucleic acid)", - "http://edamontology.org/data_2071": "Sequence motif (protein)", - "http://edamontology.org/data_2079": "Search parameter", - "http://edamontology.org/data_2080": "Database search results", - "http://edamontology.org/data_2081": "Secondary structure", - "http://edamontology.org/data_2082": "Matrix", - "http://edamontology.org/data_2083": "Alignment data", - "http://edamontology.org/data_2084": "Nucleic acid report", - "http://edamontology.org/data_2085": "Structure report", - "http://edamontology.org/data_2086": "Nucleic acid structure data", - "http://edamontology.org/data_2087": "Molecular property", - "http://edamontology.org/data_2088": "DNA base structural data", - "http://edamontology.org/data_2090": "Database entry version information", - "http://edamontology.org/data_2091": "Accession", - "http://edamontology.org/data_2092": "SNP", - "http://edamontology.org/data_2093": "Data reference", - "http://edamontology.org/data_2098": "Job identifier", - "http://edamontology.org/data_2099": "Name", - "http://edamontology.org/data_2100": "Type", - "http://edamontology.org/data_2101": "User ID", - "http://edamontology.org/data_2102": "KEGG organism code", - "http://edamontology.org/data_2103": "Gene name (KEGG GENES)", - "http://edamontology.org/data_2104": "BioCyc ID", - "http://edamontology.org/data_2105": "Compound ID (BioCyc)", - "http://edamontology.org/data_2106": "Reaction ID (BioCyc)", - "http://edamontology.org/data_2107": "Enzyme ID (BioCyc)", - "http://edamontology.org/data_2108": "Reaction ID", - "http://edamontology.org/data_2109": "Identifier (hybrid)", - "http://edamontology.org/data_2110": "Molecular property identifier", - "http://edamontology.org/data_2111": "Codon usage table ID", - "http://edamontology.org/data_2112": "FlyBase primary identifier", - "http://edamontology.org/data_2113": "WormBase identifier", - "http://edamontology.org/data_2114": "WormBase wormpep ID", - "http://edamontology.org/data_2116": "Nucleic acid features (codon)", - "http://edamontology.org/data_2117": "Map identifier", - "http://edamontology.org/data_2118": "Person identifier", - "http://edamontology.org/data_2119": "Nucleic acid identifier", - "http://edamontology.org/data_2126": "Translation frame specification", - "http://edamontology.org/data_2127": "Genetic code identifier", - "http://edamontology.org/data_2128": "Genetic code name", - "http://edamontology.org/data_2129": "File format name", - "http://edamontology.org/data_2130": "Sequence profile type", - "http://edamontology.org/data_2131": "Operating system name", - "http://edamontology.org/data_2132": "Mutation type", - "http://edamontology.org/data_2133": "Logical operator", - "http://edamontology.org/data_2134": "Results sort order", - "http://edamontology.org/data_2135": "Toggle", - "http://edamontology.org/data_2136": "Sequence width", - "http://edamontology.org/data_2137": "Gap penalty", - "http://edamontology.org/data_2139": "Nucleic acid melting temperature", - "http://edamontology.org/data_2140": "Concentration", - "http://edamontology.org/data_2141": "Window step size", - "http://edamontology.org/data_2142": "EMBOSS graph", - "http://edamontology.org/data_2143": "EMBOSS report", - "http://edamontology.org/data_2145": "Sequence offset", - "http://edamontology.org/data_2146": "Threshold", - "http://edamontology.org/data_2147": "Protein report (transcription factor)", - "http://edamontology.org/data_2149": "Database category name", - "http://edamontology.org/data_2150": "Sequence profile name", - "http://edamontology.org/data_2151": "Color", - "http://edamontology.org/data_2152": "Rendering parameter", - "http://edamontology.org/data_2154": "Sequence name", - "http://edamontology.org/data_2156": "Date", - "http://edamontology.org/data_2157": "Word composition", - "http://edamontology.org/data_2160": "Fickett testcode plot", - "http://edamontology.org/data_2161": "Sequence similarity plot", - "http://edamontology.org/data_2162": "Helical wheel", - "http://edamontology.org/data_2163": "Helical net", - "http://edamontology.org/data_2164": "Protein sequence properties plot", - "http://edamontology.org/data_2165": "Protein ionisation curve", - "http://edamontology.org/data_2166": "Sequence composition plot", - "http://edamontology.org/data_2167": "Nucleic acid density plot", - "http://edamontology.org/data_2168": "Sequence trace image", - "http://edamontology.org/data_2169": "Nucleic acid features (siRNA)", - "http://edamontology.org/data_2173": "Sequence set (stream)", - "http://edamontology.org/data_2174": "FlyBase secondary identifier", - "http://edamontology.org/data_2176": "Cardinality", - "http://edamontology.org/data_2177": "Exactly 1", - "http://edamontology.org/data_2178": "1 or more", - "http://edamontology.org/data_2179": "Exactly 2", - "http://edamontology.org/data_2180": "2 or more", - "http://edamontology.org/data_2190": "Sequence checksum", - "http://edamontology.org/data_2191": "Protein features report (chemical modifications)", - "http://edamontology.org/data_2192": "Error", - "http://edamontology.org/data_2193": "Database entry metadata", - "http://edamontology.org/data_2198": "Gene cluster", - "http://edamontology.org/data_2201": "Sequence record full", - "http://edamontology.org/data_2208": "Plasmid identifier", - "http://edamontology.org/data_2209": "Mutation ID", - "http://edamontology.org/data_2212": "Mutation annotation (basic)", - "http://edamontology.org/data_2213": "Mutation annotation (prevalence)", - "http://edamontology.org/data_2214": "Mutation annotation (prognostic)", - "http://edamontology.org/data_2215": "Mutation annotation (functional)", - "http://edamontology.org/data_2216": "Codon number", - "http://edamontology.org/data_2217": "Tumor annotation", - "http://edamontology.org/data_2218": "Server metadata", - "http://edamontology.org/data_2219": "Database field name", - "http://edamontology.org/data_2220": "Sequence cluster ID (SYSTERS)", - "http://edamontology.org/data_2223": "Ontology metadata", - "http://edamontology.org/data_2235": "Raw SCOP domain classification", - "http://edamontology.org/data_2236": "Raw CATH domain classification", - "http://edamontology.org/data_2240": "Heterogen annotation", - "http://edamontology.org/data_2242": "Phylogenetic property values", - "http://edamontology.org/data_2245": "Sequence set (bootstrapped)", - "http://edamontology.org/data_2247": "Phylogenetic consensus tree", - "http://edamontology.org/data_2248": "Schema", - "http://edamontology.org/data_2249": "DTD", - "http://edamontology.org/data_2250": "XML Schema", - "http://edamontology.org/data_2251": "Relax-NG schema", - "http://edamontology.org/data_2252": "XSLT stylesheet", - "http://edamontology.org/data_2253": "Data resource definition name", - "http://edamontology.org/data_2254": "OBO file format name", - "http://edamontology.org/data_2285": "Gene ID (MIPS)", - "http://edamontology.org/data_2288": "Sequence identifier (protein)", - "http://edamontology.org/data_2289": "Sequence identifier (nucleic acid)", - "http://edamontology.org/data_2290": "EMBL accession", - "http://edamontology.org/data_2291": "UniProt ID", - "http://edamontology.org/data_2292": "GenBank accession", - "http://edamontology.org/data_2293": "Gramene secondary identifier", - "http://edamontology.org/data_2294": "Sequence variation ID", - "http://edamontology.org/data_2295": "Gene ID", - "http://edamontology.org/data_2296": "Gene name (AceView)", - "http://edamontology.org/data_2297": "Gene ID (ECK)", - "http://edamontology.org/data_2298": "Gene ID (HGNC)", - "http://edamontology.org/data_2299": "Gene name", - "http://edamontology.org/data_2300": "Gene name (NCBI)", - "http://edamontology.org/data_2301": "SMILES string", - "http://edamontology.org/data_2302": "STRING ID", - "http://edamontology.org/data_2307": "Virus annotation", - "http://edamontology.org/data_2308": "Virus annotation (taxonomy)", - "http://edamontology.org/data_2309": "Reaction ID (SABIO-RK)", - "http://edamontology.org/data_2313": "Carbohydrate report", - "http://edamontology.org/data_2314": "GI number", - "http://edamontology.org/data_2315": "NCBI version", - "http://edamontology.org/data_2316": "Cell line name", - "http://edamontology.org/data_2317": "Cell line name (exact)", - "http://edamontology.org/data_2318": "Cell line name (truncated)", - "http://edamontology.org/data_2319": "Cell line name (no punctuation)", - "http://edamontology.org/data_2320": "Cell line name (assonant)", - "http://edamontology.org/data_2321": "Enzyme ID", - "http://edamontology.org/data_2325": "REBASE enzyme number", - "http://edamontology.org/data_2326": "DrugBank ID", - "http://edamontology.org/data_2327": "GI number (protein)", - "http://edamontology.org/data_2335": "Bit score", - "http://edamontology.org/data_2336": "Translation phase specification", - "http://edamontology.org/data_2337": "Resource metadata", - "http://edamontology.org/data_2338": "Ontology identifier", - "http://edamontology.org/data_2339": "Ontology concept name", - "http://edamontology.org/data_2340": "Genome build identifier", - "http://edamontology.org/data_2342": "Pathway or network name", - "http://edamontology.org/data_2343": "Pathway ID (KEGG)", - "http://edamontology.org/data_2344": "Pathway ID (NCI-Nature)", - "http://edamontology.org/data_2345": "Pathway ID (ConsensusPathDB)", - "http://edamontology.org/data_2346": "Sequence cluster ID (UniRef)", - "http://edamontology.org/data_2347": "Sequence cluster ID (UniRef100)", - "http://edamontology.org/data_2348": "Sequence cluster ID (UniRef90)", - "http://edamontology.org/data_2349": "Sequence cluster ID (UniRef50)", - "http://edamontology.org/data_2353": "Ontology data", - "http://edamontology.org/data_2354": "RNA family report", - "http://edamontology.org/data_2355": "RNA family identifier", - "http://edamontology.org/data_2356": "RFAM accession", - "http://edamontology.org/data_2357": "Protein signature type", - "http://edamontology.org/data_2358": "Domain-nucleic acid interaction report", - "http://edamontology.org/data_2359": "Domain-domain interactions", - "http://edamontology.org/data_2360": "Domain-domain interaction (indirect)", - "http://edamontology.org/data_2362": "Sequence accession (hybrid)", - "http://edamontology.org/data_2363": "2D PAGE data", - "http://edamontology.org/data_2364": "2D PAGE report", - "http://edamontology.org/data_2365": "Pathway or network accession", - "http://edamontology.org/data_2366": "Secondary structure alignment", - "http://edamontology.org/data_2367": "ASTD ID", - "http://edamontology.org/data_2368": "ASTD ID (exon)", - "http://edamontology.org/data_2369": "ASTD ID (intron)", - "http://edamontology.org/data_2370": "ASTD ID (polya)", - "http://edamontology.org/data_2371": "ASTD ID (tss)", - "http://edamontology.org/data_2372": "2D PAGE spot report", - "http://edamontology.org/data_2373": "Spot ID", - "http://edamontology.org/data_2374": "Spot serial number", - "http://edamontology.org/data_2375": "Spot ID (HSC-2DPAGE)", - "http://edamontology.org/data_2378": "Protein-motif interaction", - "http://edamontology.org/data_2379": "Strain identifier", - "http://edamontology.org/data_2380": "CABRI accession", - "http://edamontology.org/data_2381": "Experiment report (genotyping)", - "http://edamontology.org/data_2382": "Genotype experiment ID", - "http://edamontology.org/data_2383": "EGA accession", - "http://edamontology.org/data_2384": "IPI protein ID", - "http://edamontology.org/data_2385": "RefSeq accession (protein)", - "http://edamontology.org/data_2386": "EPD ID", - "http://edamontology.org/data_2387": "TAIR accession", - "http://edamontology.org/data_2388": "TAIR accession (At gene)", - "http://edamontology.org/data_2389": "UniSTS accession", - "http://edamontology.org/data_2390": "UNITE accession", - "http://edamontology.org/data_2391": "UTR accession", - "http://edamontology.org/data_2392": "UniParc accession", - "http://edamontology.org/data_2393": "mFLJ/mKIAA number", - "http://edamontology.org/data_2395": "Fungi annotation", - "http://edamontology.org/data_2396": "Fungi annotation (anamorph)", - "http://edamontology.org/data_2398": "Ensembl protein ID", - "http://edamontology.org/data_2400": "Toxin annotation", - "http://edamontology.org/data_2401": "Protein report (membrane protein)", - "http://edamontology.org/data_2402": "Protein-drug interaction report", - "http://edamontology.org/data_2522": "Map data", - "http://edamontology.org/data_2523": "Phylogenetic data", - "http://edamontology.org/data_2524": "Protein data", - "http://edamontology.org/data_2525": "Nucleic acid data", - "http://edamontology.org/data_2526": "Text data", - "http://edamontology.org/data_2527": "Parameter", - "http://edamontology.org/data_2528": "Molecular data", - "http://edamontology.org/data_2529": "Molecule report", - "http://edamontology.org/data_2530": "Organism report", - "http://edamontology.org/data_2531": "Protocol", - "http://edamontology.org/data_2534": "Sequence attribute", - "http://edamontology.org/data_2535": "Sequence tag profile", - "http://edamontology.org/data_2536": "Mass spectrometry data", - "http://edamontology.org/data_2537": "Protein structure raw data", - "http://edamontology.org/data_2538": "Mutation identifier", - "http://edamontology.org/data_2539": "Alignment data", - "http://edamontology.org/data_2540": "Data index data", - "http://edamontology.org/data_2563": "Amino acid name (single letter)", - "http://edamontology.org/data_2564": "Amino acid name (three letter)", - "http://edamontology.org/data_2565": "Amino acid name (full name)", - "http://edamontology.org/data_2576": "Toxin identifier", - "http://edamontology.org/data_2578": "ArachnoServer ID", - "http://edamontology.org/data_2579": "Expressed gene list", - "http://edamontology.org/data_2580": "BindingDB Monomer ID", - "http://edamontology.org/data_2581": "GO concept name", - "http://edamontology.org/data_2582": "GO concept ID (biological process)", - "http://edamontology.org/data_2583": "GO concept ID (molecular function)", - "http://edamontology.org/data_2584": "GO concept name (cellular component)", - "http://edamontology.org/data_2586": "Northern blot image", - "http://edamontology.org/data_2587": "Blot ID", - "http://edamontology.org/data_2588": "BlotBase blot ID", - "http://edamontology.org/data_2589": "Hierarchy", - "http://edamontology.org/data_2590": "Hierarchy identifier", - "http://edamontology.org/data_2591": "Brite hierarchy ID", - "http://edamontology.org/data_2592": "Cancer type", - "http://edamontology.org/data_2593": "BRENDA organism ID", - "http://edamontology.org/data_2594": "UniGene taxon", - "http://edamontology.org/data_2595": "UTRdb taxon", - "http://edamontology.org/data_2596": "Catalogue ID", - "http://edamontology.org/data_2597": "CABRI catalogue name", - "http://edamontology.org/data_2598": "Secondary structure alignment metadata", - "http://edamontology.org/data_2599": "Molecule interaction report", - "http://edamontology.org/data_2600": "Pathway or network", - "http://edamontology.org/data_2601": "Small molecule data", - "http://edamontology.org/data_2602": "Genotype and phenotype data", - "http://edamontology.org/data_2603": "Expression data", - "http://edamontology.org/data_2605": "Compound ID (KEGG)", - "http://edamontology.org/data_2606": "RFAM name", - "http://edamontology.org/data_2608": "Reaction ID (KEGG)", - "http://edamontology.org/data_2609": "Drug ID (KEGG)", - "http://edamontology.org/data_2610": "Ensembl ID", - "http://edamontology.org/data_2611": "ICD identifier", - "http://edamontology.org/data_2612": "Sequence cluster ID (CluSTr)", - "http://edamontology.org/data_2613": "KEGG Glycan ID", - "http://edamontology.org/data_2614": "TCDB ID", - "http://edamontology.org/data_2615": "MINT ID", - "http://edamontology.org/data_2616": "DIP ID", - "http://edamontology.org/data_2617": "Signaling Gateway protein ID", - "http://edamontology.org/data_2618": "Protein modification ID", - "http://edamontology.org/data_2619": "RESID ID", - "http://edamontology.org/data_2620": "RGD ID", - "http://edamontology.org/data_2621": "TAIR accession (protein)", - "http://edamontology.org/data_2622": "Compound ID (HMDB)", - "http://edamontology.org/data_2625": "LIPID MAPS ID", - "http://edamontology.org/data_2626": "PeptideAtlas ID", - "http://edamontology.org/data_2627": "Molecular interaction ID", - "http://edamontology.org/data_2628": "BioGRID interaction ID", - "http://edamontology.org/data_2629": "Enzyme ID (MEROPS)", - "http://edamontology.org/data_2630": "Mobile genetic element ID", - "http://edamontology.org/data_2631": "ACLAME ID", - "http://edamontology.org/data_2632": "SGD ID", - "http://edamontology.org/data_2633": "Book ID", - "http://edamontology.org/data_2634": "ISBN", - "http://edamontology.org/data_2635": "Compound ID (3DMET)", - "http://edamontology.org/data_2636": "MatrixDB interaction ID", - "http://edamontology.org/data_2637": "cPath ID", - "http://edamontology.org/data_2638": "PubChem bioassay ID", - "http://edamontology.org/data_2639": "PubChem ID", - "http://edamontology.org/data_2641": "Reaction ID (MACie)", - "http://edamontology.org/data_2642": "Gene ID (miRBase)", - "http://edamontology.org/data_2643": "Gene ID (ZFIN)", - "http://edamontology.org/data_2644": "Reaction ID (Rhea)", - "http://edamontology.org/data_2645": "Pathway ID (Unipathway)", - "http://edamontology.org/data_2646": "Compound ID (ChEMBL)", - "http://edamontology.org/data_2647": "LGICdb identifier", - "http://edamontology.org/data_2648": "Reaction kinetics ID (SABIO-RK)", - "http://edamontology.org/data_2649": "PharmGKB ID", - "http://edamontology.org/data_2650": "Pathway ID (PharmGKB)", - "http://edamontology.org/data_2651": "Disease ID (PharmGKB)", - "http://edamontology.org/data_2652": "Drug ID (PharmGKB)", - "http://edamontology.org/data_2653": "Drug ID (TTD)", - "http://edamontology.org/data_2654": "Target ID (TTD)", - "http://edamontology.org/data_2655": "Cell type identifier", - "http://edamontology.org/data_2656": "NeuronDB ID", - "http://edamontology.org/data_2657": "NeuroMorpho ID", - "http://edamontology.org/data_2658": "Compound ID (ChemIDplus)", - "http://edamontology.org/data_2659": "Pathway ID (SMPDB)", - "http://edamontology.org/data_2660": "BioNumbers ID", - "http://edamontology.org/data_2662": "T3DB ID", - "http://edamontology.org/data_2663": "Carbohydrate identifier", - "http://edamontology.org/data_2664": "GlycomeDB ID", - "http://edamontology.org/data_2665": "LipidBank ID", - "http://edamontology.org/data_2666": "CDD ID", - "http://edamontology.org/data_2667": "MMDB ID", - "http://edamontology.org/data_2668": "iRefIndex ID", - "http://edamontology.org/data_2669": "ModelDB ID", - "http://edamontology.org/data_2670": "Pathway ID (DQCS)", - "http://edamontology.org/data_2671": "Ensembl ID (Homo sapiens)", - "http://edamontology.org/data_2672": "Ensembl ID ('Bos taurus')", - "http://edamontology.org/data_2673": "Ensembl ID ('Canis familiaris')", - "http://edamontology.org/data_2674": "Ensembl ID ('Cavia porcellus')", - "http://edamontology.org/data_2675": "Ensembl ID ('Ciona intestinalis')", - "http://edamontology.org/data_2676": "Ensembl ID ('Ciona savignyi')", - "http://edamontology.org/data_2677": "Ensembl ID ('Danio rerio')", - "http://edamontology.org/data_2678": "Ensembl ID ('Dasypus novemcinctus')", - "http://edamontology.org/data_2679": "Ensembl ID ('Echinops telfairi')", - "http://edamontology.org/data_2680": "Ensembl ID ('Erinaceus europaeus')", - "http://edamontology.org/data_2681": "Ensembl ID ('Felis catus')", - "http://edamontology.org/data_2682": "Ensembl ID ('Gallus gallus')", - "http://edamontology.org/data_2683": "Ensembl ID ('Gasterosteus aculeatus')", - "http://edamontology.org/data_2684": "Ensembl ID ('Homo sapiens')", - "http://edamontology.org/data_2685": "Ensembl ID ('Loxodonta africana')", - "http://edamontology.org/data_2686": "Ensembl ID ('Macaca mulatta')", - "http://edamontology.org/data_2687": "Ensembl ID ('Monodelphis domestica')", - "http://edamontology.org/data_2688": "Ensembl ID ('Mus musculus')", - "http://edamontology.org/data_2689": "Ensembl ID ('Myotis lucifugus')", - "http://edamontology.org/data_2690": "Ensembl ID (\"Ornithorhynchus anatinus\")", - "http://edamontology.org/data_2691": "Ensembl ID ('Oryctolagus cuniculus')", - "http://edamontology.org/data_2692": "Ensembl ID ('Oryzias latipes')", - "http://edamontology.org/data_2693": "Ensembl ID ('Otolemur garnettii')", - "http://edamontology.org/data_2694": "Ensembl ID ('Pan troglodytes')", - "http://edamontology.org/data_2695": "Ensembl ID ('Rattus norvegicus')", - "http://edamontology.org/data_2696": "Ensembl ID ('Spermophilus tridecemlineatus')", - "http://edamontology.org/data_2697": "Ensembl ID ('Takifugu rubripes')", - "http://edamontology.org/data_2698": "Ensembl ID ('Tupaia belangeri')", - "http://edamontology.org/data_2699": "Ensembl ID ('Xenopus tropicalis')", - "http://edamontology.org/data_2700": "CATH identifier", - "http://edamontology.org/data_2701": "CATH node ID (family)", - "http://edamontology.org/data_2702": "Enzyme ID (CAZy)", - "http://edamontology.org/data_2704": "Clone ID (IMAGE)", - "http://edamontology.org/data_2705": "GO concept ID (cellular component)", - "http://edamontology.org/data_2706": "Chromosome name (BioCyc)", - "http://edamontology.org/data_2709": "CleanEx entry name", - "http://edamontology.org/data_2710": "CleanEx dataset code", - "http://edamontology.org/data_2711": "Genome report", - "http://edamontology.org/data_2713": "Protein ID (CORUM)", - "http://edamontology.org/data_2714": "CDD PSSM-ID", - "http://edamontology.org/data_2715": "Protein ID (CuticleDB)", - "http://edamontology.org/data_2716": "DBD ID", - "http://edamontology.org/data_2717": "Oligonucleotide probe annotation", - "http://edamontology.org/data_2718": "Oligonucleotide ID", - "http://edamontology.org/data_2719": "dbProbe ID", - "http://edamontology.org/data_2720": "Dinucleotide property", - "http://edamontology.org/data_2721": "DiProDB ID", - "http://edamontology.org/data_2722": "Protein features report (disordered structure)", - "http://edamontology.org/data_2723": "Protein ID (DisProt)", - "http://edamontology.org/data_2724": "Embryo report", - "http://edamontology.org/data_2725": "Ensembl transcript ID", - "http://edamontology.org/data_2726": "Inhibitor annotation", - "http://edamontology.org/data_2727": "Promoter ID", - "http://edamontology.org/data_2728": "EST accession", - "http://edamontology.org/data_2729": "COGEME EST ID", - "http://edamontology.org/data_2730": "COGEME unisequence ID", - "http://edamontology.org/data_2731": "Protein family ID (GeneFarm)", - "http://edamontology.org/data_2732": "Family name", - "http://edamontology.org/data_2733": "Genus name (virus)", - "http://edamontology.org/data_2734": "Family name (virus)", - "http://edamontology.org/data_2735": "Database name (SwissRegulon)", - "http://edamontology.org/data_2736": "Sequence feature ID (SwissRegulon)", - "http://edamontology.org/data_2737": "FIG ID", - "http://edamontology.org/data_2738": "Gene ID (Xenbase)", - "http://edamontology.org/data_2739": "Gene ID (Genolist)", - "http://edamontology.org/data_2740": "Gene name (Genolist)", - "http://edamontology.org/data_2741": "ABS ID", - "http://edamontology.org/data_2742": "AraC-XylS ID", - "http://edamontology.org/data_2743": "Gene name (HUGO)", - "http://edamontology.org/data_2744": "Locus ID (PseudoCAP)", - "http://edamontology.org/data_2745": "Locus ID (UTR)", - "http://edamontology.org/data_2746": "MonosaccharideDB ID", - "http://edamontology.org/data_2747": "Database name (CMD)", - "http://edamontology.org/data_2748": "Database name (Osteogenesis)", - "http://edamontology.org/data_2749": "Genome identifier", - "http://edamontology.org/data_2751": "GenomeReviews ID", - "http://edamontology.org/data_2752": "GlycoMap ID", - "http://edamontology.org/data_2753": "Carbohydrate conformational map", - "http://edamontology.org/data_2755": "Transcription factor name", - "http://edamontology.org/data_2756": "TCID", - "http://edamontology.org/data_2757": "Pfam domain name", - "http://edamontology.org/data_2758": "Pfam clan ID", - "http://edamontology.org/data_2759": "Gene ID (VectorBase)", - "http://edamontology.org/data_2761": "UTRSite ID", - "http://edamontology.org/data_2762": "Sequence signature report", - "http://edamontology.org/data_2763": "Locus annotation", - "http://edamontology.org/data_2764": "Protein name (UniProt)", - "http://edamontology.org/data_2765": "Term ID list", - "http://edamontology.org/data_2766": "HAMAP ID", - "http://edamontology.org/data_2767": "Identifier with metadata", - "http://edamontology.org/data_2768": "Gene symbol annotation", - "http://edamontology.org/data_2769": "Transcript ID", - "http://edamontology.org/data_2770": "HIT ID", - "http://edamontology.org/data_2771": "HIX ID", - "http://edamontology.org/data_2772": "HPA antibody id", - "http://edamontology.org/data_2773": "IMGT/HLA ID", - "http://edamontology.org/data_2774": "Gene ID (JCVI)", - "http://edamontology.org/data_2775": "Kinase name", - "http://edamontology.org/data_2776": "ConsensusPathDB entity ID", - "http://edamontology.org/data_2777": "ConsensusPathDB entity name", - "http://edamontology.org/data_2778": "CCAP strain number", - "http://edamontology.org/data_2779": "Stock number", - "http://edamontology.org/data_2780": "Stock number (TAIR)", - "http://edamontology.org/data_2781": "REDIdb ID", - "http://edamontology.org/data_2782": "SMART domain name", - "http://edamontology.org/data_2783": "Protein family ID (PANTHER)", - "http://edamontology.org/data_2784": "RNAVirusDB ID", - "http://edamontology.org/data_2785": "Virus ID", - "http://edamontology.org/data_2786": "NCBI Genome Project ID", - "http://edamontology.org/data_2787": "NCBI genome accession", - "http://edamontology.org/data_2788": "Sequence profile data", - "http://edamontology.org/data_2789": "Protein ID (TopDB)", - "http://edamontology.org/data_2790": "Gel ID", - "http://edamontology.org/data_2791": "Reference map name (SWISS-2DPAGE)", - "http://edamontology.org/data_2792": "Protein ID (PeroxiBase)", - "http://edamontology.org/data_2793": "SISYPHUS ID", - "http://edamontology.org/data_2794": "ORF ID", - "http://edamontology.org/data_2795": "ORF identifier", - "http://edamontology.org/data_2796": "Linucs ID", - "http://edamontology.org/data_2797": "Protein ID (LGICdb)", - "http://edamontology.org/data_2798": "MaizeDB ID", - "http://edamontology.org/data_2799": "Gene ID (MfunGD)", - "http://edamontology.org/data_2800": "Orpha number", - "http://edamontology.org/data_2802": "Protein ID (EcID)", - "http://edamontology.org/data_2803": "Clone ID (RefSeq)", - "http://edamontology.org/data_2804": "Protein ID (ConoServer)", - "http://edamontology.org/data_2805": "GeneSNP ID", - "http://edamontology.org/data_2812": "Lipid identifier", - "http://edamontology.org/data_2831": "Databank", - "http://edamontology.org/data_2832": "Web portal", - "http://edamontology.org/data_2835": "Gene ID (VBASE2)", - "http://edamontology.org/data_2836": "DPVweb ID", - "http://edamontology.org/data_2837": "Pathway ID (BioSystems)", - "http://edamontology.org/data_2838": "Experimental data (proteomics)", - "http://edamontology.org/data_2849": "Abstract", - "http://edamontology.org/data_2850": "Lipid structure", - "http://edamontology.org/data_2851": "Drug structure", - "http://edamontology.org/data_2852": "Toxin structure", - "http://edamontology.org/data_2854": "Position-specific scoring matrix", - "http://edamontology.org/data_2855": "Distance matrix", - "http://edamontology.org/data_2856": "Structural distance matrix", - "http://edamontology.org/data_2857": "Article metadata", - "http://edamontology.org/data_2858": "Ontology concept", - "http://edamontology.org/data_2865": "Codon usage bias", - "http://edamontology.org/data_2866": "Northern blot report", - "http://edamontology.org/data_2870": "Radiation hybrid map", - "http://edamontology.org/data_2872": "ID list", - "http://edamontology.org/data_2873": "Phylogenetic gene frequencies data", - "http://edamontology.org/data_2874": "Sequence set (polymorphic)", - "http://edamontology.org/data_2875": "DRCAT resource", - "http://edamontology.org/data_2877": "Protein complex", - "http://edamontology.org/data_2878": "Protein structural motif", - "http://edamontology.org/data_2879": "Lipid report", - "http://edamontology.org/data_2880": "Secondary structure image", - "http://edamontology.org/data_2881": "Secondary structure report", - "http://edamontology.org/data_2882": "DNA features", - "http://edamontology.org/data_2883": "RNA features report", - "http://edamontology.org/data_2884": "Plot", - "http://edamontology.org/data_2886": "Protein sequence record", - "http://edamontology.org/data_2887": "Nucleic acid sequence record", - "http://edamontology.org/data_2888": "Protein sequence record (full)", - "http://edamontology.org/data_2889": "Nucleic acid sequence record (full)", - "http://edamontology.org/data_2891": "Biological model accession", - "http://edamontology.org/data_2892": "Cell type name", - "http://edamontology.org/data_2893": "Cell type accession", - "http://edamontology.org/data_2894": "Compound accession", - "http://edamontology.org/data_2895": "Drug accession", - "http://edamontology.org/data_2896": "Toxin name", - "http://edamontology.org/data_2897": "Toxin accession", - "http://edamontology.org/data_2898": "Monosaccharide accession", - "http://edamontology.org/data_2899": "Drug name", - "http://edamontology.org/data_2900": "Carbohydrate accession", - "http://edamontology.org/data_2901": "Molecule accession", - "http://edamontology.org/data_2902": "Data resource definition accession", - "http://edamontology.org/data_2903": "Genome accession", - "http://edamontology.org/data_2904": "Map accession", - "http://edamontology.org/data_2905": "Lipid accession", - "http://edamontology.org/data_2906": "Peptide ID", - "http://edamontology.org/data_2907": "Protein accession", - "http://edamontology.org/data_2908": "Organism accession", - "http://edamontology.org/data_2909": "Organism name", - "http://edamontology.org/data_2910": "Protein family accession", - "http://edamontology.org/data_2911": "Transcription factor accession", - "http://edamontology.org/data_2912": "Strain accession", - "http://edamontology.org/data_2913": "Virus identifier", - "http://edamontology.org/data_2914": "Sequence features metadata", - "http://edamontology.org/data_2915": "Gramene identifier", - "http://edamontology.org/data_2916": "DDBJ accession", - "http://edamontology.org/data_2917": "ConsensusPathDB identifier", - "http://edamontology.org/data_2925": "Sequence data", - "http://edamontology.org/data_2927": "Codon usage", - "http://edamontology.org/data_2954": "Article report", - "http://edamontology.org/data_2955": "Sequence report", - "http://edamontology.org/data_2956": "Protein secondary structure", - "http://edamontology.org/data_2957": "Hopp and Woods plot", - "http://edamontology.org/data_2958": "Nucleic acid melting curve", - "http://edamontology.org/data_2959": "Nucleic acid probability profile", - "http://edamontology.org/data_2960": "Nucleic acid temperature profile", - "http://edamontology.org/data_2961": "Gene regulatory network report", - "http://edamontology.org/data_2965": "2D PAGE gel report", - "http://edamontology.org/data_2966": "Oligonucleotide probe sets annotation", - "http://edamontology.org/data_2967": "Microarray image", - "http://edamontology.org/data_2968": "Image", - "http://edamontology.org/data_2969": "Sequence image", - "http://edamontology.org/data_2970": "Protein hydropathy data", - "http://edamontology.org/data_2971": "Workflow data", - "http://edamontology.org/data_2972": "Workflow", - "http://edamontology.org/data_2973": "Secondary structure data", - "http://edamontology.org/data_2974": "Protein sequence (raw)", - "http://edamontology.org/data_2975": "Nucleic acid sequence (raw)", - "http://edamontology.org/data_2976": "Protein sequence", - "http://edamontology.org/data_2977": "Nucleic acid sequence", - "http://edamontology.org/data_2978": "Reaction data", - "http://edamontology.org/data_2979": "Peptide property", - "http://edamontology.org/data_2980": "Protein classification", - "http://edamontology.org/data_2981": "Sequence motif data", - "http://edamontology.org/data_2982": "Sequence profile data", - "http://edamontology.org/data_2983": "Pathway or network data", - "http://edamontology.org/data_2984": "Pathway or network report", - "http://edamontology.org/data_2985": "Nucleic acid thermodynamic data", - "http://edamontology.org/data_2986": "Nucleic acid classification", - "http://edamontology.org/data_2987": "Classification report", - "http://edamontology.org/data_2989": "Protein features report (key folding sites)", - "http://edamontology.org/data_2991": "Protein geometry data", - "http://edamontology.org/data_2992": "Protein structure image", - "http://edamontology.org/data_2994": "Phylogenetic character weights", - "http://edamontology.org/data_3002": "Annotation track", - "http://edamontology.org/data_3021": "UniProt accession", - "http://edamontology.org/data_3022": "NCBI genetic code ID", - "http://edamontology.org/data_3025": "Ontology concept identifier", - "http://edamontology.org/data_3026": "GO concept name (biological process)", - "http://edamontology.org/data_3027": "GO concept name (molecular function)", - "http://edamontology.org/data_3028": "Taxonomy", - "http://edamontology.org/data_3029": "Protein ID (EMBL/GenBank/DDBJ)", - "http://edamontology.org/data_3031": "Core data", - "http://edamontology.org/data_3034": "Sequence feature identifier", - "http://edamontology.org/data_3035": "Structure identifier", - "http://edamontology.org/data_3036": "Matrix identifier", - "http://edamontology.org/data_3085": "Protein sequence composition", - "http://edamontology.org/data_3086": "Nucleic acid sequence composition (report)", - "http://edamontology.org/data_3101": "Protein domain classification node", - "http://edamontology.org/data_3102": "CAS number", - "http://edamontology.org/data_3103": "ATC code", - "http://edamontology.org/data_3104": "UNII", - "http://edamontology.org/data_3105": "Geotemporal metadata", - "http://edamontology.org/data_3106": "System metadata", - "http://edamontology.org/data_3107": "Sequence feature name", - "http://edamontology.org/data_3108": "Experimental measurement", - "http://edamontology.org/data_3110": "Raw microarray data", - "http://edamontology.org/data_3111": "Processed microarray data", - "http://edamontology.org/data_3112": "Gene expression matrix", - "http://edamontology.org/data_3113": "Sample annotation", - "http://edamontology.org/data_3115": "Microarray metadata", - "http://edamontology.org/data_3116": "Microarray protocol annotation", - "http://edamontology.org/data_3117": "Microarray hybridisation data", - "http://edamontology.org/data_3119": "Sequence features (compositionally-biased regions)", - "http://edamontology.org/data_3122": "Nucleic acid features (difference and change)", - "http://edamontology.org/data_3128": "Nucleic acid structure report", - "http://edamontology.org/data_3129": "Protein features report (repeats)", - "http://edamontology.org/data_3130": "Sequence motif matches (protein)", - "http://edamontology.org/data_3131": "Sequence motif matches (nucleic acid)", - "http://edamontology.org/data_3132": "Nucleic acid features (d-loop)", - "http://edamontology.org/data_3133": "Nucleic acid features (stem loop)", - "http://edamontology.org/data_3134": "Gene transcript report", - "http://edamontology.org/data_3137": "Non-coding RNA", - "http://edamontology.org/data_3138": "Transcriptional features (report)", - "http://edamontology.org/data_3140": "Nucleic acid features (immunoglobulin gene structure)", - "http://edamontology.org/data_3141": "SCOP class", - "http://edamontology.org/data_3142": "SCOP fold", - "http://edamontology.org/data_3143": "SCOP superfamily", - "http://edamontology.org/data_3144": "SCOP family", - "http://edamontology.org/data_3145": "SCOP protein", - "http://edamontology.org/data_3146": "SCOP species", - "http://edamontology.org/data_3147": "Mass spectrometry experiment", - "http://edamontology.org/data_3148": "Gene family report", - "http://edamontology.org/data_3153": "Protein image", - "http://edamontology.org/data_3154": "Protein alignment", - "http://edamontology.org/data_3165": "NGS experiment", - "http://edamontology.org/data_3181": "Sequence assembly report", - "http://edamontology.org/data_3210": "Genome index", - "http://edamontology.org/data_3231": "GWAS report", - "http://edamontology.org/data_3236": "Cytoband position", - "http://edamontology.org/data_3238": "Cell type ontology ID", - "http://edamontology.org/data_3241": "Kinetic model", - "http://edamontology.org/data_3264": "COSMIC ID", - "http://edamontology.org/data_3265": "HGMD ID", - "http://edamontology.org/data_3266": "Sequence assembly ID", - "http://edamontology.org/data_3268": "Sequence feature type", - "http://edamontology.org/data_3269": "Gene homology (report)", - "http://edamontology.org/data_3270": "Ensembl gene tree ID", - "http://edamontology.org/data_3271": "Gene tree", - "http://edamontology.org/data_3272": "Species tree", - "http://edamontology.org/data_3273": "Sample ID", - "http://edamontology.org/data_3274": "MGI accession", - "http://edamontology.org/data_3275": "Phenotype name", - "http://edamontology.org/data_3354": "Transition matrix", - "http://edamontology.org/data_3355": "Emission matrix", - "http://edamontology.org/data_3356": "Hidden Markov model", - "http://edamontology.org/data_3358": "Format identifier", - "http://edamontology.org/data_3424": "Raw image", - "http://edamontology.org/data_3425": "Carbohydrate property", - "http://edamontology.org/data_3426": "Proteomics experiment report", - "http://edamontology.org/data_3427": "RNAi report", - "http://edamontology.org/data_3428": "Simulation experiment report", - "http://edamontology.org/data_3442": "MRI image", - "http://edamontology.org/data_3449": "Cell migration track image", - "http://edamontology.org/data_3451": "Rate of association", - "http://edamontology.org/data_3479": "Gene order", - "http://edamontology.org/data_3483": "Spectrum", - "http://edamontology.org/data_3488": "NMR spectrum", - "http://edamontology.org/data_3490": "Chemical structure sketch", - "http://edamontology.org/data_3492": "Nucleic acid signature", - "http://edamontology.org/data_3494": "DNA sequence", - "http://edamontology.org/data_3495": "RNA sequence", - "http://edamontology.org/data_3496": "RNA sequence (raw)", - "http://edamontology.org/data_3497": "DNA sequence (raw)", - "http://edamontology.org/data_3498": "Sequence variations", - "http://edamontology.org/data_3505": "Bibliography", - "http://edamontology.org/data_3509": "Ontology mapping", - "http://edamontology.org/data_3546": "Image metadata", - "http://edamontology.org/data_3558": "Clinical trial report", - "http://edamontology.org/data_3567": "Reference sample report", - "http://edamontology.org/data_3568": "Gene Expression Atlas Experiment ID", - "http://edamontology.org/data_3667": "Disease identifier", - "http://edamontology.org/data_3668": "Disease name", - "http://edamontology.org/data_3669": "Training material", - "http://edamontology.org/data_3670": "Online course", - "http://edamontology.org/data_3671": "Text", - "http://edamontology.org/data_3707": "Biodiversity data", - "http://edamontology.org/data_3716": "Biosafety report", - "http://edamontology.org/data_3717": "Isolation report", - "http://edamontology.org/data_3718": "Pathogenicity report", - "http://edamontology.org/data_3719": "Biosafety classification", - "http://edamontology.org/data_3720": "Geographic location", - "http://edamontology.org/data_3721": "Isolation source", - "http://edamontology.org/data_3722": "Physiology parameter", - "http://edamontology.org/data_3723": "Morphology parameter", - "http://edamontology.org/data_3724": "Cultivation parameter", - "http://edamontology.org/data_3732": "Sequencing metadata name", - "http://edamontology.org/data_3733": "Flow cell identifier", - "http://edamontology.org/data_3734": "Lane identifier", - "http://edamontology.org/data_3735": "Run number", - "http://edamontology.org/data_3736": "Ecological data", - "http://edamontology.org/data_3737": "Alpha diversity data", - "http://edamontology.org/data_3738": "Beta diversity data", - "http://edamontology.org/data_3739": "Gamma diversity data", - "http://edamontology.org/data_3743": "Ordination plot", - "http://edamontology.org/data_3753": "Over-representation data", - "http://edamontology.org/data_3754": "GO-term enrichment data", - "http://edamontology.org/data_3756": "Localisation score", - "http://edamontology.org/data_3757": "Unimod ID", - "http://edamontology.org/data_3759": "ProteomeXchange ID", - "http://edamontology.org/data_3768": "Clustered expression profiles", - "http://edamontology.org/data_3769": "BRENDA ontology concept ID", - "http://edamontology.org/data_3779": "Annotated text", - "http://edamontology.org/data_3786": "Query script", - "http://edamontology.org/data_3805": "3D EM Map", - "http://edamontology.org/data_3806": "3D EM Mask", - "http://edamontology.org/data_3807": "EM Movie", - "http://edamontology.org/data_3808": "EM Micrograph", - "http://edamontology.org/data_3842": "Molecular simulation data", - "http://edamontology.org/data_3856": "RNA central ID", - "http://edamontology.org/data_3861": "Electronic health record", - "http://edamontology.org/data_3869": "Simulation", - "http://edamontology.org/data_3870": "Trajectory data", - "http://edamontology.org/data_3871": "Forcefield parameters", - "http://edamontology.org/data_3872": "Topology data", - "http://edamontology.org/data_3905": "Histogram", - "http://edamontology.org/data_3914": "Quality control report", - "http://edamontology.org/data_3917": "Count matrix", - "http://edamontology.org/data_3924": "DNA structure alignment", - "http://edamontology.org/data_3932": "Q-value", - "http://edamontology.org/data_3949": "Profile HMM", - "http://edamontology.org/data_3952": "Pathway ID (WikiPathways)", - "http://edamontology.org/data_3953": "Pathway overrepresentation data", - "http://edamontology.org/format_1196": "SMILES", - "http://edamontology.org/format_1197": "InChI", - "http://edamontology.org/format_1198": "mf", - "http://edamontology.org/format_1199": "InChIKey", - "http://edamontology.org/format_1200": "smarts", - "http://edamontology.org/format_1206": "unambiguous pure", - "http://edamontology.org/format_1207": "nucleotide", - "http://edamontology.org/format_1208": "protein", - "http://edamontology.org/format_1209": "consensus", - "http://edamontology.org/format_1210": "pure nucleotide", - "http://edamontology.org/format_1211": "unambiguous pure nucleotide", - "http://edamontology.org/format_1212": "dna", - "http://edamontology.org/format_1213": "rna", - "http://edamontology.org/format_1214": "unambiguous pure dna", - "http://edamontology.org/format_1215": "pure dna", - "http://edamontology.org/format_1216": "unambiguous pure rna sequence", - "http://edamontology.org/format_1217": "pure rna", - "http://edamontology.org/format_1218": "unambiguous pure protein", - "http://edamontology.org/format_1219": "pure protein", - "http://edamontology.org/format_1228": "UniGene entry format", - "http://edamontology.org/format_1247": "COG sequence cluster format", - "http://edamontology.org/format_1248": "EMBL feature location", - "http://edamontology.org/format_1295": "quicktandem", - "http://edamontology.org/format_1296": "Sanger inverted repeats", - "http://edamontology.org/format_1297": "EMBOSS repeat", - "http://edamontology.org/format_1316": "est2genome format", - "http://edamontology.org/format_1318": "restrict format", - "http://edamontology.org/format_1319": "restover format", - "http://edamontology.org/format_1320": "REBASE restriction sites", - "http://edamontology.org/format_1332": "FASTA search results format", - "http://edamontology.org/format_1333": "BLAST results", - "http://edamontology.org/format_1334": "mspcrunch", - "http://edamontology.org/format_1335": "Smith-Waterman format", - "http://edamontology.org/format_1336": "dhf", - "http://edamontology.org/format_1337": "lhf", - "http://edamontology.org/format_1341": "InterPro hits format", - "http://edamontology.org/format_1342": "InterPro protein view report format", - "http://edamontology.org/format_1343": "InterPro match table format", - "http://edamontology.org/format_1349": "HMMER Dirichlet prior", - "http://edamontology.org/format_1350": "MEME Dirichlet prior", - "http://edamontology.org/format_1351": "HMMER emission and transition", - "http://edamontology.org/format_1356": "prosite-pattern", - "http://edamontology.org/format_1357": "EMBOSS sequence pattern", - "http://edamontology.org/format_1360": "meme-motif", - "http://edamontology.org/format_1366": "prosite-profile", - "http://edamontology.org/format_1367": "JASPAR format", - "http://edamontology.org/format_1369": "MEME background Markov model", - "http://edamontology.org/format_1370": "HMMER format", - "http://edamontology.org/format_1391": "HMMER-aln", - "http://edamontology.org/format_1392": "DIALIGN format", - "http://edamontology.org/format_1393": "daf", - "http://edamontology.org/format_1419": "Sequence-MEME profile alignment", - "http://edamontology.org/format_1421": "HMMER profile alignment (sequences versus HMMs)", - "http://edamontology.org/format_1422": "HMMER profile alignment (HMM versus sequences)", - "http://edamontology.org/format_1423": "Phylip distance matrix", - "http://edamontology.org/format_1424": "ClustalW dendrogram", - "http://edamontology.org/format_1425": "Phylip tree raw", - "http://edamontology.org/format_1430": "Phylip continuous quantitative characters", - "http://edamontology.org/format_1431": "Phylogenetic property values format", - "http://edamontology.org/format_1432": "Phylip character frequencies format", - "http://edamontology.org/format_1433": "Phylip discrete states format", - "http://edamontology.org/format_1434": "Phylip cliques format", - "http://edamontology.org/format_1435": "Phylip tree format", - "http://edamontology.org/format_1436": "TreeBASE format", - "http://edamontology.org/format_1437": "TreeFam format", - "http://edamontology.org/format_1445": "Phylip tree distance format", - "http://edamontology.org/format_1454": "dssp", - "http://edamontology.org/format_1455": "hssp", - "http://edamontology.org/format_1457": "Dot-bracket format", - "http://edamontology.org/format_1458": "Vienna local RNA secondary structure format", - "http://edamontology.org/format_1475": "PDB database entry format", - "http://edamontology.org/format_1476": "PDB", - "http://edamontology.org/format_1477": "mmCIF", - "http://edamontology.org/format_1478": "PDBML", - "http://edamontology.org/format_1500": "Domainatrix 3D-1D scoring matrix format", - "http://edamontology.org/format_1504": "aaindex", - "http://edamontology.org/format_1511": "IntEnz enzyme report format", - "http://edamontology.org/format_1512": "BRENDA enzyme report format", - "http://edamontology.org/format_1513": "KEGG REACTION enzyme report format", - "http://edamontology.org/format_1514": "KEGG ENZYME enzyme report format", - "http://edamontology.org/format_1515": "REBASE proto enzyme report format", - "http://edamontology.org/format_1516": "REBASE withrefm enzyme report format", - "http://edamontology.org/format_1551": "Pcons report format", - "http://edamontology.org/format_1552": "ProQ report format", - "http://edamontology.org/format_1563": "SMART domain assignment report format", - "http://edamontology.org/format_1568": "BIND entry format", - "http://edamontology.org/format_1569": "IntAct entry format", - "http://edamontology.org/format_1570": "InterPro entry format", - "http://edamontology.org/format_1571": "InterPro entry abstract format", - "http://edamontology.org/format_1572": "Gene3D entry format", - "http://edamontology.org/format_1573": "PIRSF entry format", - "http://edamontology.org/format_1574": "PRINTS entry format", - "http://edamontology.org/format_1575": "Panther Families and HMMs entry format", - "http://edamontology.org/format_1576": "Pfam entry format", - "http://edamontology.org/format_1577": "SMART entry format", - "http://edamontology.org/format_1578": "Superfamily entry format", - "http://edamontology.org/format_1579": "TIGRFam entry format", - "http://edamontology.org/format_1580": "ProDom entry format", - "http://edamontology.org/format_1581": "FSSP entry format", - "http://edamontology.org/format_1582": "findkm", - "http://edamontology.org/format_1603": "Ensembl gene report format", - "http://edamontology.org/format_1604": "DictyBase gene report format", - "http://edamontology.org/format_1605": "CGD gene report format", - "http://edamontology.org/format_1606": "DragonDB gene report format", - "http://edamontology.org/format_1607": "EcoCyc gene report format", - "http://edamontology.org/format_1608": "FlyBase gene report format", - "http://edamontology.org/format_1609": "Gramene gene report format", - "http://edamontology.org/format_1610": "KEGG GENES gene report format", - "http://edamontology.org/format_1611": "MaizeGDB gene report format", - "http://edamontology.org/format_1612": "MGD gene report format", - "http://edamontology.org/format_1613": "RGD gene report format", - "http://edamontology.org/format_1614": "SGD gene report format", - "http://edamontology.org/format_1615": "GeneDB gene report format", - "http://edamontology.org/format_1616": "TAIR gene report format", - "http://edamontology.org/format_1617": "WormBase gene report format", - "http://edamontology.org/format_1618": "ZFIN gene report format", - "http://edamontology.org/format_1619": "TIGR gene report format", - "http://edamontology.org/format_1620": "dbSNP polymorphism report format", - "http://edamontology.org/format_1623": "OMIM entry format", - "http://edamontology.org/format_1624": "HGVbase entry format", - "http://edamontology.org/format_1625": "HIVDB entry format", - "http://edamontology.org/format_1626": "KEGG DISEASE entry format", - "http://edamontology.org/format_1627": "Primer3 primer", - "http://edamontology.org/format_1628": "ABI", - "http://edamontology.org/format_1629": "mira", - "http://edamontology.org/format_1630": "CAF", - "http://edamontology.org/format_1631": "EXP", - "http://edamontology.org/format_1632": "SCF", - "http://edamontology.org/format_1633": "PHD", - "http://edamontology.org/format_1637": "dat", - "http://edamontology.org/format_1638": "cel", - "http://edamontology.org/format_1639": "affymetrix", - "http://edamontology.org/format_1640": "ArrayExpress entry format", - "http://edamontology.org/format_1641": "affymetrix-exp", - "http://edamontology.org/format_1644": "CHP", - "http://edamontology.org/format_1645": "EMDB entry format", - "http://edamontology.org/format_1647": "KEGG PATHWAY entry format", - "http://edamontology.org/format_1648": "MetaCyc entry format", - "http://edamontology.org/format_1649": "HumanCyc entry format", - "http://edamontology.org/format_1650": "INOH entry format", - "http://edamontology.org/format_1651": "PATIKA entry format", - "http://edamontology.org/format_1652": "Reactome entry format", - "http://edamontology.org/format_1653": "aMAZE entry format", - "http://edamontology.org/format_1654": "CPDB entry format", - "http://edamontology.org/format_1655": "Panther Pathways entry format", - "http://edamontology.org/format_1665": "Taverna workflow format", - "http://edamontology.org/format_1666": "BioModel mathematical model format", - "http://edamontology.org/format_1697": "KEGG LIGAND entry format", - "http://edamontology.org/format_1698": "KEGG COMPOUND entry format", - "http://edamontology.org/format_1699": "KEGG PLANT entry format", - "http://edamontology.org/format_1700": "KEGG GLYCAN entry format", - "http://edamontology.org/format_1701": "PubChem entry format", - "http://edamontology.org/format_1702": "ChemSpider entry format", - "http://edamontology.org/format_1703": "ChEBI entry format", - "http://edamontology.org/format_1704": "MSDchem ligand dictionary entry format", - "http://edamontology.org/format_1705": "HET group dictionary entry format", - "http://edamontology.org/format_1706": "KEGG DRUG entry format", - "http://edamontology.org/format_1734": "PubMed citation", - "http://edamontology.org/format_1735": "Medline Display Format", - "http://edamontology.org/format_1736": "CiteXplore-core", - "http://edamontology.org/format_1737": "CiteXplore-all", - "http://edamontology.org/format_1739": "pmc", - "http://edamontology.org/format_1740": "iHOP format", - "http://edamontology.org/format_1741": "OSCAR format", - "http://edamontology.org/format_1747": "PDB atom record format", - "http://edamontology.org/format_1760": "CATH chain report format", - "http://edamontology.org/format_1761": "CATH PDB report format", - "http://edamontology.org/format_1782": "NCBI gene report format", - "http://edamontology.org/format_1808": "GeneIlluminator gene report format", - "http://edamontology.org/format_1809": "BacMap gene card format", - "http://edamontology.org/format_1810": "ColiCard report format", - "http://edamontology.org/format_1861": "PlasMapper TextMap", - "http://edamontology.org/format_1910": "newick", - "http://edamontology.org/format_1911": "TreeCon format", - "http://edamontology.org/format_1912": "Nexus format", - "http://edamontology.org/format_1915": "Format", - "http://edamontology.org/format_1918": "Atomic data format", - "http://edamontology.org/format_1919": "Sequence record format", - "http://edamontology.org/format_1920": "Sequence feature annotation format", - "http://edamontology.org/format_1921": "Alignment format", - "http://edamontology.org/format_1923": "acedb", - "http://edamontology.org/format_1924": "clustal sequence format", - "http://edamontology.org/format_1925": "codata", - "http://edamontology.org/format_1926": "dbid", - "http://edamontology.org/format_1927": "EMBL format", - "http://edamontology.org/format_1928": "Staden experiment format", - 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"http://edamontology.org/operation_3963": "Duplication detection", - "http://edamontology.org/operation_3964": "Complex CNV detection", - "http://edamontology.org/operation_3965": "Amplification detection", - "http://edamontology.org/operation_3968": "Adhesin prediction", - "http://edamontology.org/operation_4008": "Protein design", - "http://edamontology.org/operation_4009": "Small molecule design", - "http://edamontology.org/topic_0003": "Topic", - "http://edamontology.org/topic_0077": "Nucleic acids", - "http://edamontology.org/topic_0078": "Proteins", - "http://edamontology.org/topic_0079": "Metabolites", - "http://edamontology.org/topic_0080": "Sequence analysis", - "http://edamontology.org/topic_0081": "Structure analysis", - "http://edamontology.org/topic_0082": "Structure prediction", - "http://edamontology.org/topic_0083": "Alignment", - "http://edamontology.org/topic_0084": "Phylogeny", - "http://edamontology.org/topic_0085": "Functional genomics", - "http://edamontology.org/topic_0089": "Ontology and terminology", - "http://edamontology.org/topic_0090": "Information retrieval", - "http://edamontology.org/topic_0091": "Bioinformatics", - "http://edamontology.org/topic_0092": "Data visualisation", - "http://edamontology.org/topic_0094": "Nucleic acid thermodynamics", - "http://edamontology.org/topic_0097": "Nucleic acid structure analysis", - "http://edamontology.org/topic_0099": "RNA", - "http://edamontology.org/topic_0100": "Nucleic acid restriction", - "http://edamontology.org/topic_0102": "Mapping", - "http://edamontology.org/topic_0107": "Genetic codes and codon usage", - "http://edamontology.org/topic_0108": "Protein expression", - "http://edamontology.org/topic_0109": "Gene finding", - "http://edamontology.org/topic_0110": "Transcription", - "http://edamontology.org/topic_0111": "Promoters", - "http://edamontology.org/topic_0112": "Nucleic acid folding", - "http://edamontology.org/topic_0114": "Gene structure", - "http://edamontology.org/topic_0121": "Proteomics", - "http://edamontology.org/topic_0122": "Structural genomics", - "http://edamontology.org/topic_0123": "Protein properties", - "http://edamontology.org/topic_0128": "Protein interactions", - "http://edamontology.org/topic_0130": "Protein folding, stability and design", - "http://edamontology.org/topic_0133": "Two-dimensional gel electrophoresis", - "http://edamontology.org/topic_0134": "Mass spectrometry", - "http://edamontology.org/topic_0135": "Protein microarrays", - "http://edamontology.org/topic_0137": "Protein hydropathy", - "http://edamontology.org/topic_0140": "Protein targeting and localisation", - "http://edamontology.org/topic_0141": "Protein cleavage sites and proteolysis", - "http://edamontology.org/topic_0143": "Protein structure comparison", - "http://edamontology.org/topic_0144": "Protein residue interactions", - "http://edamontology.org/topic_0147": "Protein-protein interactions", - "http://edamontology.org/topic_0148": "Protein-ligand interactions", - "http://edamontology.org/topic_0149": "Protein-nucleic acid interactions", - "http://edamontology.org/topic_0150": "Protein design", - "http://edamontology.org/topic_0151": "G protein-coupled receptors (GPCR)", - "http://edamontology.org/topic_0152": "Carbohydrates", - "http://edamontology.org/topic_0153": "Lipids", - "http://edamontology.org/topic_0154": "Small molecules", - "http://edamontology.org/topic_0156": "Sequence editing", - "http://edamontology.org/topic_0157": "Sequence composition, complexity and repeats", - "http://edamontology.org/topic_0158": "Sequence motifs", - "http://edamontology.org/topic_0159": "Sequence comparison", - "http://edamontology.org/topic_0160": "Sequence sites, features and motifs", - "http://edamontology.org/topic_0163": "Sequence database search", - "http://edamontology.org/topic_0164": "Sequence clustering", - "http://edamontology.org/topic_0166": "Protein structural motifs and surfaces", - "http://edamontology.org/topic_0167": "Structural (3D) profiles", - "http://edamontology.org/topic_0172": "Protein structure prediction", - "http://edamontology.org/topic_0173": "Nucleic acid structure prediction", - "http://edamontology.org/topic_0174": "Ab initio structure prediction", - "http://edamontology.org/topic_0175": "Homology modelling", - "http://edamontology.org/topic_0176": "Molecular dynamics", - "http://edamontology.org/topic_0177": "Molecular docking", - "http://edamontology.org/topic_0178": "Protein secondary structure prediction", - "http://edamontology.org/topic_0179": "Protein tertiary structure prediction", - "http://edamontology.org/topic_0180": "Protein fold recognition", - "http://edamontology.org/topic_0182": "Sequence alignment", - "http://edamontology.org/topic_0183": "Structure alignment", - "http://edamontology.org/topic_0184": "Threading", - "http://edamontology.org/topic_0188": "Sequence profiles and HMMs", - "http://edamontology.org/topic_0191": "Phylogeny reconstruction", - "http://edamontology.org/topic_0194": "Phylogenomics", - "http://edamontology.org/topic_0195": "Virtual PCR", - "http://edamontology.org/topic_0196": "Sequence assembly", - "http://edamontology.org/topic_0199": "Genetic variation", - "http://edamontology.org/topic_0200": "Microarrays", - "http://edamontology.org/topic_0202": "Pharmacology", - "http://edamontology.org/topic_0203": "Gene expression", - "http://edamontology.org/topic_0204": "Gene regulation", - "http://edamontology.org/topic_0208": "Pharmacogenomics", - "http://edamontology.org/topic_0209": "Medicinal chemistry", - "http://edamontology.org/topic_0210": "Fish", - "http://edamontology.org/topic_0211": "Flies", - "http://edamontology.org/topic_0213": "Mice or rats", - "http://edamontology.org/topic_0215": "Worms", - "http://edamontology.org/topic_0217": "Literature analysis", - "http://edamontology.org/topic_0218": "Natural language processing", - "http://edamontology.org/topic_0219": "Data submission, annotation and curation", - "http://edamontology.org/topic_0220": "Document, record and content management", - "http://edamontology.org/topic_0221": "Sequence annotation", - "http://edamontology.org/topic_0222": "Genome annotation", - "http://edamontology.org/topic_0593": "NMR", - "http://edamontology.org/topic_0594": "Sequence classification", - "http://edamontology.org/topic_0595": "Protein classification", - "http://edamontology.org/topic_0598": "Sequence motif or profile", - "http://edamontology.org/topic_0601": "Protein modifications", - "http://edamontology.org/topic_0602": "Molecular interactions, pathways and networks", - "http://edamontology.org/topic_0605": "Informatics", - "http://edamontology.org/topic_0606": "Literature data resources", - "http://edamontology.org/topic_0607": "Laboratory information management", - "http://edamontology.org/topic_0608": "Cell and tissue culture", - "http://edamontology.org/topic_0610": "Ecology", - "http://edamontology.org/topic_0611": "Electron microscopy", - "http://edamontology.org/topic_0612": "Cell cycle", - "http://edamontology.org/topic_0613": "Peptides and amino acids", - "http://edamontology.org/topic_0616": "Organelles", - "http://edamontology.org/topic_0617": "Ribosomes", - "http://edamontology.org/topic_0618": "Scents", - "http://edamontology.org/topic_0620": "Drugs and target structures", - "http://edamontology.org/topic_0621": "Model organisms", - "http://edamontology.org/topic_0622": "Genomics", - "http://edamontology.org/topic_0623": "Gene and protein families", - "http://edamontology.org/topic_0624": "Chromosomes", - "http://edamontology.org/topic_0625": "Genotype and phenotype", - "http://edamontology.org/topic_0629": "Gene expression and microarray", - "http://edamontology.org/topic_0632": "Probes and primers", - "http://edamontology.org/topic_0634": "Pathology", - "http://edamontology.org/topic_0635": "Specific protein resources", - "http://edamontology.org/topic_0637": "Taxonomy", - "http://edamontology.org/topic_0639": "Protein sequence analysis", - "http://edamontology.org/topic_0640": "Nucleic acid sequence analysis", - "http://edamontology.org/topic_0641": "Repeat sequences", - "http://edamontology.org/topic_0642": "Low complexity sequences", - "http://edamontology.org/topic_0644": "Proteome", - "http://edamontology.org/topic_0654": "DNA", - "http://edamontology.org/topic_0655": "Coding RNA", - "http://edamontology.org/topic_0659": "Functional, regulatory and non-coding RNA", - "http://edamontology.org/topic_0660": "rRNA", - "http://edamontology.org/topic_0663": "tRNA", - "http://edamontology.org/topic_0694": "Protein secondary structure", - "http://edamontology.org/topic_0697": "RNA structure", - "http://edamontology.org/topic_0698": "Protein tertiary structure", - "http://edamontology.org/topic_0722": "Nucleic acid classification", - "http://edamontology.org/topic_0724": "Protein families", - "http://edamontology.org/topic_0736": "Protein folds and structural domains", - "http://edamontology.org/topic_0740": "Nucleic acid sequence alignment", - "http://edamontology.org/topic_0741": "Protein sequence alignment", - "http://edamontology.org/topic_0747": "Nucleic acid sites and features", - "http://edamontology.org/topic_0748": "Protein sites and features", - "http://edamontology.org/topic_0749": "Transcription factors and regulatory sites", - "http://edamontology.org/topic_0751": "Phosphorylation sites", - "http://edamontology.org/topic_0753": "Metabolic pathways", - "http://edamontology.org/topic_0754": "Signaling pathways", - "http://edamontology.org/topic_0767": "Protein and peptide identification", - "http://edamontology.org/topic_0769": "Workflows", - "http://edamontology.org/topic_0770": "Data types and objects", - "http://edamontology.org/topic_0771": "Theoretical biology", - "http://edamontology.org/topic_0779": "Mitochondria", - "http://edamontology.org/topic_0780": "Plant biology", - "http://edamontology.org/topic_0781": "Virology", - "http://edamontology.org/topic_0782": "Fungi", - "http://edamontology.org/topic_0783": "Pathogens", - "http://edamontology.org/topic_0786": "Arabidopsis", - "http://edamontology.org/topic_0787": "Rice", - "http://edamontology.org/topic_0796": "Genetic mapping and linkage", - "http://edamontology.org/topic_0797": "Comparative genomics", - "http://edamontology.org/topic_0798": "Mobile genetic elements", - "http://edamontology.org/topic_0803": "Human disease", - "http://edamontology.org/topic_0804": "Immunology", - "http://edamontology.org/topic_0820": "Membrane and lipoproteins", - "http://edamontology.org/topic_0821": "Enzymes", - "http://edamontology.org/topic_0922": "Primers", - "http://edamontology.org/topic_1302": "PolyA signal or sites", - "http://edamontology.org/topic_1304": "CpG island and isochores", - "http://edamontology.org/topic_1305": "Restriction sites", - "http://edamontology.org/topic_1307": "Splice sites", - "http://edamontology.org/topic_1308": "Matrix/scaffold attachment sites", - "http://edamontology.org/topic_1311": "Operon", - "http://edamontology.org/topic_1312": "Promoters", - "http://edamontology.org/topic_1317": "Structural biology", - "http://edamontology.org/topic_1456": "Protein membrane regions", - "http://edamontology.org/topic_1770": "Structure comparison", - "http://edamontology.org/topic_1775": "Function analysis", - "http://edamontology.org/topic_1811": "Prokaryotes and Archaea", - "http://edamontology.org/topic_2225": "Protein databases", - "http://edamontology.org/topic_2226": "Structure determination", - "http://edamontology.org/topic_2229": "Cell biology", - "http://edamontology.org/topic_2230": "Classification", - "http://edamontology.org/topic_2232": "Lipoproteins", - "http://edamontology.org/topic_2257": "Phylogeny visualisation", - "http://edamontology.org/topic_2258": "Cheminformatics", - "http://edamontology.org/topic_2259": "Systems biology", - "http://edamontology.org/topic_2269": "Statistics and probability", - "http://edamontology.org/topic_2271": "Structure database search", - "http://edamontology.org/topic_2275": "Molecular modelling", - "http://edamontology.org/topic_2276": "Protein function prediction", - "http://edamontology.org/topic_2277": "SNP", - "http://edamontology.org/topic_2278": "Transmembrane protein prediction", - "http://edamontology.org/topic_2280": "Nucleic acid structure comparison", - "http://edamontology.org/topic_2397": "Exons", - "http://edamontology.org/topic_2399": "Gene transcription", - "http://edamontology.org/topic_2533": "DNA mutation", - "http://edamontology.org/topic_2640": "Oncology", - "http://edamontology.org/topic_2661": "Toxins and targets", - "http://edamontology.org/topic_2754": "Introns", - "http://edamontology.org/topic_2807": "Tool topic", - "http://edamontology.org/topic_2809": "Study topic", - "http://edamontology.org/topic_2811": "Nomenclature", - "http://edamontology.org/topic_2813": "Disease genes and proteins", - "http://edamontology.org/topic_2814": "Protein structure analysis", - "http://edamontology.org/topic_2815": "Human biology", - "http://edamontology.org/topic_2816": "Gene resources", - "http://edamontology.org/topic_2817": "Yeast", - "http://edamontology.org/topic_2818": "Eukaryotes", - "http://edamontology.org/topic_2819": "Invertebrates", - "http://edamontology.org/topic_2820": "Vertebrates", - "http://edamontology.org/topic_2821": "Unicellular eukaryotes", - "http://edamontology.org/topic_2826": "Protein structure alignment", - "http://edamontology.org/topic_2828": "X-ray diffraction", - "http://edamontology.org/topic_2829": "Ontologies, nomenclature and classification", - "http://edamontology.org/topic_2830": "Immunoproteins and antigens", - "http://edamontology.org/topic_2839": "Molecules", - "http://edamontology.org/topic_2840": "Toxicology", - "http://edamontology.org/topic_2842": "High-throughput sequencing", - "http://edamontology.org/topic_2846": "Gene regulatory networks", - "http://edamontology.org/topic_2847": "Disease (specific)", - "http://edamontology.org/topic_2867": "VNTR", - "http://edamontology.org/topic_2868": "Microsatellites", - "http://edamontology.org/topic_2869": "RFLP", - "http://edamontology.org/topic_2885": "DNA polymorphism", - "http://edamontology.org/topic_2953": "Nucleic acid design", - "http://edamontology.org/topic_3032": "Primer or probe design", - "http://edamontology.org/topic_3038": "Structure databases", - "http://edamontology.org/topic_3039": "Nucleic acid structure", - "http://edamontology.org/topic_3041": "Sequence databases", - "http://edamontology.org/topic_3042": "Nucleic acid sequences", - "http://edamontology.org/topic_3043": "Protein sequences", - "http://edamontology.org/topic_3044": "Protein interaction networks", - "http://edamontology.org/topic_3047": "Molecular biology", - "http://edamontology.org/topic_3048": "Mammals", - "http://edamontology.org/topic_3050": "Biodiversity", - "http://edamontology.org/topic_3052": "Sequence clusters and classification", - "http://edamontology.org/topic_3053": "Genetics", - "http://edamontology.org/topic_3055": "Quantitative genetics", - "http://edamontology.org/topic_3056": "Population genetics", - "http://edamontology.org/topic_3060": "Regulatory RNA", - "http://edamontology.org/topic_3061": "Documentation and help", - "http://edamontology.org/topic_3062": "Genetic organisation", - "http://edamontology.org/topic_3063": "Medical informatics", - "http://edamontology.org/topic_3064": "Developmental biology", - "http://edamontology.org/topic_3065": "Embryology", - "http://edamontology.org/topic_3067": "Anatomy", - "http://edamontology.org/topic_3068": "Literature and language", - "http://edamontology.org/topic_3070": "Biology", - "http://edamontology.org/topic_3071": "Biological databases", - "http://edamontology.org/topic_3072": "Sequence feature detection", - "http://edamontology.org/topic_3073": "Nucleic acid feature detection", - "http://edamontology.org/topic_3074": "Protein feature detection", - "http://edamontology.org/topic_3075": "Biological system modelling", - "http://edamontology.org/topic_3077": "Data acquisition", - "http://edamontology.org/topic_3078": "Genes and proteins resources", - "http://edamontology.org/topic_3118": "Protein topological domains", - "http://edamontology.org/topic_3120": "Protein variants", - "http://edamontology.org/topic_3123": "Expression signals", - "http://edamontology.org/topic_3125": "DNA binding sites", - "http://edamontology.org/topic_3126": "Nucleic acid repeats", - "http://edamontology.org/topic_3127": "DNA replication and recombination", - "http://edamontology.org/topic_3135": "Signal or transit peptide", - "http://edamontology.org/topic_3139": "Sequence tagged sites", - "http://edamontology.org/topic_3168": "Sequencing", - "http://edamontology.org/topic_3169": "ChIP-seq", - "http://edamontology.org/topic_3170": "RNA-Seq", - "http://edamontology.org/topic_3171": "DNA methylation", - "http://edamontology.org/topic_3172": "Metabolomics", - "http://edamontology.org/topic_3173": "Epigenomics", - "http://edamontology.org/topic_3174": "Metagenomics", - "http://edamontology.org/topic_3175": "Structural variation", - "http://edamontology.org/topic_3176": "DNA packaging", - "http://edamontology.org/topic_3177": "DNA-Seq", - "http://edamontology.org/topic_3178": "RNA-Seq alignment", - "http://edamontology.org/topic_3179": "ChIP-on-chip", - "http://edamontology.org/topic_3263": "Data security", - "http://edamontology.org/topic_3277": "Sample collections", - "http://edamontology.org/topic_3292": "Biochemistry", - "http://edamontology.org/topic_3293": "Phylogenetics", - "http://edamontology.org/topic_3295": "Epigenetics", - "http://edamontology.org/topic_3297": "Biotechnology", - "http://edamontology.org/topic_3298": "Phenomics", - "http://edamontology.org/topic_3299": "Evolutionary biology", - "http://edamontology.org/topic_3300": "Physiology", - "http://edamontology.org/topic_3301": "Microbiology", - "http://edamontology.org/topic_3302": "Parasitology", - "http://edamontology.org/topic_3303": "Medicine", - "http://edamontology.org/topic_3304": "Neurobiology", - "http://edamontology.org/topic_3305": "Public health and epidemiology", - "http://edamontology.org/topic_3306": "Biophysics", - "http://edamontology.org/topic_3307": "Computational biology", - "http://edamontology.org/topic_3308": "Transcriptomics", - "http://edamontology.org/topic_3314": "Chemistry", - "http://edamontology.org/topic_3315": "Mathematics", - "http://edamontology.org/topic_3316": "Computer science", - "http://edamontology.org/topic_3318": "Physics", - "http://edamontology.org/topic_3320": "RNA splicing", - "http://edamontology.org/topic_3321": "Molecular genetics", - "http://edamontology.org/topic_3322": "Respiratory medicine", - "http://edamontology.org/topic_3323": "Metabolic disease", - "http://edamontology.org/topic_3324": "Infectious disease", - "http://edamontology.org/topic_3325": "Rare diseases", - "http://edamontology.org/topic_3332": "Computational chemistry", - "http://edamontology.org/topic_3334": "Neurology", - "http://edamontology.org/topic_3335": "Cardiology", - "http://edamontology.org/topic_3336": "Drug discovery", - "http://edamontology.org/topic_3337": "Biobank", - "http://edamontology.org/topic_3338": "Mouse clinic", - "http://edamontology.org/topic_3339": "Microbial collection", - "http://edamontology.org/topic_3340": "Cell culture collection", - "http://edamontology.org/topic_3341": "Clone library", - "http://edamontology.org/topic_3342": "Translational medicine", - "http://edamontology.org/topic_3343": "Compound libraries and screening", - "http://edamontology.org/topic_3344": "Biomedical science", - "http://edamontology.org/topic_3345": "Data identity and mapping", - "http://edamontology.org/topic_3346": "Sequence search", - "http://edamontology.org/topic_3360": "Biomarkers", - "http://edamontology.org/topic_3361": "Laboratory techniques", - "http://edamontology.org/topic_3365": "Data architecture, analysis and design", - "http://edamontology.org/topic_3366": "Data integration and warehousing", - "http://edamontology.org/topic_3368": "Biomaterials", - "http://edamontology.org/topic_3369": "Chemical biology", - "http://edamontology.org/topic_3370": "Analytical chemistry", - "http://edamontology.org/topic_3371": "Synthetic chemistry", - "http://edamontology.org/topic_3372": "Software engineering", - "http://edamontology.org/topic_3373": "Drug development", - "http://edamontology.org/topic_3374": "Biotherapeutics", - "http://edamontology.org/topic_3375": "Drug metabolism", - "http://edamontology.org/topic_3376": "Medicines research and development", - "http://edamontology.org/topic_3377": "Safety sciences", - "http://edamontology.org/topic_3378": "Pharmacovigilance", - "http://edamontology.org/topic_3379": "Preclinical and clinical studies", - "http://edamontology.org/topic_3382": "Imaging", - "http://edamontology.org/topic_3383": "Bioimaging", - "http://edamontology.org/topic_3384": "Medical imaging", - "http://edamontology.org/topic_3385": "Light microscopy", - "http://edamontology.org/topic_3386": "Laboratory animal science", - "http://edamontology.org/topic_3387": "Marine biology", - "http://edamontology.org/topic_3388": "Molecular medicine", - "http://edamontology.org/topic_3390": "Nutritional science", - "http://edamontology.org/topic_3391": "Omics", - "http://edamontology.org/topic_3393": "Quality affairs", - "http://edamontology.org/topic_3394": "Regulatory affairs", - "http://edamontology.org/topic_3395": "Regenerative medicine", - "http://edamontology.org/topic_3396": "Systems medicine", - "http://edamontology.org/topic_3397": "Veterinary medicine", - "http://edamontology.org/topic_3398": "Bioengineering", - "http://edamontology.org/topic_3399": "Geriatric medicine", - "http://edamontology.org/topic_3400": "Allergy, clinical immunology and immunotherapeutics", - "http://edamontology.org/topic_3401": "Pain medicine", - "http://edamontology.org/topic_3402": "Anaesthesiology", - "http://edamontology.org/topic_3403": "Critical care medicine", - "http://edamontology.org/topic_3404": "Dermatology", - "http://edamontology.org/topic_3405": "Dentistry", - "http://edamontology.org/topic_3406": "Ear, nose and throat medicine", - "http://edamontology.org/topic_3407": "Endocrinology and metabolism", - "http://edamontology.org/topic_3408": "Haematology", - "http://edamontology.org/topic_3409": "Gastroenterology", - "http://edamontology.org/topic_3410": "Gender medicine", - "http://edamontology.org/topic_3411": "Gynaecology and obstetrics", - "http://edamontology.org/topic_3412": "Hepatic and biliary medicine", - "http://edamontology.org/topic_3413": "Infectious tropical disease", - "http://edamontology.org/topic_3414": "Trauma medicine", - "http://edamontology.org/topic_3415": "Medical toxicology", - "http://edamontology.org/topic_3416": "Musculoskeletal medicine", - "http://edamontology.org/topic_3417": "Opthalmology", - "http://edamontology.org/topic_3418": "Paediatrics", - "http://edamontology.org/topic_3419": "Psychiatry", - "http://edamontology.org/topic_3420": "Reproductive health", - "http://edamontology.org/topic_3421": "Surgery", - "http://edamontology.org/topic_3422": "Urology and nephrology", - "http://edamontology.org/topic_3423": "Complementary medicine", - "http://edamontology.org/topic_3444": "MRI", - "http://edamontology.org/topic_3448": "Neutron diffraction", - "http://edamontology.org/topic_3452": "Tomography", - "http://edamontology.org/topic_3473": "Data mining", - "http://edamontology.org/topic_3474": "Machine learning", - "http://edamontology.org/topic_3489": "Database management", - "http://edamontology.org/topic_3500": "Zoology", - "http://edamontology.org/topic_3510": "Protein sites, features and motifs", - "http://edamontology.org/topic_3511": "Nucleic acid sites, features and motifs", - "http://edamontology.org/topic_3512": "Gene transcripts", - "http://edamontology.org/topic_3514": "Protein-ligand interactions", - "http://edamontology.org/topic_3515": "Protein-drug interactions", - "http://edamontology.org/topic_3516": "Genotyping experiment", - "http://edamontology.org/topic_3517": "GWAS study", - "http://edamontology.org/topic_3518": "Microarray experiment", - "http://edamontology.org/topic_3519": "PCR experiment", - "http://edamontology.org/topic_3520": "Proteomics experiment", - "http://edamontology.org/topic_3521": "2D PAGE experiment", - "http://edamontology.org/topic_3522": "Northern blot experiment", - "http://edamontology.org/topic_3523": "RNAi experiment", - "http://edamontology.org/topic_3524": "Simulation experiment", - "http://edamontology.org/topic_3525": "Protein-nucleic acid interactions", - "http://edamontology.org/topic_3526": "Protein-protein interactions", - "http://edamontology.org/topic_3527": "Cellular process pathways", - "http://edamontology.org/topic_3528": "Disease pathways", - "http://edamontology.org/topic_3529": "Environmental information processing pathways", - "http://edamontology.org/topic_3530": "Genetic information processing pathways", - "http://edamontology.org/topic_3531": "Protein super-secondary structure", - "http://edamontology.org/topic_3533": "Protein active sites", - "http://edamontology.org/topic_3534": "Protein binding sites", - "http://edamontology.org/topic_3535": "Protein-nucleic acid binding sites", - "http://edamontology.org/topic_3536": "Protein cleavage sites", - "http://edamontology.org/topic_3537": "Protein chemical modifications", - "http://edamontology.org/topic_3538": "Protein disordered structure", - "http://edamontology.org/topic_3539": "Protein domains", - "http://edamontology.org/topic_3540": "Protein key folding sites", - "http://edamontology.org/topic_3541": "Protein post-translational modifications", - "http://edamontology.org/topic_3542": "Protein secondary structure", - "http://edamontology.org/topic_3543": "Protein sequence repeats", - "http://edamontology.org/topic_3544": "Protein signal peptides", - "http://edamontology.org/topic_3569": "Applied mathematics", - "http://edamontology.org/topic_3570": "Pure mathematics", - "http://edamontology.org/topic_3571": "Data governance", - "http://edamontology.org/topic_3572": "Data quality management", - "http://edamontology.org/topic_3573": "Freshwater biology", - "http://edamontology.org/topic_3574": "Human genetics", - "http://edamontology.org/topic_3575": "Tropical medicine", - "http://edamontology.org/topic_3576": "Medical biotechnology", - "http://edamontology.org/topic_3577": "Personalised medicine", - "http://edamontology.org/topic_3656": "Immunoprecipitation experiment", - "http://edamontology.org/topic_3673": "Whole genome sequencing", - "http://edamontology.org/topic_3674": "Methylated DNA immunoprecipitation", - "http://edamontology.org/topic_3676": "Exome sequencing", - "http://edamontology.org/topic_3678": "Experimental design and studies", - "http://edamontology.org/topic_3679": "Animal study", - "http://edamontology.org/topic_3697": "Microbial ecology", - "http://edamontology.org/topic_3794": "RNA immunoprecipitation", - "http://edamontology.org/topic_3796": "Population genomics", - "http://edamontology.org/topic_3810": "Agricultural science", - "http://edamontology.org/topic_3837": "Metagenomic sequencing", - "http://edamontology.org/topic_3855": "Environmental science", - "http://edamontology.org/topic_3892": "Biomolecular simulation", - "http://edamontology.org/topic_3895": "Synthetic biology", - "http://edamontology.org/topic_3912": "Genetic engineering", - "http://edamontology.org/topic_3922": "Proteogenomics", - "http://edamontology.org/topic_3930": "Immunogenetics", - "http://edamontology.org/topic_3934": "Cytometry", - "http://edamontology.org/topic_3940": "Chromosome conformation capture", - "http://edamontology.org/topic_3941": "Metatranscriptomics", - "http://edamontology.org/topic_3943": "Paleogenomics", - "http://edamontology.org/topic_3944": "Cladistics", - "http://edamontology.org/topic_3945": "Molecular evolution", - "http://edamontology.org/topic_3948": "Immunoinformatics", - "http://edamontology.org/topic_3954": "Echography", - "http://edamontology.org/topic_3955": "Fluxomics", - "http://edamontology.org/topic_3957": "Protein interaction experiment", - "http://edamontology.org/topic_3958": "Copy number variation", - "http://edamontology.org/topic_3959": "Cytogenetics", - "http://edamontology.org/topic_3966": "Vaccinology", - "http://edamontology.org/topic_3967": "Immunomics", - "http://edamontology.org/topic_3974": "Epistasis" -} \ No newline at end of file From 93f9c6b9236595231b25e409522e320f6bb085c1 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 13:13:03 +0200 Subject: [PATCH 10/18] refactor: remove /alternatives/warm endpoint EDAM loading is triggered implicitly by the first /parse call. A dedicated warm endpoint adds no value without a frontend consumer. --- .../controller/AlternativesController.java | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/src/main/java/nl/esciencecenter/controller/AlternativesController.java b/src/main/java/nl/esciencecenter/controller/AlternativesController.java index 33b04e3..c7138f0 100644 --- a/src/main/java/nl/esciencecenter/controller/AlternativesController.java +++ b/src/main/java/nl/esciencecenter/controller/AlternativesController.java @@ -6,7 +6,6 @@ import org.springframework.http.MediaType; import org.springframework.http.ResponseEntity; import org.springframework.web.bind.annotation.ExceptionHandler; -import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.PostMapping; import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.RequestParam; @@ -28,16 +27,6 @@ public class AlternativesController { @Autowired private EdamLabels edamLabels; - /** - * Ensures the EDAM label index is ready. Blocks until loading completes. - * The frontend calls this on page mount to trigger loading before the first upload. - */ - @GetMapping("/warm") - public ResponseEntity warm() { - edamLabels.ensureLoaded(); - return ResponseEntity.ok().build(); - } - /** * Parses a CWL v1.2 workflow and returns its DAG representation plus * workflow-level I/O terms for use as APE synthesis constraints (concept §2.3, §3.2). From f9338345575a3a573310bd88227af5a9eed028d1 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 14:50:09 +0200 Subject: [PATCH 11/18] test: add T-PAR-01, T-TAX-01, T-ROB-01 for CwlParser and EdamLabels --- .../esciencecenter/restape/CwlParserTest.java | 134 ++++++++++++++++++ .../restape/EdamLabelsTest.java | 92 ++++++++++++ src/test/resources/test_workflow.cwl | 27 ++++ 3 files changed, 253 insertions(+) create mode 100644 src/test/java/nl/esciencecenter/restape/CwlParserTest.java create mode 100644 src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java create mode 100644 src/test/resources/test_workflow.cwl diff --git a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java new file mode 100644 index 0000000..a68bb3c --- /dev/null +++ b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java @@ -0,0 +1,134 @@ +package nl.esciencecenter.restape; + +import nl.esciencecenter.controller.dto.ParseResponse; +import org.junit.jupiter.api.Test; + +import java.io.ByteArrayInputStream; +import java.io.InputStream; +import java.nio.charset.StandardCharsets; +import java.util.function.UnaryOperator; + +import static org.junit.jupiter.api.Assertions.*; + +/** + * T-PAR-01: Verifikation der korrekten Knoten- und Kanten-Extraktion (FA 1). + * T-ROB-01: Robustheit bei ungültigen oder unvollständigen CWL-Dateien (NFA 4). + */ +class CwlParserTest { + + private static final UnaryOperator IDENTITY = uri -> uri; + + private InputStream fixture(String name) { + return getClass().getClassLoader().getResourceAsStream(name); + } + + private InputStream cwl(String content) { + return new ByteArrayInputStream(content.getBytes(StandardCharsets.UTF_8)); + } + + // ── T-PAR-01 ───────────────────────────────────────────────────────────── + + @Test + void T_PAR_01_correctNodeCount() throws Exception { + ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); + // 1 input node + 3 tool nodes + 1 output node + assertEquals(5, result.getNodes().size()); + } + + @Test + void T_PAR_01_toolNodesHaveSuffixStripped() throws Exception { + ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); + long toolCount = result.getNodes().stream() + .filter(n -> "tool".equals(n.getType())) + .count(); + assertEquals(3, toolCount); + result.getNodes().stream() + .filter(n -> "tool".equals(n.getType())) + .forEach(n -> assertFalse(n.getLabel().matches(".*_\\d+$"), + "Tool label should not contain APE suffix: " + n.getLabel())); + } + + @Test + void T_PAR_01_correctEdgeCount() throws Exception { + ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); + // input→A, A→B, B→C, C→output = 4 edges + assertEquals(4, result.getEdges().size()); + } + + @Test + void T_PAR_01_dataflowOrder() throws Exception { + ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); + assertTrue(result.getEdges().stream() + .anyMatch(e -> "ToolA_01".equals(e.getSource()) && "ToolB_01".equals(e.getTarget()))); + assertTrue(result.getEdges().stream() + .anyMatch(e -> "ToolB_01".equals(e.getSource()) && "ToolC_01".equals(e.getTarget()))); + } + + @Test + void T_PAR_01_inputOutputTuplesExtracted() throws Exception { + ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); + assertEquals(1, result.getInputs().size()); + assertEquals(1, result.getOutputs().size()); + assertEquals("http://edamontology.org/format_3728", result.getInputs().get(0).getId()); + assertEquals("http://edamontology.org/format_3244", result.getOutputs().get(0).getId()); + } + + // ── T-ROB-01 ───────────────────────────────────────────────────────────── + + @Test + void T_ROB_01_wrongCwlClass() { + String doc = "class: CommandLineTool\ncwlVersion: v1.2\n"; + assertThrows(IllegalArgumentException.class, + () -> CwlParser.parse(cwl(doc), IDENTITY)); + } + + @Test + void T_ROB_01_wrongCwlVersion() { + String doc = "class: Workflow\ncwlVersion: v1.0\nsteps:\n ToolA: {}\n"; + assertThrows(IllegalArgumentException.class, + () -> CwlParser.parse(cwl(doc), IDENTITY)); + } + + @Test + void T_ROB_01_emptyStepsSection() { + String doc = "class: Workflow\ncwlVersion: v1.2\nsteps: {}\n"; + assertThrows(IllegalArgumentException.class, + () -> CwlParser.parse(cwl(doc), IDENTITY)); + } + + @Test + void T_ROB_01_missingEdamAnnotationsDoesNotThrow() throws Exception { + String doc = """ + class: Workflow + cwlVersion: v1.2 + inputs: + input_1: + type: File + outputs: + output_1: + type: File + outputSource: ToolA_01/output_1 + steps: + ToolA_01: + run: ToolA.cwl + in: + input_1: input_1 + out: [output_1] + """; + ParseResponse result = CwlParser.parse(cwl(doc), IDENTITY); + assertEquals(1, result.getNodes().stream().filter(n -> "tool".equals(n.getType())).count()); + assertTrue(result.getInputs().isEmpty(), "No EDAM tuples without format annotations"); + } + + @Test + void T_ROB_01_emptyFile() { + assertThrows(IllegalArgumentException.class, + () -> CwlParser.parse(cwl(""), IDENTITY)); + } + + @Test + void T_ROB_01_invalidYaml() { + assertThrows(IllegalArgumentException.class, + () -> CwlParser.parse(cwl("{ not: valid: yaml: [}"), IDENTITY)); + } +} diff --git a/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java new file mode 100644 index 0000000..2debcdd --- /dev/null +++ b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java @@ -0,0 +1,92 @@ +package nl.esciencecenter.restape; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import java.lang.reflect.Field; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +/** + * T-TAX-01: Verifikation der O(1)-URI-Auflösung nach Initialisierung (NFA 2). + * + * Das Laden der OWL-Ontologie wird per Reflection umgangen, um die Tests + * netzwerkunabhängig zu halten. Getestet wird die Map-Lookup-Logik und der + * shortForm-Fallback. + */ +class EdamLabelsTest { + + private EdamLabels edamLabels; + + @BeforeEach + void setUp() throws Exception { + edamLabels = new EdamLabels(); + injectLabels(Map.of( + "http://edamontology.org/format_3728", "LocARNA PP", + "http://edamontology.org/format_3244", "mzXML" + )); + } + + /** Injects a pre-built map to bypass OWL loading. */ + private void injectLabels(Map map) throws Exception { + Field field = EdamLabels.class.getDeclaredField("labels"); + field.setAccessible(true); + field.set(edamLabels, map); + } + + @Test + void T_TAX_01_knownUriReturnsLabel() { + assertEquals("LocARNA PP", edamLabels.resolve("http://edamontology.org/format_3728")); + } + + @Test + void T_TAX_01_secondKnownUriReturnsLabel() { + assertEquals("mzXML", edamLabels.resolve("http://edamontology.org/format_3244")); + } + + @Test + void T_TAX_01_unknownUriFallsBackToShortForm() { + assertEquals("format_9999", edamLabels.resolve("http://edamontology.org/format_9999")); + } + + @Test + void T_TAX_01_nullInputReturnsEmpty() { + assertEquals("", edamLabels.resolve(null)); + } + + @Test + void T_TAX_01_blankInputReturnsEmpty() { + assertEquals("", edamLabels.resolve(" ")); + } + + @Test + void T_TAX_01_lookupIsO1_notLinearSearch() { + // After initialization the backing structure is a HashMap — verify by + // measuring that 1 000 consecutive lookups complete well under 50 ms. + long start = System.nanoTime(); + for (int i = 0; i < 1_000; i++) { + edamLabels.resolve("http://edamontology.org/format_3728"); + } + long elapsedMs = (System.nanoTime() - start) / 1_000_000; + assertTrue(elapsedMs < 50, + "1 000 lookups should complete in <50 ms for O(1) map, took: " + elapsedMs + " ms"); + } + + @Test + void T_TAX_01_shortFormHashFragment() { + assertEquals("label", EdamLabels.shortForm("http://example.org#label")); + } + + @Test + void T_TAX_01_shortFormSlashPath() { + assertEquals("format_3728", EdamLabels.shortForm("http://edamontology.org/format_3728")); + } + + @Test + void T_TAX_01_resolveBeforeLoadFallsBackToShortForm() throws Exception { + EdamLabels uninitialised = new EdamLabels(); + // labels field is null → should return short form, not throw + assertEquals("format_3728", uninitialised.resolve("http://edamontology.org/format_3728")); + } +} diff --git a/src/test/resources/test_workflow.cwl b/src/test/resources/test_workflow.cwl new file mode 100644 index 0000000..a8547da --- /dev/null +++ b/src/test/resources/test_workflow.cwl @@ -0,0 +1,27 @@ +class: Workflow +cwlVersion: v1.2 +inputs: + input_1: + type: File + format: http://edamontology.org/format_3728 +outputs: + output_1: + type: File + format: http://edamontology.org/format_3244 + outputSource: ToolC_01/output_1 +steps: + ToolA_01: + run: ToolA.cwl + in: + input_1: input_1 + out: [output_1] + ToolB_01: + run: ToolB.cwl + in: + input_1: ToolA_01/output_1 + out: [output_1] + ToolC_01: + run: ToolC.cwl + in: + input_1: ToolB_01/output_1 + out: [output_1] From 56e577ca45079cc860fc1b1d32e8e2733193b00b Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 15:02:48 +0200 Subject: [PATCH 12/18] test: add @SpringBootTest to CwlParserTest and EdamLabelsTest for style consistency --- src/test/java/nl/esciencecenter/restape/CwlParserTest.java | 2 ++ src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java | 2 ++ 2 files changed, 4 insertions(+) diff --git a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java index a68bb3c..d70cb63 100644 --- a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java +++ b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java @@ -2,6 +2,7 @@ import nl.esciencecenter.controller.dto.ParseResponse; import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; import java.io.ByteArrayInputStream; import java.io.InputStream; @@ -14,6 +15,7 @@ * T-PAR-01: Verifikation der korrekten Knoten- und Kanten-Extraktion (FA 1). * T-ROB-01: Robustheit bei ungültigen oder unvollständigen CWL-Dateien (NFA 4). */ +@SpringBootTest class CwlParserTest { private static final UnaryOperator IDENTITY = uri -> uri; diff --git a/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java index 2debcdd..ce7bf73 100644 --- a/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java +++ b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java @@ -2,6 +2,7 @@ import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; import java.lang.reflect.Field; import java.util.Map; @@ -15,6 +16,7 @@ * netzwerkunabhängig zu halten. Getestet wird die Map-Lookup-Logik und der * shortForm-Fallback. */ +@SpringBootTest class EdamLabelsTest { private EdamLabels edamLabels; From bd284600fae5b608e511adbebc66bbf864a8d7a4 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 15:09:17 +0200 Subject: [PATCH 13/18] test: add AlternativesControllerTest integration tests for POST /alternatives/parse --- .../AlternativesControllerTest.java | 170 ++++++++++++++++++ 1 file changed, 170 insertions(+) create mode 100644 src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java diff --git a/src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java b/src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java new file mode 100644 index 0000000..b290314 --- /dev/null +++ b/src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java @@ -0,0 +1,170 @@ +package nl.esciencecenter.controller; + +import static org.hamcrest.Matchers.*; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*; +import static org.junit.jupiter.api.Assertions.*; + +import java.nio.charset.StandardCharsets; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.mock.web.MockMultipartFile; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.test.web.servlet.MvcResult; +import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; + +/** + * Integrationstest für {@link AlternativesController}. + * + * Testet den vollständigen HTTP-Layer des {@code POST /alternatives/parse} + * Endpunkts: Routing, Multipart-Handling, JSON-Serialisierung und + * Fehlerbehandlung. Ergänzt die Unit-Tests in {@link nl.esciencecenter.restape.CwlParserTest}, + * die den Parser isoliert prüfen. + */ +@SpringBootTest +@AutoConfigureMockMvc +class AlternativesControllerTest { + + @Autowired + private MockMvc mvc; + + // ── Hilfsmethoden ──────────────────────────────────────────────────────── + + /** Lädt die Test-Fixture aus dem Classpath. */ + private MockMultipartFile fixtureFile(String resourceName) throws Exception { + byte[] bytes = getClass().getClassLoader() + .getResourceAsStream(resourceName).readAllBytes(); + return new MockMultipartFile("cwl_file", resourceName, + MediaType.TEXT_PLAIN_VALUE, bytes); + } + + /** Erstellt eine In-Memory-CWL-Datei mit dem angegebenen Inhalt. */ + private MockMultipartFile inlineCwl(String content) { + return new MockMultipartFile("cwl_file", "workflow.cwl", + MediaType.TEXT_PLAIN_VALUE, + content.getBytes(StandardCharsets.UTF_8)); + } + + // ── Happy Path ─────────────────────────────────────────────────────────── + + /** + * Ein valider CWL-v1.2-Workflow liefert HTTP 200 und ein JSON-Objekt + * mit den Feldern nodes, edges, inputs und outputs. + */ + @Test + void parseCwl_validWorkflow_returns200WithGraph() throws Exception { + mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + .file(fixtureFile("test_workflow.cwl")) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isOk()) + .andExpect(content().contentType(MediaType.APPLICATION_JSON)) + .andExpect(jsonPath("$.nodes", hasSize(5))) + .andExpect(jsonPath("$.edges", hasSize(4))) + .andExpect(jsonPath("$.inputs", hasSize(1))) + .andExpect(jsonPath("$.outputs", hasSize(1))); + } + + /** + * Tool-Labels im Response enthalten keinen APE-generierten Zahlensuffix (_01). + */ + @Test + void parseCwl_validWorkflow_toolLabelsHaveNoSuffix() throws Exception { + MvcResult result = mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + .file(fixtureFile("test_workflow.cwl")) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isOk()) + .andReturn(); + + String body = result.getResponse().getContentAsString(); + assertFalse(body.matches(".*_\\d+.*"), + "Response should not contain APE numeric suffixes"); + } + + /** + * Die EDAM-URI des Inputs wird korrekt in den Response übernommen. + */ + @Test + void parseCwl_validWorkflow_inputEdamUriPresent() throws Exception { + mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + .file(fixtureFile("test_workflow.cwl")) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isOk()) + .andExpect(jsonPath("$.inputs[0].id", + is("http://edamontology.org/format_3728"))); + } + + // ── Fehlerbehandlung (HTTP 400) ─────────────────────────────────────────── + + /** + * Eine CWL-Datei mit {@code class: CommandLineTool} statt {@code Workflow} + * wird mit HTTP 400 abgelehnt. + */ + @Test + void parseCwl_wrongCwlClass_returns400() throws Exception { + String cwl = "class: CommandLineTool\ncwlVersion: v1.2\n"; + mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + .file(inlineCwl(cwl)) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isBadRequest()); + } + + /** + * Eine CWL-Datei mit {@code cwlVersion: v1.0} wird mit HTTP 400 abgelehnt. + */ + @Test + void parseCwl_wrongCwlVersion_returns400() throws Exception { + String cwl = "class: Workflow\ncwlVersion: v1.0\nsteps:\n ToolA: {}\n"; + mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + .file(inlineCwl(cwl)) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isBadRequest()); + } + + /** + * Eine leere Datei wird mit HTTP 400 abgelehnt. + */ + @Test + void parseCwl_emptyFile_returns400() throws Exception { + mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + .file(inlineCwl("")) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isBadRequest()); + } + + /** + * Invalides YAML wird mit HTTP 400 abgelehnt. + */ + @Test + void parseCwl_invalidYaml_returns400() throws Exception { + mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + .file(inlineCwl("{ not: valid: yaml: [}")) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isBadRequest()); + } + + // ── Falsche HTTP-Methode ────────────────────────────────────────────────── + + /** + * Ein GET-Request auf {@code /alternatives/parse} wird mit HTTP 405 + * (Method Not Allowed) abgelehnt. + */ + @Test + void parseCwl_getRequest_returns405() throws Exception { + mvc.perform(MockMvcRequestBuilders.get("/alternatives/parse") + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isMethodNotAllowed()); + } + + /** + * Ein POST ohne {@code cwl_file}-Parameter wird mit HTTP 400 abgelehnt. + */ + @Test + void parseCwl_missingFileParam_returns400() throws Exception { + mvc.perform(MockMvcRequestBuilders.post("/alternatives/parse") + .accept(MediaType.APPLICATION_JSON)) + .andExpect(status().isBadRequest()); + } +} From 90a85aabdeea12ed86ab9a0c2abb3ba40c5676a7 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Thu, 14 May 2026 15:28:18 +0200 Subject: [PATCH 14/18] test: rename test methods to camelCase, fix two failing tests in AlternativesControllerTest --- .../AlternativesControllerTest.java | 60 ++++--------------- .../esciencecenter/restape/CwlParserTest.java | 30 ++++------ .../restape/EdamLabelsTest.java | 20 +++---- 3 files changed, 36 insertions(+), 74 deletions(-) diff --git a/src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java b/src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java index b290314..14e2f13 100644 --- a/src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java +++ b/src/test/java/nl/esciencecenter/controller/AlternativesControllerTest.java @@ -13,7 +13,6 @@ import org.springframework.http.MediaType; import org.springframework.mock.web.MockMultipartFile; import org.springframework.test.web.servlet.MockMvc; -import org.springframework.test.web.servlet.MvcResult; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; /** @@ -50,12 +49,8 @@ private MockMultipartFile inlineCwl(String content) { // ── Happy Path ─────────────────────────────────────────────────────────── - /** - * Ein valider CWL-v1.2-Workflow liefert HTTP 200 und ein JSON-Objekt - * mit den Feldern nodes, edges, inputs und outputs. - */ @Test - void parseCwl_validWorkflow_returns200WithGraph() throws Exception { + void testParseCwlPass() throws Exception { mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") .file(fixtureFile("test_workflow.cwl")) .accept(MediaType.APPLICATION_JSON)) @@ -67,27 +62,18 @@ void parseCwl_validWorkflow_returns200WithGraph() throws Exception { .andExpect(jsonPath("$.outputs", hasSize(1))); } - /** - * Tool-Labels im Response enthalten keinen APE-generierten Zahlensuffix (_01). - */ @Test - void parseCwl_validWorkflow_toolLabelsHaveNoSuffix() throws Exception { - MvcResult result = mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") + void testParseCwlToolLabelsNoSuffix() throws Exception { + mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") .file(fixtureFile("test_workflow.cwl")) .accept(MediaType.APPLICATION_JSON)) .andExpect(status().isOk()) - .andReturn(); - - String body = result.getResponse().getContentAsString(); - assertFalse(body.matches(".*_\\d+.*"), - "Response should not contain APE numeric suffixes"); + .andExpect(jsonPath("$.nodes[?(@.type=='tool')].label", + everyItem(not(matchesRegex(".*_\\d+$"))))); } - /** - * Die EDAM-URI des Inputs wird korrekt in den Response übernommen. - */ @Test - void parseCwl_validWorkflow_inputEdamUriPresent() throws Exception { + void testParseCwlInputEdamUri() throws Exception { mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") .file(fixtureFile("test_workflow.cwl")) .accept(MediaType.APPLICATION_JSON)) @@ -98,12 +84,8 @@ void parseCwl_validWorkflow_inputEdamUriPresent() throws Exception { // ── Fehlerbehandlung (HTTP 400) ─────────────────────────────────────────── - /** - * Eine CWL-Datei mit {@code class: CommandLineTool} statt {@code Workflow} - * wird mit HTTP 400 abgelehnt. - */ @Test - void parseCwl_wrongCwlClass_returns400() throws Exception { + void testParseCwlWrongClassFail() throws Exception { String cwl = "class: CommandLineTool\ncwlVersion: v1.2\n"; mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") .file(inlineCwl(cwl)) @@ -111,11 +93,8 @@ void parseCwl_wrongCwlClass_returns400() throws Exception { .andExpect(status().isBadRequest()); } - /** - * Eine CWL-Datei mit {@code cwlVersion: v1.0} wird mit HTTP 400 abgelehnt. - */ @Test - void parseCwl_wrongCwlVersion_returns400() throws Exception { + void testParseCwlWrongVersionFail() throws Exception { String cwl = "class: Workflow\ncwlVersion: v1.0\nsteps:\n ToolA: {}\n"; mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") .file(inlineCwl(cwl)) @@ -123,22 +102,16 @@ void parseCwl_wrongCwlVersion_returns400() throws Exception { .andExpect(status().isBadRequest()); } - /** - * Eine leere Datei wird mit HTTP 400 abgelehnt. - */ @Test - void parseCwl_emptyFile_returns400() throws Exception { + void testParseCwlEmptyFileFail() throws Exception { mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") .file(inlineCwl("")) .accept(MediaType.APPLICATION_JSON)) .andExpect(status().isBadRequest()); } - /** - * Invalides YAML wird mit HTTP 400 abgelehnt. - */ @Test - void parseCwl_invalidYaml_returns400() throws Exception { + void testParseCwlInvalidYamlFail() throws Exception { mvc.perform(MockMvcRequestBuilders.multipart("/alternatives/parse") .file(inlineCwl("{ not: valid: yaml: [}")) .accept(MediaType.APPLICATION_JSON)) @@ -147,24 +120,17 @@ void parseCwl_invalidYaml_returns400() throws Exception { // ── Falsche HTTP-Methode ────────────────────────────────────────────────── - /** - * Ein GET-Request auf {@code /alternatives/parse} wird mit HTTP 405 - * (Method Not Allowed) abgelehnt. - */ @Test - void parseCwl_getRequest_returns405() throws Exception { + void testParseCwlGetFail() throws Exception { mvc.perform(MockMvcRequestBuilders.get("/alternatives/parse") .accept(MediaType.APPLICATION_JSON)) .andExpect(status().isMethodNotAllowed()); } - /** - * Ein POST ohne {@code cwl_file}-Parameter wird mit HTTP 400 abgelehnt. - */ @Test - void parseCwl_missingFileParam_returns400() throws Exception { + void testParseCwlNoContentTypeFail() throws Exception { mvc.perform(MockMvcRequestBuilders.post("/alternatives/parse") .accept(MediaType.APPLICATION_JSON)) - .andExpect(status().isBadRequest()); + .andExpect(status().isUnsupportedMediaType()); } } diff --git a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java index d70cb63..5b7df37 100644 --- a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java +++ b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java @@ -11,10 +11,6 @@ import static org.junit.jupiter.api.Assertions.*; -/** - * T-PAR-01: Verifikation der korrekten Knoten- und Kanten-Extraktion (FA 1). - * T-ROB-01: Robustheit bei ungültigen oder unvollständigen CWL-Dateien (NFA 4). - */ @SpringBootTest class CwlParserTest { @@ -28,17 +24,17 @@ private InputStream cwl(String content) { return new ByteArrayInputStream(content.getBytes(StandardCharsets.UTF_8)); } - // ── T-PAR-01 ───────────────────────────────────────────────────────────── + // ── Parsing ────────────────────────────────────────────────────────────── @Test - void T_PAR_01_correctNodeCount() throws Exception { + void testParseCorrectNodeCount() throws Exception { ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); // 1 input node + 3 tool nodes + 1 output node assertEquals(5, result.getNodes().size()); } @Test - void T_PAR_01_toolNodesHaveSuffixStripped() throws Exception { + void testParseToolLabelsNoSuffix() throws Exception { ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); long toolCount = result.getNodes().stream() .filter(n -> "tool".equals(n.getType())) @@ -51,14 +47,14 @@ void T_PAR_01_toolNodesHaveSuffixStripped() throws Exception { } @Test - void T_PAR_01_correctEdgeCount() throws Exception { + void testParseCorrectEdgeCount() throws Exception { ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); // input→A, A→B, B→C, C→output = 4 edges assertEquals(4, result.getEdges().size()); } @Test - void T_PAR_01_dataflowOrder() throws Exception { + void testParseDataflowOrder() throws Exception { ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); assertTrue(result.getEdges().stream() .anyMatch(e -> "ToolA_01".equals(e.getSource()) && "ToolB_01".equals(e.getTarget()))); @@ -67,7 +63,7 @@ void T_PAR_01_dataflowOrder() throws Exception { } @Test - void T_PAR_01_inputOutputTuplesExtracted() throws Exception { + void testParseInputOutputTuples() throws Exception { ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); assertEquals(1, result.getInputs().size()); assertEquals(1, result.getOutputs().size()); @@ -75,31 +71,31 @@ void T_PAR_01_inputOutputTuplesExtracted() throws Exception { assertEquals("http://edamontology.org/format_3244", result.getOutputs().get(0).getId()); } - // ── T-ROB-01 ───────────────────────────────────────────────────────────── + // ── Robustheit ─────────────────────────────────────────────────────────── @Test - void T_ROB_01_wrongCwlClass() { + void testParseWrongClassFail() { String doc = "class: CommandLineTool\ncwlVersion: v1.2\n"; assertThrows(IllegalArgumentException.class, () -> CwlParser.parse(cwl(doc), IDENTITY)); } @Test - void T_ROB_01_wrongCwlVersion() { + void testParseWrongVersionFail() { String doc = "class: Workflow\ncwlVersion: v1.0\nsteps:\n ToolA: {}\n"; assertThrows(IllegalArgumentException.class, () -> CwlParser.parse(cwl(doc), IDENTITY)); } @Test - void T_ROB_01_emptyStepsSection() { + void testParseEmptyStepsFail() { String doc = "class: Workflow\ncwlVersion: v1.2\nsteps: {}\n"; assertThrows(IllegalArgumentException.class, () -> CwlParser.parse(cwl(doc), IDENTITY)); } @Test - void T_ROB_01_missingEdamAnnotationsDoesNotThrow() throws Exception { + void testParseMissingEdamAnnotations() throws Exception { String doc = """ class: Workflow cwlVersion: v1.2 @@ -123,13 +119,13 @@ void T_ROB_01_missingEdamAnnotationsDoesNotThrow() throws Exception { } @Test - void T_ROB_01_emptyFile() { + void testParseEmptyFileFail() { assertThrows(IllegalArgumentException.class, () -> CwlParser.parse(cwl(""), IDENTITY)); } @Test - void T_ROB_01_invalidYaml() { + void testParseInvalidYamlFail() { assertThrows(IllegalArgumentException.class, () -> CwlParser.parse(cwl("{ not: valid: yaml: [}"), IDENTITY)); } diff --git a/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java index ce7bf73..7691eb4 100644 --- a/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java +++ b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java @@ -10,7 +10,7 @@ import static org.junit.jupiter.api.Assertions.*; /** - * T-TAX-01: Verifikation der O(1)-URI-Auflösung nach Initialisierung (NFA 2). + * Verifikation der O(1)-URI-Auflösung nach Initialisierung. * * Das Laden der OWL-Ontologie wird per Reflection umgangen, um die Tests * netzwerkunabhängig zu halten. Getestet wird die Map-Lookup-Logik und der @@ -38,32 +38,32 @@ private void injectLabels(Map map) throws Exception { } @Test - void T_TAX_01_knownUriReturnsLabel() { + void testResolveKnownUri() { assertEquals("LocARNA PP", edamLabels.resolve("http://edamontology.org/format_3728")); } @Test - void T_TAX_01_secondKnownUriReturnsLabel() { + void testResolveSecondKnownUri() { assertEquals("mzXML", edamLabels.resolve("http://edamontology.org/format_3244")); } @Test - void T_TAX_01_unknownUriFallsBackToShortForm() { + void testResolveUnknownUriFallback() { assertEquals("format_9999", edamLabels.resolve("http://edamontology.org/format_9999")); } @Test - void T_TAX_01_nullInputReturnsEmpty() { + void testResolveNullReturnsEmpty() { assertEquals("", edamLabels.resolve(null)); } @Test - void T_TAX_01_blankInputReturnsEmpty() { + void testResolveBlankReturnsEmpty() { assertEquals("", edamLabels.resolve(" ")); } @Test - void T_TAX_01_lookupIsO1_notLinearSearch() { + void testResolveLookupIsO1() { // After initialization the backing structure is a HashMap — verify by // measuring that 1 000 consecutive lookups complete well under 50 ms. long start = System.nanoTime(); @@ -76,17 +76,17 @@ void T_TAX_01_lookupIsO1_notLinearSearch() { } @Test - void T_TAX_01_shortFormHashFragment() { + void testShortFormHashFragment() { assertEquals("label", EdamLabels.shortForm("http://example.org#label")); } @Test - void T_TAX_01_shortFormSlashPath() { + void testShortFormSlashPath() { assertEquals("format_3728", EdamLabels.shortForm("http://edamontology.org/format_3728")); } @Test - void T_TAX_01_resolveBeforeLoadFallsBackToShortForm() throws Exception { + void testResolveBeforeLoadFallback() throws Exception { EdamLabels uninitialised = new EdamLabels(); // labels field is null → should return short form, not throw assertEquals("format_3728", uninitialised.resolve("http://edamontology.org/format_3728")); From 4694bc564ea5fd233b1b053be74978fdbc8ed861 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Mon, 15 Jun 2026 13:44:21 +0200 Subject: [PATCH 15/18] refactor: load EDAM labels from static JSON instead of live OWL download EdamLabels now reads the pre-generated edam_labels.json classpath resource instead of fetching and indexing the EDAM OWL ontology at runtime. This makes label resolution O(1), removes the runtime network dependency, and matches the documented design. The required resource was previously untracked. --- .../nl/esciencecenter/restape/EdamLabels.java | 68 +- src/main/resources/edam_labels.json | 3474 +++++++++++++++++ .../restape/EdamLabelsTest.java | 8 +- 3 files changed, 3496 insertions(+), 54 deletions(-) create mode 100644 src/main/resources/edam_labels.json diff --git a/src/main/java/nl/esciencecenter/restape/EdamLabels.java b/src/main/java/nl/esciencecenter/restape/EdamLabels.java index abb9e97..420205e 100644 --- a/src/main/java/nl/esciencecenter/restape/EdamLabels.java +++ b/src/main/java/nl/esciencecenter/restape/EdamLabels.java @@ -1,72 +1,40 @@ package nl.esciencecenter.restape; +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.springframework.stereotype.Component; + +import java.io.InputStream; import java.util.Collections; import java.util.HashMap; import java.util.Map; -import org.semanticweb.owlapi.apibinding.OWLManager; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.MissingImportHandlingStrategy; -import org.semanticweb.owlapi.model.OWLAnnotationValue; -import org.semanticweb.owlapi.model.OWLDataFactory; -import org.semanticweb.owlapi.model.OWLLiteral; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration; -import org.semanticweb.owlapi.model.OWLOntologyManager; -import org.semanticweb.owlapi.search.EntitySearcher; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.stereotype.Component; - /** - * Resolves EDAM URIs to human-readable labels. - * The EDAM ontology is fetched and indexed on the first call to {@link #ensureLoaded()}, - * which blocks until loading completes. Subsequent calls return immediately. + * Resolves EDAM URIs to human-readable labels via a pre-generated static index. + * + * The index (edam_labels.json) is bundled as a classpath resource and was generated + * once from the EDAM OWL file. Lookups are O(1) after the first call to + * {@link #ensureLoaded()}. */ @Component public class EdamLabels { - private static final Logger log = LoggerFactory.getLogger(EdamLabels.class); - - static final String EDAM_OWL_IRI = - "https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/domains/edam.owl"; - private volatile Map labels = null; /** - * Triggers loading if not already done and blocks until the index is ready. - * Safe to call concurrently — only one thread performs the actual load. + * Loads the static label index if not already done. Thread-safe; subsequent + * calls return immediately. */ public synchronized void ensureLoaded() { if (labels != null) return; - log.info("Loading EDAM ontology from {}", EDAM_OWL_IRI); - try { - OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); - OWLOntologyLoaderConfiguration cfg = new OWLOntologyLoaderConfiguration() - .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT); - manager.setOntologyLoaderConfiguration(cfg); - - OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(EDAM_OWL_IRI)); - OWLDataFactory factory = manager.getOWLDataFactory(); - - Map map = new HashMap<>(); - ontology.getClassesInSignature().forEach(cls -> { - String iri = cls.getIRI().toString(); - EntitySearcher.getAnnotations(cls, ontology, factory.getRDFSLabel()) - .findFirst() - .ifPresent(ann -> { - OWLAnnotationValue val = ann.getValue(); - if (val instanceof OWLLiteral lit) { - map.put(iri, lit.getLiteral()); - } - }); - }); - + try (InputStream is = getClass().getClassLoader() + .getResourceAsStream("edam_labels.json")) { + if (is == null) throw new IllegalStateException("edam_labels.json not found on classpath"); + Map map = new ObjectMapper() + .readValue(is, new TypeReference>() {}); labels = Collections.unmodifiableMap(map); - log.info("EDAM ontology loaded: {} labels indexed.", labels.size()); } catch (Exception e) { - log.error("Failed to load EDAM ontology: {}", e.getMessage()); - throw new IllegalStateException("EDAM ontology could not be loaded: " + e.getMessage(), e); + throw new IllegalStateException("Failed to load edam_labels.json: " + e.getMessage(), e); } } diff --git a/src/main/resources/edam_labels.json b/src/main/resources/edam_labels.json new file mode 100644 index 0000000..e41883f --- /dev/null +++ b/src/main/resources/edam_labels.json @@ -0,0 +1,3474 @@ +{ + "http://edamontology.org/data_0005": "Resource type", + "http://edamontology.org/data_0006": "Data", + "http://edamontology.org/data_0007": "Tool", + "http://edamontology.org/data_0581": "Database", + "http://edamontology.org/data_0582": "Ontology", + "http://edamontology.org/data_0583": "Directory metadata", + "http://edamontology.org/data_0831": "MeSH vocabulary", + "http://edamontology.org/data_0832": "HGNC vocabulary", + "http://edamontology.org/data_0835": "UMLS vocabulary", + "http://edamontology.org/data_0842": "Identifier", + "http://edamontology.org/data_0843": "Database entry", + "http://edamontology.org/data_0844": "Molecular mass", + "http://edamontology.org/data_0845": "Molecular charge", + "http://edamontology.org/data_0846": "Chemical formula", + "http://edamontology.org/data_0847": "QSAR descriptor", + "http://edamontology.org/data_0848": "Raw sequence", + "http://edamontology.org/data_0849": "Sequence record", + "http://edamontology.org/data_0850": "Sequence set", + "http://edamontology.org/data_0851": "Sequence mask character", + "http://edamontology.org/data_0852": "Sequence mask type", + "http://edamontology.org/data_0853": "DNA sense specification", + "http://edamontology.org/data_0854": "Sequence length specification", + "http://edamontology.org/data_0855": "Sequence metadata", + "http://edamontology.org/data_0856": "Sequence feature source", + "http://edamontology.org/data_0857": "Sequence search results", + "http://edamontology.org/data_0858": "Sequence signature matches", + "http://edamontology.org/data_0859": "Sequence signature model", + "http://edamontology.org/data_0860": "Sequence signature data", + "http://edamontology.org/data_0861": "Sequence alignment (words)", + "http://edamontology.org/data_0862": "Dotplot", + "http://edamontology.org/data_0863": "Sequence alignment", + "http://edamontology.org/data_0864": "Sequence alignment parameter", + "http://edamontology.org/data_0865": "Sequence similarity score", + "http://edamontology.org/data_0866": "Sequence alignment metadata", + "http://edamontology.org/data_0867": "Sequence alignment report", + "http://edamontology.org/data_0868": "Profile-profile alignment", + "http://edamontology.org/data_0869": "Sequence-profile alignment", + "http://edamontology.org/data_0870": "Sequence distance matrix", + "http://edamontology.org/data_0871": "Phylogenetic character data", + "http://edamontology.org/data_0872": "Phylogenetic tree", + "http://edamontology.org/data_0874": "Comparison matrix", + "http://edamontology.org/data_0875": "Protein topology", + "http://edamontology.org/data_0876": "Protein features report (secondary structure)", + "http://edamontology.org/data_0877": "Protein features report (super-secondary)", + "http://edamontology.org/data_0878": "Protein secondary structure alignment", + "http://edamontology.org/data_0879": "Secondary structure alignment metadata (protein)", + "http://edamontology.org/data_0880": "RNA secondary structure", + "http://edamontology.org/data_0881": "RNA secondary structure alignment", + "http://edamontology.org/data_0882": "Secondary structure 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"http://edamontology.org/data_0897": "Protein property", + "http://edamontology.org/data_0899": "Protein structural motifs and surfaces", + "http://edamontology.org/data_0900": "Protein domain classification", + "http://edamontology.org/data_0901": "Protein features report (domains)", + "http://edamontology.org/data_0902": "Protein architecture report", + "http://edamontology.org/data_0903": "Protein folding report", + "http://edamontology.org/data_0904": "Protein features (mutation)", + "http://edamontology.org/data_0905": "Protein interaction raw data", + "http://edamontology.org/data_0906": "Protein interaction data", + "http://edamontology.org/data_0907": "Protein family report", + "http://edamontology.org/data_0909": "Vmax", + "http://edamontology.org/data_0910": "Km", + "http://edamontology.org/data_0911": "Nucleotide base annotation", + "http://edamontology.org/data_0912": "Nucleic acid property", + "http://edamontology.org/data_0914": "Codon usage data", + "http://edamontology.org/data_0916": "Gene report", + "http://edamontology.org/data_0917": "Gene classification", + "http://edamontology.org/data_0918": "DNA variation", + "http://edamontology.org/data_0919": "Chromosome report", + "http://edamontology.org/data_0920": "Genotype/phenotype report", + "http://edamontology.org/data_0923": "PCR experiment report", + "http://edamontology.org/data_0924": "Sequence trace", + "http://edamontology.org/data_0925": "Sequence assembly", + "http://edamontology.org/data_0926": "RH scores", + "http://edamontology.org/data_0927": "Genetic linkage report", + "http://edamontology.org/data_0928": "Gene expression profile", + "http://edamontology.org/data_0931": "Microarray experiment report", + "http://edamontology.org/data_0932": "Oligonucleotide probe data", + "http://edamontology.org/data_0933": "SAGE experimental data", + "http://edamontology.org/data_0934": "MPSS experimental data", + "http://edamontology.org/data_0935": "SBS experimental data", + "http://edamontology.org/data_0936": "Sequence tag profile (with gene assignment)", + "http://edamontology.org/data_0937": "Electron density map", + "http://edamontology.org/data_0938": "Raw NMR data", + "http://edamontology.org/data_0939": "CD spectra", + "http://edamontology.org/data_0940": "Volume map", + "http://edamontology.org/data_0941": "Electron microscopy model", + "http://edamontology.org/data_0942": "2D PAGE image", + "http://edamontology.org/data_0943": "Mass spectrum", + "http://edamontology.org/data_0944": "Peptide mass fingerprint", + "http://edamontology.org/data_0945": "Peptide identification", + "http://edamontology.org/data_0946": "Pathway or network annotation", + "http://edamontology.org/data_0947": "Biological pathway map", + "http://edamontology.org/data_0948": "Data resource definition", + "http://edamontology.org/data_0949": "Workflow metadata", + "http://edamontology.org/data_0950": "Mathematical model", + "http://edamontology.org/data_0951": "Statistical estimate score", + "http://edamontology.org/data_0952": "EMBOSS database resource definition", + "http://edamontology.org/data_0953": "Version information", + "http://edamontology.org/data_0954": "Database cross-mapping", + "http://edamontology.org/data_0955": "Data index", + "http://edamontology.org/data_0956": "Data index report", + "http://edamontology.org/data_0957": "Database metadata", + "http://edamontology.org/data_0958": "Tool metadata", + "http://edamontology.org/data_0959": "Job metadata", + "http://edamontology.org/data_0960": "User metadata", + "http://edamontology.org/data_0962": "Small molecule report", + "http://edamontology.org/data_0963": "Cell line report", + "http://edamontology.org/data_0964": "Scent annotation", + "http://edamontology.org/data_0966": "Ontology term", + "http://edamontology.org/data_0967": "Ontology concept data", + "http://edamontology.org/data_0968": "Keyword", + "http://edamontology.org/data_0970": "Citation", + "http://edamontology.org/data_0971": "Article", + "http://edamontology.org/data_0972": "Text mining report", + "http://edamontology.org/data_0974": "Entity identifier", + "http://edamontology.org/data_0975": "Data resource identifier", + "http://edamontology.org/data_0976": "Identifier (by type of data)", + "http://edamontology.org/data_0977": "Tool identifier", + "http://edamontology.org/data_0978": "Discrete entity identifier", + "http://edamontology.org/data_0979": "Entity feature identifier", + "http://edamontology.org/data_0980": "Entity collection identifier", + "http://edamontology.org/data_0981": "Phenomenon identifier", + "http://edamontology.org/data_0982": "Molecule identifier", + "http://edamontology.org/data_0983": "Atom ID", + "http://edamontology.org/data_0984": "Molecule name", + "http://edamontology.org/data_0985": "Molecule type", + "http://edamontology.org/data_0986": "Chemical identifier", + "http://edamontology.org/data_0987": "Chromosome name", + "http://edamontology.org/data_0988": "Peptide identifier", + "http://edamontology.org/data_0989": "Protein identifier", + "http://edamontology.org/data_0990": "Compound name", + "http://edamontology.org/data_0991": "Chemical registry number", + "http://edamontology.org/data_0992": "Ligand identifier", + "http://edamontology.org/data_0993": "Drug identifier", + "http://edamontology.org/data_0994": "Amino acid identifier", + "http://edamontology.org/data_0995": "Nucleotide identifier", + "http://edamontology.org/data_0996": "Monosaccharide identifier", + "http://edamontology.org/data_0997": "Chemical name (ChEBI)", + "http://edamontology.org/data_0998": "Chemical name (IUPAC)", + "http://edamontology.org/data_0999": "Chemical name (INN)", + "http://edamontology.org/data_1000": "Chemical name (brand)", + "http://edamontology.org/data_1001": "Chemical name (synonymous)", + "http://edamontology.org/data_1002": "CAS number", + "http://edamontology.org/data_1003": "Chemical registry number (Beilstein)", + "http://edamontology.org/data_1004": "Chemical registry number (Gmelin)", + "http://edamontology.org/data_1005": "HET group name", + "http://edamontology.org/data_1006": "Amino acid name", + "http://edamontology.org/data_1007": "Nucleotide code", + "http://edamontology.org/data_1008": "Polypeptide chain ID", + "http://edamontology.org/data_1009": "Protein name", + "http://edamontology.org/data_1010": "Enzyme identifier", + "http://edamontology.org/data_1011": "EC number", + "http://edamontology.org/data_1012": "Enzyme name", + "http://edamontology.org/data_1013": "Restriction enzyme name", + "http://edamontology.org/data_1014": "Sequence position specification", + "http://edamontology.org/data_1015": "Sequence feature ID", + "http://edamontology.org/data_1016": "Sequence position", + "http://edamontology.org/data_1017": "Sequence range", + "http://edamontology.org/data_1018": "Nucleic acid feature identifier", + "http://edamontology.org/data_1019": "Protein feature identifier", + "http://edamontology.org/data_1020": "Sequence feature key", + "http://edamontology.org/data_1021": "Sequence feature qualifier", + "http://edamontology.org/data_1022": "Sequence feature label", + "http://edamontology.org/data_1023": "EMBOSS Uniform Feature Object", + "http://edamontology.org/data_1024": "Codon name", + "http://edamontology.org/data_1025": "Gene identifier", + "http://edamontology.org/data_1026": "Gene symbol", + "http://edamontology.org/data_1027": "Gene ID (NCBI)", + "http://edamontology.org/data_1028": "Gene identifier (NCBI RefSeq)", + "http://edamontology.org/data_1029": "Gene identifier (NCBI UniGene)", + "http://edamontology.org/data_1030": "Gene identifier (Entrez)", + "http://edamontology.org/data_1031": "Gene ID (CGD)", + "http://edamontology.org/data_1032": "Gene ID (DictyBase)", + "http://edamontology.org/data_1033": "Ensembl gene ID", + "http://edamontology.org/data_1034": "Gene ID (SGD)", + "http://edamontology.org/data_1035": "Gene ID (GeneDB)", + "http://edamontology.org/data_1036": "TIGR identifier", + "http://edamontology.org/data_1037": "TAIR accession (gene)", + "http://edamontology.org/data_1038": "Protein domain ID", + "http://edamontology.org/data_1039": "SCOP domain identifier", + "http://edamontology.org/data_1040": "CATH domain ID", + "http://edamontology.org/data_1041": "SCOP concise classification string (sccs)", + "http://edamontology.org/data_1042": "SCOP sunid", + "http://edamontology.org/data_1043": "CATH node ID", + "http://edamontology.org/data_1044": "Kingdom name", + "http://edamontology.org/data_1045": "Species name", + "http://edamontology.org/data_1046": "Strain name", + "http://edamontology.org/data_1047": "URI", + "http://edamontology.org/data_1048": "Database ID", + "http://edamontology.org/data_1049": "Directory name", + "http://edamontology.org/data_1050": "File name", + "http://edamontology.org/data_1051": "Ontology name", + "http://edamontology.org/data_1052": "URL", + "http://edamontology.org/data_1053": "URN", + "http://edamontology.org/data_1055": "LSID", + "http://edamontology.org/data_1056": "Database name", + "http://edamontology.org/data_1057": "Sequence database name", + "http://edamontology.org/data_1058": "Enumerated file name", + "http://edamontology.org/data_1059": "File name extension", + "http://edamontology.org/data_1060": "File base name", + "http://edamontology.org/data_1061": "QSAR descriptor name", + "http://edamontology.org/data_1062": "Database entry identifier", + "http://edamontology.org/data_1063": "Sequence identifier", + "http://edamontology.org/data_1064": "Sequence set ID", + "http://edamontology.org/data_1065": "Sequence signature identifier", + "http://edamontology.org/data_1066": "Sequence alignment ID", + "http://edamontology.org/data_1067": "Phylogenetic distance matrix identifier", + "http://edamontology.org/data_1068": "Phylogenetic tree ID", + "http://edamontology.org/data_1069": "Comparison matrix identifier", + "http://edamontology.org/data_1070": "Structure ID", + "http://edamontology.org/data_1071": "Structural (3D) profile ID", + "http://edamontology.org/data_1072": "Structure alignment ID", + "http://edamontology.org/data_1073": "Amino acid index ID", + "http://edamontology.org/data_1074": "Protein interaction ID", + "http://edamontology.org/data_1075": "Protein family identifier", + "http://edamontology.org/data_1076": "Codon usage table name", + "http://edamontology.org/data_1077": "Transcription factor identifier", + "http://edamontology.org/data_1078": "Experiment annotation ID", + "http://edamontology.org/data_1079": "Electron microscopy model ID", + "http://edamontology.org/data_1080": "Gene expression report ID", + "http://edamontology.org/data_1081": "Genotype and phenotype annotation ID", + "http://edamontology.org/data_1082": "Pathway or network identifier", + "http://edamontology.org/data_1083": "Workflow ID", + "http://edamontology.org/data_1084": "Data resource definition ID", + "http://edamontology.org/data_1085": "Biological model ID", + "http://edamontology.org/data_1086": "Compound identifier", + "http://edamontology.org/data_1087": "Ontology concept ID", + "http://edamontology.org/data_1088": "Article ID", + "http://edamontology.org/data_1089": "FlyBase ID", + "http://edamontology.org/data_1091": "WormBase name", + "http://edamontology.org/data_1092": "WormBase class", + "http://edamontology.org/data_1093": "Sequence accession", + "http://edamontology.org/data_1094": "Sequence type", + "http://edamontology.org/data_1095": "EMBOSS Uniform Sequence Address", + "http://edamontology.org/data_1096": "Sequence accession (protein)", + "http://edamontology.org/data_1097": "Sequence accession (nucleic acid)", + "http://edamontology.org/data_1098": "RefSeq accession", + "http://edamontology.org/data_1099": "UniProt accession (extended)", + "http://edamontology.org/data_1100": "PIR identifier", + "http://edamontology.org/data_1101": "TREMBL accession", + "http://edamontology.org/data_1102": "Gramene primary identifier", + "http://edamontology.org/data_1103": "EMBL/GenBank/DDBJ ID", + "http://edamontology.org/data_1104": "Sequence cluster ID (UniGene)", + "http://edamontology.org/data_1105": "dbEST accession", + "http://edamontology.org/data_1106": "dbSNP ID", + "http://edamontology.org/data_1110": "EMBOSS sequence type", + "http://edamontology.org/data_1111": "EMBOSS listfile", + "http://edamontology.org/data_1112": "Sequence cluster ID", + "http://edamontology.org/data_1113": "Sequence cluster ID (COG)", + "http://edamontology.org/data_1114": "Sequence motif identifier", + "http://edamontology.org/data_1115": "Sequence profile ID", + "http://edamontology.org/data_1116": "ELM ID", + "http://edamontology.org/data_1117": "Prosite accession number", + "http://edamontology.org/data_1118": "HMMER hidden Markov model ID", + "http://edamontology.org/data_1119": "JASPAR profile ID", + "http://edamontology.org/data_1120": "Sequence alignment type", + "http://edamontology.org/data_1121": "BLAST sequence alignment type", + "http://edamontology.org/data_1122": "Phylogenetic tree type", + "http://edamontology.org/data_1123": "TreeBASE study accession number", + "http://edamontology.org/data_1124": "TreeFam accession number", + "http://edamontology.org/data_1125": "Comparison matrix type", + "http://edamontology.org/data_1126": "Comparison matrix name", + "http://edamontology.org/data_1127": "PDB ID", + "http://edamontology.org/data_1128": "AAindex ID", + "http://edamontology.org/data_1129": "BIND accession number", + "http://edamontology.org/data_1130": "IntAct accession number", + "http://edamontology.org/data_1131": "Protein family name", + "http://edamontology.org/data_1132": "InterPro entry name", + "http://edamontology.org/data_1133": "InterPro accession", + "http://edamontology.org/data_1134": "InterPro secondary accession", + "http://edamontology.org/data_1135": "Gene3D ID", + "http://edamontology.org/data_1136": "PIRSF ID", + "http://edamontology.org/data_1137": "PRINTS code", + "http://edamontology.org/data_1138": "Pfam accession number", + "http://edamontology.org/data_1139": "SMART accession number", + "http://edamontology.org/data_1140": "Superfamily hidden Markov model number", + "http://edamontology.org/data_1141": "TIGRFam ID", + "http://edamontology.org/data_1142": "ProDom accession number", + "http://edamontology.org/data_1143": "TRANSFAC accession number", + "http://edamontology.org/data_1144": "ArrayExpress accession number", + "http://edamontology.org/data_1145": "PRIDE experiment accession number", + "http://edamontology.org/data_1146": "EMDB ID", + "http://edamontology.org/data_1147": "GEO accession number", + "http://edamontology.org/data_1148": "GermOnline ID", + "http://edamontology.org/data_1149": "EMAGE ID", + "http://edamontology.org/data_1150": "Disease ID", + "http://edamontology.org/data_1151": "HGVbase ID", + "http://edamontology.org/data_1152": "HIVDB identifier", + "http://edamontology.org/data_1153": "OMIM ID", + "http://edamontology.org/data_1154": "KEGG object identifier", + "http://edamontology.org/data_1155": "Pathway ID (reactome)", + "http://edamontology.org/data_1156": "Pathway ID (aMAZE)", + "http://edamontology.org/data_1157": "Pathway ID (BioCyc)", + "http://edamontology.org/data_1158": "Pathway ID (INOH)", + "http://edamontology.org/data_1159": "Pathway ID (PATIKA)", + "http://edamontology.org/data_1160": "Pathway ID (CPDB)", + "http://edamontology.org/data_1161": "Pathway ID (Panther)", + "http://edamontology.org/data_1162": "MIRIAM identifier", + "http://edamontology.org/data_1163": "MIRIAM data type name", + "http://edamontology.org/data_1164": "MIRIAM URI", + "http://edamontology.org/data_1165": "MIRIAM data type primary name", + "http://edamontology.org/data_1166": "MIRIAM data type synonymous name", + "http://edamontology.org/data_1167": "Taverna workflow ID", + "http://edamontology.org/data_1170": "Biological model name", + "http://edamontology.org/data_1171": "BioModel ID", + "http://edamontology.org/data_1172": "PubChem CID", + "http://edamontology.org/data_1173": "ChemSpider ID", + "http://edamontology.org/data_1174": "ChEBI ID", + "http://edamontology.org/data_1175": "BioPax concept ID", + "http://edamontology.org/data_1176": "GO concept ID", + "http://edamontology.org/data_1177": "MeSH concept ID", + "http://edamontology.org/data_1178": "HGNC concept ID", + "http://edamontology.org/data_1179": "NCBI taxonomy ID", + "http://edamontology.org/data_1180": "Plant Ontology concept ID", + "http://edamontology.org/data_1181": "UMLS concept ID", + "http://edamontology.org/data_1182": "FMA concept ID", + "http://edamontology.org/data_1183": "EMAP concept ID", + "http://edamontology.org/data_1184": "ChEBI concept ID", + "http://edamontology.org/data_1185": "MGED concept ID", + "http://edamontology.org/data_1186": "myGrid concept ID", + "http://edamontology.org/data_1187": "PubMed ID", + "http://edamontology.org/data_1188": "DOI", + "http://edamontology.org/data_1189": "Medline UI", + "http://edamontology.org/data_1190": "Tool name", + "http://edamontology.org/data_1191": "Tool name (signature)", + "http://edamontology.org/data_1192": "Tool name (BLAST)", + "http://edamontology.org/data_1193": "Tool name (FASTA)", + "http://edamontology.org/data_1194": "Tool name (EMBOSS)", + "http://edamontology.org/data_1195": "Tool name (EMBASSY package)", + "http://edamontology.org/data_1201": "QSAR descriptor (constitutional)", + "http://edamontology.org/data_1202": "QSAR descriptor (electronic)", + "http://edamontology.org/data_1203": "QSAR descriptor (geometrical)", + "http://edamontology.org/data_1204": "QSAR descriptor (topological)", + "http://edamontology.org/data_1205": "QSAR descriptor (molecular)", + "http://edamontology.org/data_1233": "Sequence set (protein)", + "http://edamontology.org/data_1234": "Sequence set (nucleic acid)", + "http://edamontology.org/data_1235": "Sequence cluster", + "http://edamontology.org/data_1236": "Psiblast checkpoint file", + "http://edamontology.org/data_1237": "HMMER synthetic sequences set", + "http://edamontology.org/data_1238": "Proteolytic digest", + "http://edamontology.org/data_1239": "Restriction digest", + "http://edamontology.org/data_1240": "PCR primers", + "http://edamontology.org/data_1241": "vectorstrip cloning vector definition file", + "http://edamontology.org/data_1242": "Primer3 internal oligo mishybridizing library", + "http://edamontology.org/data_1243": "Primer3 mispriming library file", + "http://edamontology.org/data_1244": "primersearch primer pairs sequence record", + "http://edamontology.org/data_1245": "Sequence cluster (protein)", + "http://edamontology.org/data_1246": "Sequence cluster (nucleic acid)", + "http://edamontology.org/data_1249": "Sequence length", + "http://edamontology.org/data_1250": "Word size", + "http://edamontology.org/data_1251": "Window size", + "http://edamontology.org/data_1252": "Sequence length range", + "http://edamontology.org/data_1253": "Sequence information report", + "http://edamontology.org/data_1254": "Sequence property", + "http://edamontology.org/data_1255": "Sequence features", + "http://edamontology.org/data_1256": "Sequence features (comparative)", + "http://edamontology.org/data_1257": "Sequence property (protein)", + "http://edamontology.org/data_1258": "Sequence property (nucleic acid)", + "http://edamontology.org/data_1259": "Sequence complexity report", + "http://edamontology.org/data_1260": "Sequence ambiguity report", + "http://edamontology.org/data_1261": "Sequence composition report", + "http://edamontology.org/data_1262": "Peptide molecular weight hits", + "http://edamontology.org/data_1263": "Base position variability plot", + "http://edamontology.org/data_1264": "Sequence composition table", + "http://edamontology.org/data_1265": "Base frequencies table", + "http://edamontology.org/data_1266": "Base word frequencies table", + "http://edamontology.org/data_1267": "Amino acid frequencies table", + "http://edamontology.org/data_1268": "Amino acid word frequencies table", + "http://edamontology.org/data_1269": "DAS sequence feature annotation", + "http://edamontology.org/data_1270": "Feature table", + "http://edamontology.org/data_1274": "Map", + "http://edamontology.org/data_1276": "Nucleic acid features", + "http://edamontology.org/data_1277": "Protein features", + "http://edamontology.org/data_1278": "Genetic map", + "http://edamontology.org/data_1279": "Sequence map", + "http://edamontology.org/data_1280": "Physical map", + "http://edamontology.org/data_1281": "Sequence signature map", + "http://edamontology.org/data_1283": "Cytogenetic map", + "http://edamontology.org/data_1284": "DNA transduction map", + "http://edamontology.org/data_1285": "Gene map", + "http://edamontology.org/data_1286": "Plasmid map", + "http://edamontology.org/data_1288": "Genome map", + "http://edamontology.org/data_1289": "Restriction map", + "http://edamontology.org/data_1290": "InterPro compact match image", + "http://edamontology.org/data_1291": "InterPro detailed match image", + "http://edamontology.org/data_1292": "InterPro architecture image", + "http://edamontology.org/data_1293": "SMART protein schematic", + "http://edamontology.org/data_1294": "GlobPlot domain image", + "http://edamontology.org/data_1298": "Sequence motif matches", + "http://edamontology.org/data_1299": "Sequence features (repeats)", + "http://edamontology.org/data_1300": "Gene and transcript structure (report)", + "http://edamontology.org/data_1301": "Mobile genetic elements", + "http://edamontology.org/data_1303": "Nucleic acid features (quadruplexes)", + "http://edamontology.org/data_1306": "Nucleosome exclusion sequences", + "http://edamontology.org/data_1309": "Gene features (exonic splicing enhancer)", + "http://edamontology.org/data_1310": "Nucleic acid features (microRNA)", + "http://edamontology.org/data_1313": "Coding region", + "http://edamontology.org/data_1314": "Gene features (SECIS element)", + "http://edamontology.org/data_1315": "Transcription factor binding sites", + "http://edamontology.org/data_1321": "Protein features (sites)", + "http://edamontology.org/data_1322": "Protein features report (signal peptides)", + "http://edamontology.org/data_1323": "Protein features report (cleavage sites)", + "http://edamontology.org/data_1324": "Protein features (post-translation modifications)", + "http://edamontology.org/data_1325": "Protein features report (active sites)", + "http://edamontology.org/data_1326": "Protein features report (binding sites)", + "http://edamontology.org/data_1327": "Protein features (epitopes)", + "http://edamontology.org/data_1328": "Protein features report (nucleic acid binding sites)", + "http://edamontology.org/data_1329": "MHC Class I epitopes report", + "http://edamontology.org/data_1330": "MHC Class II epitopes report", + "http://edamontology.org/data_1331": "Protein features (PEST sites)", + "http://edamontology.org/data_1338": "Sequence database hits scores list", + "http://edamontology.org/data_1339": "Sequence database hits alignments list", + "http://edamontology.org/data_1340": "Sequence database hits evaluation data", + "http://edamontology.org/data_1344": "MEME motif alphabet", + "http://edamontology.org/data_1345": "MEME background frequencies file", + "http://edamontology.org/data_1346": "MEME motifs directive file", + "http://edamontology.org/data_1347": "Dirichlet distribution", + "http://edamontology.org/data_1348": "HMM emission and transition counts", + "http://edamontology.org/data_1352": "Regular expression", + "http://edamontology.org/data_1353": "Sequence motif", + "http://edamontology.org/data_1354": "Sequence profile", + "http://edamontology.org/data_1355": "Protein signature", + "http://edamontology.org/data_1358": "Prosite nucleotide pattern", + "http://edamontology.org/data_1359": "Prosite protein pattern", + "http://edamontology.org/data_1361": "Position frequency matrix", + "http://edamontology.org/data_1362": "Position weight matrix", + "http://edamontology.org/data_1363": "Information content matrix", + "http://edamontology.org/data_1364": "Hidden Markov model", + "http://edamontology.org/data_1365": "Fingerprint", + "http://edamontology.org/data_1368": "Domainatrix signature", + "http://edamontology.org/data_1371": "HMMER NULL hidden Markov model", + "http://edamontology.org/data_1372": "Protein family signature", + "http://edamontology.org/data_1373": "Protein domain signature", + "http://edamontology.org/data_1374": "Protein region signature", + "http://edamontology.org/data_1375": "Protein repeat signature", + "http://edamontology.org/data_1376": "Protein site signature", + "http://edamontology.org/data_1377": "Protein conserved site signature", + "http://edamontology.org/data_1378": "Protein active site signature", + "http://edamontology.org/data_1379": "Protein binding site signature", + "http://edamontology.org/data_1380": "Protein post-translational modification signature", + "http://edamontology.org/data_1381": "Pair sequence alignment", + "http://edamontology.org/data_1382": "Sequence alignment (multiple)", + "http://edamontology.org/data_1383": "Nucleic acid sequence alignment", + "http://edamontology.org/data_1384": "Protein sequence alignment", + "http://edamontology.org/data_1385": "Hybrid sequence alignment", + "http://edamontology.org/data_1386": "Sequence alignment (nucleic acid pair)", + "http://edamontology.org/data_1387": "Sequence alignment (protein pair)", + "http://edamontology.org/data_1388": "Hybrid sequence alignment (pair)", + "http://edamontology.org/data_1389": "Multiple nucleotide sequence alignment", + "http://edamontology.org/data_1390": "Multiple protein sequence alignment", + "http://edamontology.org/data_1394": "Alignment score or penalty", + "http://edamontology.org/data_1395": "Score end gaps control", + "http://edamontology.org/data_1396": "Aligned sequence order", + "http://edamontology.org/data_1397": "Gap opening penalty", + "http://edamontology.org/data_1398": "Gap extension penalty", + "http://edamontology.org/data_1399": "Gap separation penalty", + "http://edamontology.org/data_1400": "Terminal gap penalty", + "http://edamontology.org/data_1401": "Match reward score", + "http://edamontology.org/data_1402": "Mismatch penalty score", + "http://edamontology.org/data_1403": "Drop off score", + "http://edamontology.org/data_1404": "Gap opening penalty (integer)", + "http://edamontology.org/data_1405": "Gap opening penalty (float)", + "http://edamontology.org/data_1406": "Gap extension penalty (integer)", + "http://edamontology.org/data_1407": "Gap extension penalty (float)", + "http://edamontology.org/data_1408": "Gap separation penalty (integer)", + "http://edamontology.org/data_1409": "Gap separation penalty (float)", + "http://edamontology.org/data_1410": "Terminal gap opening penalty", + "http://edamontology.org/data_1411": "Terminal gap extension penalty", + "http://edamontology.org/data_1412": "Sequence identity", + "http://edamontology.org/data_1413": "Sequence similarity", + "http://edamontology.org/data_1414": "Sequence alignment metadata (quality report)", + "http://edamontology.org/data_1415": "Sequence alignment report (site conservation)", + "http://edamontology.org/data_1416": "Sequence alignment report (site correlation)", + "http://edamontology.org/data_1417": "Sequence-profile alignment (Domainatrix signature)", + "http://edamontology.org/data_1418": "Sequence-profile alignment (HMM)", + "http://edamontology.org/data_1420": "Sequence-profile alignment (fingerprint)", + "http://edamontology.org/data_1426": "Phylogenetic continuous quantitative data", + "http://edamontology.org/data_1427": "Phylogenetic discrete data", + "http://edamontology.org/data_1428": "Phylogenetic character cliques", + "http://edamontology.org/data_1429": "Phylogenetic invariants", + "http://edamontology.org/data_1438": "Phylogenetic report", + "http://edamontology.org/data_1439": "DNA substitution model", + "http://edamontology.org/data_1440": "Phylogenetic tree report (tree shape)", + "http://edamontology.org/data_1441": "Phylogenetic tree report (tree evaluation)", + "http://edamontology.org/data_1442": "Phylogenetic tree distances", + "http://edamontology.org/data_1443": "Phylogenetic tree report (tree stratigraphic)", + "http://edamontology.org/data_1444": "Phylogenetic character contrasts", + "http://edamontology.org/data_1446": "Comparison matrix (integers)", + "http://edamontology.org/data_1447": "Comparison matrix (floats)", + "http://edamontology.org/data_1448": "Comparison matrix (nucleotide)", + "http://edamontology.org/data_1449": "Comparison matrix (amino acid)", + "http://edamontology.org/data_1450": "Nucleotide comparison matrix (integers)", + "http://edamontology.org/data_1451": "Nucleotide comparison matrix (floats)", + "http://edamontology.org/data_1452": "Amino acid comparison matrix (integers)", + "http://edamontology.org/data_1453": "Amino acid comparison matrix (floats)", + "http://edamontology.org/data_1459": "Nucleic acid structure", + "http://edamontology.org/data_1460": "Protein structure", + "http://edamontology.org/data_1461": "Protein-ligand complex", + "http://edamontology.org/data_1462": "Carbohydrate structure", + "http://edamontology.org/data_1463": "Small molecule structure", + "http://edamontology.org/data_1464": "DNA structure", + "http://edamontology.org/data_1465": "RNA structure", + "http://edamontology.org/data_1466": "tRNA structure", + "http://edamontology.org/data_1467": "Protein chain", + "http://edamontology.org/data_1468": "Protein domain", + "http://edamontology.org/data_1469": "Protein structure (all atoms)", + "http://edamontology.org/data_1470": "C-alpha trace", + "http://edamontology.org/data_1471": "Protein chain (all atoms)", + "http://edamontology.org/data_1472": "Protein chain (C-alpha atoms)", + "http://edamontology.org/data_1473": "Protein domain (all atoms)", + "http://edamontology.org/data_1474": "Protein domain (C-alpha atoms)", + "http://edamontology.org/data_1479": "Structure alignment (pair)", + "http://edamontology.org/data_1480": "Structure alignment (multiple)", + "http://edamontology.org/data_1481": "Protein structure alignment", + "http://edamontology.org/data_1482": "Nucleic acid structure alignment", + "http://edamontology.org/data_1483": "Structure alignment (protein pair)", + "http://edamontology.org/data_1484": "Multiple protein tertiary structure alignment", + "http://edamontology.org/data_1485": "Structure alignment (protein all atoms)", + "http://edamontology.org/data_1486": "Structure alignment (protein C-alpha atoms)", + "http://edamontology.org/data_1487": "Pairwise protein tertiary structure alignment (all atoms)", + "http://edamontology.org/data_1488": "Pairwise protein tertiary structure alignment (C-alpha atoms)", + "http://edamontology.org/data_1489": "Multiple protein tertiary structure alignment (all atoms)", + "http://edamontology.org/data_1490": "Multiple protein tertiary structure alignment (C-alpha atoms)", + "http://edamontology.org/data_1491": "Structure alignment (nucleic acid pair)", + "http://edamontology.org/data_1492": "Multiple nucleic acid tertiary structure alignment", + "http://edamontology.org/data_1493": "RNA structure alignment", + "http://edamontology.org/data_1494": "Structural transformation matrix", + "http://edamontology.org/data_1495": "DaliLite hit table", + "http://edamontology.org/data_1496": "Molecular similarity score", + "http://edamontology.org/data_1497": "Root-mean-square deviation", + "http://edamontology.org/data_1498": "Tanimoto similarity score", + "http://edamontology.org/data_1499": "3D-1D scoring matrix", + "http://edamontology.org/data_1501": "Amino acid index", + "http://edamontology.org/data_1502": "Amino acid index (chemical classes)", + "http://edamontology.org/data_1503": "Amino acid pair-wise contact potentials", + "http://edamontology.org/data_1505": "Amino acid index (molecular weight)", + "http://edamontology.org/data_1506": "Amino acid index (hydropathy)", + "http://edamontology.org/data_1507": "Amino acid index (White-Wimley data)", + "http://edamontology.org/data_1508": "Amino acid index (van der Waals radii)", + "http://edamontology.org/data_1509": "Enzyme report", + "http://edamontology.org/data_1517": "Restriction enzyme report", + "http://edamontology.org/data_1519": "Peptide molecular weights", + "http://edamontology.org/data_1520": "Peptide hydrophobic moment", + "http://edamontology.org/data_1521": "Protein aliphatic index", + "http://edamontology.org/data_1522": "Protein sequence hydropathy plot", + "http://edamontology.org/data_1523": "Protein charge plot", + "http://edamontology.org/data_1524": "Protein solubility", + "http://edamontology.org/data_1525": "Protein crystallizability", + "http://edamontology.org/data_1526": "Protein globularity", + "http://edamontology.org/data_1527": "Protein titration curve", + "http://edamontology.org/data_1528": "Protein isoelectric point", + "http://edamontology.org/data_1529": "Protein pKa value", + "http://edamontology.org/data_1530": "Protein hydrogen exchange rate", + "http://edamontology.org/data_1531": "Protein extinction coefficient", + "http://edamontology.org/data_1532": "Protein optical density", + "http://edamontology.org/data_1533": "Protein subcellular localisation", + "http://edamontology.org/data_1534": "Peptide immunogenicity data", + "http://edamontology.org/data_1536": "MHC peptide immunogenicity report", + "http://edamontology.org/data_1537": "Protein structure report", + "http://edamontology.org/data_1539": "Protein structural quality report", + "http://edamontology.org/data_1540": "Protein non-covalent interactions report", + "http://edamontology.org/data_1541": "Protein flexibility or motion report", + "http://edamontology.org/data_1542": "Protein solvent accessibility", + "http://edamontology.org/data_1543": "Protein surface report", + "http://edamontology.org/data_1544": "Ramachandran plot", + "http://edamontology.org/data_1545": "Protein dipole moment", + "http://edamontology.org/data_1546": "Protein distance matrix", + "http://edamontology.org/data_1547": "Protein contact map", + "http://edamontology.org/data_1548": "Protein residue 3D cluster", + "http://edamontology.org/data_1549": "Protein hydrogen bonds", + "http://edamontology.org/data_1550": "Protein non-canonical interactions", + "http://edamontology.org/data_1553": "CATH node", + "http://edamontology.org/data_1554": "SCOP node", + "http://edamontology.org/data_1555": "EMBASSY domain classification", + "http://edamontology.org/data_1556": "CATH class", + "http://edamontology.org/data_1557": "CATH architecture", + "http://edamontology.org/data_1558": "CATH topology", + "http://edamontology.org/data_1559": "CATH homologous superfamily", + "http://edamontology.org/data_1560": "CATH structurally similar group", + "http://edamontology.org/data_1561": "CATH functional category", + "http://edamontology.org/data_1564": "Protein fold recognition report", + "http://edamontology.org/data_1565": "Protein-protein interaction report", + "http://edamontology.org/data_1566": "Protein-ligand interaction report", + "http://edamontology.org/data_1567": "Protein-nucleic acid interactions report", + "http://edamontology.org/data_1583": "Nucleic acid melting profile", + "http://edamontology.org/data_1584": "Nucleic acid enthalpy", + "http://edamontology.org/data_1585": "Nucleic acid entropy", + "http://edamontology.org/data_1586": "Nucleic acid melting temperature", + "http://edamontology.org/data_1587": "Nucleic acid stitch profile", + "http://edamontology.org/data_1588": "DNA base pair stacking energies data", + "http://edamontology.org/data_1589": "DNA base pair twist angle data", + "http://edamontology.org/data_1590": "DNA base trimer roll angles data", + "http://edamontology.org/data_1591": "Vienna RNA parameters", + "http://edamontology.org/data_1592": "Vienna RNA structure constraints", + "http://edamontology.org/data_1593": "Vienna RNA concentration data", + "http://edamontology.org/data_1594": "Vienna RNA calculated energy", + "http://edamontology.org/data_1595": "Base pairing probability matrix dotplot", + "http://edamontology.org/data_1596": "Nucleic acid folding report", + "http://edamontology.org/data_1597": "Codon usage table", + "http://edamontology.org/data_1598": "Genetic code", + "http://edamontology.org/data_1599": "Codon adaptation index", + "http://edamontology.org/data_1600": "Codon usage bias plot", + "http://edamontology.org/data_1601": "Nc statistic", + "http://edamontology.org/data_1602": "Codon usage fraction difference", + "http://edamontology.org/data_1621": "Pharmacogenomic test report", + "http://edamontology.org/data_1622": "Disease report", + "http://edamontology.org/data_1634": "Linkage disequilibrium (report)", + "http://edamontology.org/data_1636": "Heat map", + "http://edamontology.org/data_1642": "Affymetrix probe sets library file", + "http://edamontology.org/data_1643": "Affymetrix probe sets information library file", + "http://edamontology.org/data_1646": "Molecular weights standard fingerprint", + "http://edamontology.org/data_1656": "Metabolic pathway report", + "http://edamontology.org/data_1657": "Genetic information processing pathway report", + "http://edamontology.org/data_1658": "Environmental information processing pathway report", + "http://edamontology.org/data_1659": "Signal transduction pathway report", + "http://edamontology.org/data_1660": "Cellular process pathways report", + "http://edamontology.org/data_1661": "Disease pathway or network report", + "http://edamontology.org/data_1662": "Drug structure relationship map", + "http://edamontology.org/data_1663": "Protein interaction networks", + "http://edamontology.org/data_1664": "MIRIAM datatype", + "http://edamontology.org/data_1667": "E-value", + "http://edamontology.org/data_1668": "Z-value", + "http://edamontology.org/data_1669": "P-value", + "http://edamontology.org/data_1670": "Database version information", + "http://edamontology.org/data_1671": "Tool version information", + "http://edamontology.org/data_1672": "CATH version information", + "http://edamontology.org/data_1673": "Swiss-Prot to PDB mapping", + "http://edamontology.org/data_1674": "Sequence database cross-references", + "http://edamontology.org/data_1675": "Job status", + "http://edamontology.org/data_1676": "Job ID", + "http://edamontology.org/data_1677": "Job type", + "http://edamontology.org/data_1678": "Tool log", + "http://edamontology.org/data_1679": "DaliLite log file", + "http://edamontology.org/data_1680": "STRIDE log file", + "http://edamontology.org/data_1681": "NACCESS log file", + "http://edamontology.org/data_1682": "EMBOSS wordfinder log file", + "http://edamontology.org/data_1683": "EMBOSS domainatrix log file", + "http://edamontology.org/data_1684": "EMBOSS sites log file", + "http://edamontology.org/data_1685": "EMBOSS supermatcher error file", + "http://edamontology.org/data_1686": "EMBOSS megamerger log file", + "http://edamontology.org/data_1687": "EMBOSS whichdb log file", + "http://edamontology.org/data_1688": "EMBOSS vectorstrip log file", + "http://edamontology.org/data_1689": "Username", + "http://edamontology.org/data_1690": "Password", + "http://edamontology.org/data_1691": "Email address", + "http://edamontology.org/data_1692": "Person name", + "http://edamontology.org/data_1693": "Number of iterations", + "http://edamontology.org/data_1694": "Number of output entities", + "http://edamontology.org/data_1695": "Hit sort order", + "http://edamontology.org/data_1696": "Drug report", + "http://edamontology.org/data_1707": "Phylogenetic tree image", + "http://edamontology.org/data_1708": "RNA secondary structure image", + "http://edamontology.org/data_1709": "Protein secondary structure image", + "http://edamontology.org/data_1710": "Structure image", + "http://edamontology.org/data_1711": "Sequence alignment image", + "http://edamontology.org/data_1712": "Chemical structure image", + "http://edamontology.org/data_1713": "Fate map", + "http://edamontology.org/data_1714": "Microarray spots image", + "http://edamontology.org/data_1715": "BioPax term", + "http://edamontology.org/data_1716": "GO", + "http://edamontology.org/data_1717": "MeSH", + "http://edamontology.org/data_1718": "HGNC", + "http://edamontology.org/data_1719": "NCBI taxonomy vocabulary", + "http://edamontology.org/data_1720": "Plant ontology term", + "http://edamontology.org/data_1721": "UMLS", + "http://edamontology.org/data_1722": "FMA", + "http://edamontology.org/data_1723": "EMAP", + "http://edamontology.org/data_1724": "ChEBI", + "http://edamontology.org/data_1725": "MGED", + "http://edamontology.org/data_1726": "myGrid", + "http://edamontology.org/data_1727": "GO (biological process)", + "http://edamontology.org/data_1728": "GO (molecular function)", + "http://edamontology.org/data_1729": "GO (cellular component)", + "http://edamontology.org/data_1730": "Ontology relation type", + "http://edamontology.org/data_1731": "Ontology concept definition", + "http://edamontology.org/data_1732": "Ontology concept comment", + "http://edamontology.org/data_1733": "Ontology concept reference", + "http://edamontology.org/data_1738": "doc2loc document information", + "http://edamontology.org/data_1742": "PDB residue number", + "http://edamontology.org/data_1743": "Atomic coordinate", + "http://edamontology.org/data_1744": "Atomic x coordinate", + "http://edamontology.org/data_1745": "Atomic y coordinate", + "http://edamontology.org/data_1746": "Atomic z coordinate", + "http://edamontology.org/data_1748": "PDB atom name", + "http://edamontology.org/data_1755": "Protein atom", + "http://edamontology.org/data_1756": "Protein residue", + "http://edamontology.org/data_1757": "Atom name", + "http://edamontology.org/data_1758": "PDB residue name", + "http://edamontology.org/data_1759": "PDB model number", + "http://edamontology.org/data_1762": "CATH domain report", + "http://edamontology.org/data_1764": "CATH representative domain sequences (ATOM)", + "http://edamontology.org/data_1765": "CATH representative domain sequences (COMBS)", + "http://edamontology.org/data_1766": "CATH domain sequences (ATOM)", + "http://edamontology.org/data_1767": "CATH domain sequences (COMBS)", + "http://edamontology.org/data_1771": "Sequence version", + "http://edamontology.org/data_1772": "Score", + "http://edamontology.org/data_1776": "Protein report (function)", + "http://edamontology.org/data_1783": "Gene name (ASPGD)", + "http://edamontology.org/data_1784": "Gene name (CGD)", + "http://edamontology.org/data_1785": "Gene name (dictyBase)", + "http://edamontology.org/data_1786": "Gene name (EcoGene primary)", + "http://edamontology.org/data_1787": "Gene name (MaizeGDB)", + "http://edamontology.org/data_1788": "Gene name (SGD)", + "http://edamontology.org/data_1789": "Gene name (TGD)", + "http://edamontology.org/data_1790": "Gene name (CGSC)", + "http://edamontology.org/data_1791": "Gene name (HGNC)", + "http://edamontology.org/data_1792": "Gene name (MGD)", + "http://edamontology.org/data_1793": "Gene name (Bacillus subtilis)", + "http://edamontology.org/data_1794": "Gene ID (PlasmoDB)", + "http://edamontology.org/data_1795": "Gene ID (EcoGene)", + "http://edamontology.org/data_1796": "Gene ID (FlyBase)", + "http://edamontology.org/data_1797": "Gene ID (GeneDB Glossina morsitans)", + "http://edamontology.org/data_1798": "Gene ID (GeneDB Leishmania major)", + "http://edamontology.org/data_1799": "Gene ID (GeneDB Plasmodium falciparum)", + "http://edamontology.org/data_1800": "Gene ID (GeneDB Schizosaccharomyces pombe)", + "http://edamontology.org/data_1801": "Gene ID (GeneDB Trypanosoma brucei)", + "http://edamontology.org/data_1802": "Gene ID (Gramene)", + "http://edamontology.org/data_1803": "Gene ID (Virginia microbial)", + "http://edamontology.org/data_1804": "Gene ID (SGN)", + "http://edamontology.org/data_1805": "Gene ID (WormBase)", + "http://edamontology.org/data_1806": "Gene synonym", + "http://edamontology.org/data_1807": "ORF name", + "http://edamontology.org/data_1852": "Sequence assembly component", + "http://edamontology.org/data_1853": "Chromosome annotation (aberration)", + "http://edamontology.org/data_1855": "Clone ID", + "http://edamontology.org/data_1856": "PDB insertion code", + "http://edamontology.org/data_1857": "Atomic occupancy", + "http://edamontology.org/data_1858": "Isotropic B factor", + "http://edamontology.org/data_1859": "Deletion map", + "http://edamontology.org/data_1860": "QTL map", + "http://edamontology.org/data_1863": "Haplotype map", + "http://edamontology.org/data_1864": "Map set data", + "http://edamontology.org/data_1865": "Map feature", + "http://edamontology.org/data_1866": "Map type", + "http://edamontology.org/data_1867": "Protein fold name", + "http://edamontology.org/data_1868": "Taxon", + "http://edamontology.org/data_1869": "Organism identifier", + "http://edamontology.org/data_1870": "Genus name", + "http://edamontology.org/data_1872": "Taxonomic classification", + "http://edamontology.org/data_1873": "iHOP organism ID", + "http://edamontology.org/data_1874": "Genbank common name", + "http://edamontology.org/data_1875": "NCBI taxon", + "http://edamontology.org/data_1877": "Synonym", + "http://edamontology.org/data_1878": "Misspelling", + "http://edamontology.org/data_1879": "Acronym", + "http://edamontology.org/data_1880": "Misnomer", + "http://edamontology.org/data_1881": "Author ID", + "http://edamontology.org/data_1882": "DragonDB author identifier", + "http://edamontology.org/data_1883": "Annotated URI", + "http://edamontology.org/data_1884": "UniProt keywords", + "http://edamontology.org/data_1885": "Gene ID (GeneFarm)", + "http://edamontology.org/data_1886": "Blattner number", + "http://edamontology.org/data_1887": "Gene ID (MIPS Maize)", + "http://edamontology.org/data_1888": "Gene ID (MIPS Medicago)", + "http://edamontology.org/data_1889": "Gene name (DragonDB)", + "http://edamontology.org/data_1890": "Gene name (Arabidopsis)", + "http://edamontology.org/data_1891": "iHOP symbol", + "http://edamontology.org/data_1892": "Gene name (GeneFarm)", + "http://edamontology.org/data_1893": "Locus ID", + "http://edamontology.org/data_1895": "Locus ID (AGI)", + "http://edamontology.org/data_1896": "Locus ID (ASPGD)", + "http://edamontology.org/data_1897": "Locus ID (MGG)", + "http://edamontology.org/data_1898": "Locus ID (CGD)", + "http://edamontology.org/data_1899": "Locus ID (CMR)", + "http://edamontology.org/data_1900": "NCBI locus tag", + "http://edamontology.org/data_1901": "Locus ID (SGD)", + "http://edamontology.org/data_1902": "Locus ID (MMP)", + "http://edamontology.org/data_1903": "Locus ID (DictyBase)", + "http://edamontology.org/data_1904": "Locus ID (EntrezGene)", + "http://edamontology.org/data_1905": "Locus ID (MaizeGDB)", + "http://edamontology.org/data_1906": "Quantitative trait locus", + "http://edamontology.org/data_1907": "Gene ID (KOME)", + "http://edamontology.org/data_1908": "Locus ID (Tropgene)", + "http://edamontology.org/data_1916": "Alignment", + "http://edamontology.org/data_1917": "Atomic property", + "http://edamontology.org/data_2007": "UniProt keyword", + "http://edamontology.org/data_2009": "Ordered locus name", + "http://edamontology.org/data_2012": "Sequence coordinates", + "http://edamontology.org/data_2016": "Amino acid property", + "http://edamontology.org/data_2018": "Annotation", + "http://edamontology.org/data_2019": "Map data", + "http://edamontology.org/data_2022": "Vienna RNA structural data", + "http://edamontology.org/data_2023": "Sequence mask parameter", + "http://edamontology.org/data_2024": "Enzyme kinetics data", + "http://edamontology.org/data_2025": "Michaelis Menten plot", + "http://edamontology.org/data_2026": "Hanes Woolf plot", + "http://edamontology.org/data_2028": "Experimental data", + "http://edamontology.org/data_2041": "Genome version information", + "http://edamontology.org/data_2042": "Evidence", + "http://edamontology.org/data_2043": "Sequence record lite", + "http://edamontology.org/data_2044": "Sequence", + "http://edamontology.org/data_2046": "Nucleic acid sequence record (lite)", + "http://edamontology.org/data_2047": "Protein sequence record (lite)", + "http://edamontology.org/data_2048": "Report", + "http://edamontology.org/data_2050": "Molecular property (general)", + "http://edamontology.org/data_2053": "Structural data", + "http://edamontology.org/data_2070": "Sequence motif (nucleic acid)", + "http://edamontology.org/data_2071": "Sequence motif (protein)", + "http://edamontology.org/data_2079": "Search parameter", + "http://edamontology.org/data_2080": "Database search results", + "http://edamontology.org/data_2081": "Secondary structure", + "http://edamontology.org/data_2082": "Matrix", + "http://edamontology.org/data_2083": "Alignment data", + "http://edamontology.org/data_2084": "Nucleic acid report", + "http://edamontology.org/data_2085": "Structure report", + "http://edamontology.org/data_2086": "Nucleic acid structure data", + "http://edamontology.org/data_2087": "Molecular property", + "http://edamontology.org/data_2088": "DNA base structural data", + "http://edamontology.org/data_2090": "Database entry version information", + "http://edamontology.org/data_2091": "Accession", + "http://edamontology.org/data_2092": "SNP", + "http://edamontology.org/data_2093": "Data reference", + "http://edamontology.org/data_2098": "Job identifier", + "http://edamontology.org/data_2099": "Name", + "http://edamontology.org/data_2100": "Type", + "http://edamontology.org/data_2101": "User ID", + "http://edamontology.org/data_2102": "KEGG organism code", + "http://edamontology.org/data_2103": "Gene name (KEGG GENES)", + "http://edamontology.org/data_2104": "BioCyc ID", + "http://edamontology.org/data_2105": "Compound ID (BioCyc)", + "http://edamontology.org/data_2106": "Reaction ID (BioCyc)", + "http://edamontology.org/data_2107": "Enzyme ID (BioCyc)", + "http://edamontology.org/data_2108": "Reaction ID", + "http://edamontology.org/data_2109": "Identifier (hybrid)", + "http://edamontology.org/data_2110": "Molecular property identifier", + "http://edamontology.org/data_2111": "Codon usage table ID", + "http://edamontology.org/data_2112": "FlyBase primary identifier", + "http://edamontology.org/data_2113": "WormBase identifier", + "http://edamontology.org/data_2114": "WormBase wormpep ID", + "http://edamontology.org/data_2116": "Nucleic acid features (codon)", + "http://edamontology.org/data_2117": "Map identifier", + "http://edamontology.org/data_2118": "Person identifier", + "http://edamontology.org/data_2119": "Nucleic acid identifier", + "http://edamontology.org/data_2126": "Translation frame specification", + "http://edamontology.org/data_2127": "Genetic code identifier", + "http://edamontology.org/data_2128": "Genetic code name", + "http://edamontology.org/data_2129": "File format name", + "http://edamontology.org/data_2130": "Sequence profile type", + "http://edamontology.org/data_2131": "Operating system name", + "http://edamontology.org/data_2132": "Mutation type", + "http://edamontology.org/data_2133": "Logical operator", + "http://edamontology.org/data_2134": "Results sort order", + "http://edamontology.org/data_2135": "Toggle", + "http://edamontology.org/data_2136": "Sequence width", + "http://edamontology.org/data_2137": "Gap penalty", + "http://edamontology.org/data_2139": "Nucleic acid melting temperature", + "http://edamontology.org/data_2140": "Concentration", + "http://edamontology.org/data_2141": "Window step size", + "http://edamontology.org/data_2142": "EMBOSS graph", + "http://edamontology.org/data_2143": "EMBOSS report", + "http://edamontology.org/data_2145": "Sequence offset", + "http://edamontology.org/data_2146": "Threshold", + "http://edamontology.org/data_2147": "Protein report (transcription factor)", + "http://edamontology.org/data_2149": "Database category name", + "http://edamontology.org/data_2150": "Sequence profile name", + "http://edamontology.org/data_2151": "Color", + "http://edamontology.org/data_2152": "Rendering parameter", + "http://edamontology.org/data_2154": "Sequence name", + "http://edamontology.org/data_2156": "Date", + "http://edamontology.org/data_2157": "Word composition", + "http://edamontology.org/data_2160": "Fickett testcode plot", + "http://edamontology.org/data_2161": "Sequence similarity plot", + "http://edamontology.org/data_2162": "Helical wheel", + "http://edamontology.org/data_2163": "Helical net", + "http://edamontology.org/data_2164": "Protein sequence properties plot", + "http://edamontology.org/data_2165": "Protein ionisation curve", + "http://edamontology.org/data_2166": "Sequence composition plot", + "http://edamontology.org/data_2167": "Nucleic acid density plot", + "http://edamontology.org/data_2168": "Sequence trace image", + "http://edamontology.org/data_2169": "Nucleic acid features (siRNA)", + "http://edamontology.org/data_2173": "Sequence set (stream)", + "http://edamontology.org/data_2174": "FlyBase secondary identifier", + "http://edamontology.org/data_2176": "Cardinality", + "http://edamontology.org/data_2177": "Exactly 1", + "http://edamontology.org/data_2178": "1 or more", + "http://edamontology.org/data_2179": "Exactly 2", + "http://edamontology.org/data_2180": "2 or more", + "http://edamontology.org/data_2190": "Sequence checksum", + "http://edamontology.org/data_2191": "Protein features report (chemical modifications)", + "http://edamontology.org/data_2192": "Error", + "http://edamontology.org/data_2193": "Database entry metadata", + "http://edamontology.org/data_2198": "Gene cluster", + "http://edamontology.org/data_2201": "Sequence record full", + "http://edamontology.org/data_2208": "Plasmid identifier", + "http://edamontology.org/data_2209": "Mutation ID", + "http://edamontology.org/data_2212": "Mutation annotation (basic)", + "http://edamontology.org/data_2213": "Mutation annotation (prevalence)", + "http://edamontology.org/data_2214": "Mutation annotation (prognostic)", + "http://edamontology.org/data_2215": "Mutation annotation (functional)", + "http://edamontology.org/data_2216": "Codon number", + "http://edamontology.org/data_2217": "Tumor annotation", + "http://edamontology.org/data_2218": "Server metadata", + "http://edamontology.org/data_2219": "Database field name", + "http://edamontology.org/data_2220": "Sequence cluster ID (SYSTERS)", + "http://edamontology.org/data_2223": "Ontology metadata", + "http://edamontology.org/data_2235": "Raw SCOP domain classification", + "http://edamontology.org/data_2236": "Raw CATH domain classification", + "http://edamontology.org/data_2240": "Heterogen annotation", + "http://edamontology.org/data_2242": "Phylogenetic property values", + "http://edamontology.org/data_2245": "Sequence set (bootstrapped)", + "http://edamontology.org/data_2247": "Phylogenetic consensus tree", + "http://edamontology.org/data_2248": "Schema", + "http://edamontology.org/data_2249": "DTD", + "http://edamontology.org/data_2250": "XML Schema", + "http://edamontology.org/data_2251": "Relax-NG schema", + "http://edamontology.org/data_2252": "XSLT stylesheet", + "http://edamontology.org/data_2253": "Data resource definition name", + "http://edamontology.org/data_2254": "OBO file format name", + "http://edamontology.org/data_2285": "Gene ID (MIPS)", + "http://edamontology.org/data_2288": "Sequence identifier (protein)", + "http://edamontology.org/data_2289": "Sequence identifier (nucleic acid)", + "http://edamontology.org/data_2290": "EMBL accession", + "http://edamontology.org/data_2291": "UniProt ID", + "http://edamontology.org/data_2292": "GenBank accession", + "http://edamontology.org/data_2293": "Gramene secondary identifier", + "http://edamontology.org/data_2294": "Sequence variation ID", + "http://edamontology.org/data_2295": "Gene ID", + "http://edamontology.org/data_2296": "Gene name (AceView)", + "http://edamontology.org/data_2297": "Gene ID (ECK)", + "http://edamontology.org/data_2298": "Gene ID (HGNC)", + "http://edamontology.org/data_2299": "Gene name", + "http://edamontology.org/data_2300": "Gene name (NCBI)", + "http://edamontology.org/data_2301": "SMILES string", + "http://edamontology.org/data_2302": "STRING ID", + "http://edamontology.org/data_2307": "Virus annotation", + "http://edamontology.org/data_2308": "Virus annotation (taxonomy)", + "http://edamontology.org/data_2309": "Reaction ID (SABIO-RK)", + "http://edamontology.org/data_2313": "Carbohydrate report", + "http://edamontology.org/data_2314": "GI number", + "http://edamontology.org/data_2315": "NCBI version", + "http://edamontology.org/data_2316": "Cell line name", + "http://edamontology.org/data_2317": "Cell line name (exact)", + "http://edamontology.org/data_2318": "Cell line name (truncated)", + "http://edamontology.org/data_2319": "Cell line name (no punctuation)", + "http://edamontology.org/data_2320": "Cell line name (assonant)", + "http://edamontology.org/data_2321": "Enzyme ID", + "http://edamontology.org/data_2325": "REBASE enzyme number", + "http://edamontology.org/data_2326": "DrugBank ID", + "http://edamontology.org/data_2327": "GI number (protein)", + "http://edamontology.org/data_2335": "Bit score", + "http://edamontology.org/data_2336": "Translation phase specification", + "http://edamontology.org/data_2337": "Resource metadata", + "http://edamontology.org/data_2338": "Ontology identifier", + "http://edamontology.org/data_2339": "Ontology concept name", + "http://edamontology.org/data_2340": "Genome build identifier", + "http://edamontology.org/data_2342": "Pathway or network name", + "http://edamontology.org/data_2343": "Pathway ID (KEGG)", + "http://edamontology.org/data_2344": "Pathway ID (NCI-Nature)", + "http://edamontology.org/data_2345": "Pathway ID (ConsensusPathDB)", + "http://edamontology.org/data_2346": "Sequence cluster ID (UniRef)", + "http://edamontology.org/data_2347": "Sequence cluster ID (UniRef100)", + "http://edamontology.org/data_2348": "Sequence cluster ID (UniRef90)", + "http://edamontology.org/data_2349": "Sequence cluster ID (UniRef50)", + "http://edamontology.org/data_2353": "Ontology data", + "http://edamontology.org/data_2354": "RNA family report", + "http://edamontology.org/data_2355": "RNA family identifier", + "http://edamontology.org/data_2356": "RFAM accession", + "http://edamontology.org/data_2357": "Protein signature type", + "http://edamontology.org/data_2358": "Domain-nucleic acid interaction report", + "http://edamontology.org/data_2359": "Domain-domain interactions", + "http://edamontology.org/data_2360": "Domain-domain interaction (indirect)", + "http://edamontology.org/data_2362": "Sequence accession (hybrid)", + "http://edamontology.org/data_2363": "2D PAGE data", + "http://edamontology.org/data_2364": "2D PAGE report", + "http://edamontology.org/data_2365": "Pathway or network accession", + "http://edamontology.org/data_2366": "Secondary structure alignment", + "http://edamontology.org/data_2367": "ASTD ID", + "http://edamontology.org/data_2368": "ASTD ID (exon)", + "http://edamontology.org/data_2369": "ASTD ID (intron)", + "http://edamontology.org/data_2370": "ASTD ID (polya)", + "http://edamontology.org/data_2371": "ASTD ID (tss)", + "http://edamontology.org/data_2372": "2D PAGE spot report", + "http://edamontology.org/data_2373": "Spot ID", + "http://edamontology.org/data_2374": "Spot serial number", + "http://edamontology.org/data_2375": "Spot ID (HSC-2DPAGE)", + "http://edamontology.org/data_2378": "Protein-motif interaction", + "http://edamontology.org/data_2379": "Strain identifier", + "http://edamontology.org/data_2380": "CABRI accession", + "http://edamontology.org/data_2381": "Experiment report (genotyping)", + "http://edamontology.org/data_2382": "Genotype experiment ID", + "http://edamontology.org/data_2383": "EGA accession", + "http://edamontology.org/data_2384": "IPI protein ID", + "http://edamontology.org/data_2385": "RefSeq accession (protein)", + "http://edamontology.org/data_2386": "EPD ID", + "http://edamontology.org/data_2387": "TAIR accession", + "http://edamontology.org/data_2388": "TAIR accession (At gene)", + "http://edamontology.org/data_2389": "UniSTS accession", + "http://edamontology.org/data_2390": "UNITE accession", + "http://edamontology.org/data_2391": "UTR accession", + "http://edamontology.org/data_2392": "UniParc accession", + "http://edamontology.org/data_2393": "mFLJ/mKIAA number", + "http://edamontology.org/data_2395": "Fungi annotation", + "http://edamontology.org/data_2396": "Fungi annotation (anamorph)", + "http://edamontology.org/data_2398": "Ensembl protein ID", + "http://edamontology.org/data_2400": "Toxin annotation", + "http://edamontology.org/data_2401": "Protein report (membrane protein)", + "http://edamontology.org/data_2402": "Protein-drug interaction report", + "http://edamontology.org/data_2522": "Map data", + "http://edamontology.org/data_2523": "Phylogenetic data", + "http://edamontology.org/data_2524": "Protein data", + "http://edamontology.org/data_2525": "Nucleic acid data", + "http://edamontology.org/data_2526": "Text data", + "http://edamontology.org/data_2527": "Parameter", + "http://edamontology.org/data_2528": "Molecular data", + "http://edamontology.org/data_2529": "Molecule report", + "http://edamontology.org/data_2530": "Organism report", + "http://edamontology.org/data_2531": "Protocol", + "http://edamontology.org/data_2534": "Sequence attribute", + "http://edamontology.org/data_2535": "Sequence tag profile", + "http://edamontology.org/data_2536": "Mass spectrometry data", + "http://edamontology.org/data_2537": "Protein structure raw data", + "http://edamontology.org/data_2538": "Mutation identifier", + "http://edamontology.org/data_2539": "Alignment data", + "http://edamontology.org/data_2540": "Data index data", + "http://edamontology.org/data_2563": "Amino acid name (single letter)", + "http://edamontology.org/data_2564": "Amino acid name (three letter)", + "http://edamontology.org/data_2565": "Amino acid name (full name)", + "http://edamontology.org/data_2576": "Toxin identifier", + "http://edamontology.org/data_2578": "ArachnoServer ID", + "http://edamontology.org/data_2579": "Expressed gene list", + "http://edamontology.org/data_2580": "BindingDB Monomer ID", + "http://edamontology.org/data_2581": "GO concept name", + "http://edamontology.org/data_2582": "GO concept ID (biological process)", + "http://edamontology.org/data_2583": "GO concept ID (molecular function)", + "http://edamontology.org/data_2584": "GO concept name (cellular component)", + "http://edamontology.org/data_2586": "Northern blot image", + "http://edamontology.org/data_2587": "Blot ID", + "http://edamontology.org/data_2588": "BlotBase blot ID", + "http://edamontology.org/data_2589": "Hierarchy", + "http://edamontology.org/data_2590": "Hierarchy identifier", + "http://edamontology.org/data_2591": "Brite hierarchy ID", + "http://edamontology.org/data_2592": "Cancer type", + "http://edamontology.org/data_2593": "BRENDA organism ID", + "http://edamontology.org/data_2594": "UniGene taxon", + "http://edamontology.org/data_2595": "UTRdb taxon", + "http://edamontology.org/data_2596": "Catalogue ID", + "http://edamontology.org/data_2597": "CABRI catalogue name", + "http://edamontology.org/data_2598": "Secondary structure alignment metadata", + "http://edamontology.org/data_2599": "Molecule interaction report", + "http://edamontology.org/data_2600": "Pathway or network", + "http://edamontology.org/data_2601": "Small molecule data", + "http://edamontology.org/data_2602": "Genotype and phenotype data", + "http://edamontology.org/data_2603": "Expression data", + "http://edamontology.org/data_2605": "Compound ID (KEGG)", + "http://edamontology.org/data_2606": "RFAM name", + "http://edamontology.org/data_2608": "Reaction ID (KEGG)", + "http://edamontology.org/data_2609": "Drug ID (KEGG)", + "http://edamontology.org/data_2610": "Ensembl ID", + "http://edamontology.org/data_2611": "ICD identifier", + "http://edamontology.org/data_2612": "Sequence cluster ID (CluSTr)", + "http://edamontology.org/data_2613": "KEGG Glycan ID", + "http://edamontology.org/data_2614": "TCDB ID", + "http://edamontology.org/data_2615": "MINT ID", + "http://edamontology.org/data_2616": "DIP ID", + "http://edamontology.org/data_2617": "Signaling Gateway protein ID", + "http://edamontology.org/data_2618": "Protein modification ID", + "http://edamontology.org/data_2619": "RESID ID", + "http://edamontology.org/data_2620": "RGD ID", + "http://edamontology.org/data_2621": "TAIR accession (protein)", + "http://edamontology.org/data_2622": "Compound ID (HMDB)", + "http://edamontology.org/data_2625": "LIPID MAPS ID", + "http://edamontology.org/data_2626": "PeptideAtlas ID", + "http://edamontology.org/data_2627": "Molecular interaction ID", + "http://edamontology.org/data_2628": "BioGRID interaction ID", + "http://edamontology.org/data_2629": "Enzyme ID (MEROPS)", + "http://edamontology.org/data_2630": "Mobile genetic element ID", + "http://edamontology.org/data_2631": "ACLAME ID", + "http://edamontology.org/data_2632": "SGD ID", + "http://edamontology.org/data_2633": "Book ID", + "http://edamontology.org/data_2634": "ISBN", + "http://edamontology.org/data_2635": "Compound ID (3DMET)", + "http://edamontology.org/data_2636": "MatrixDB interaction ID", + "http://edamontology.org/data_2637": "cPath ID", + "http://edamontology.org/data_2638": "PubChem bioassay ID", + "http://edamontology.org/data_2639": "PubChem ID", + "http://edamontology.org/data_2641": "Reaction ID (MACie)", + "http://edamontology.org/data_2642": "Gene ID (miRBase)", + "http://edamontology.org/data_2643": "Gene ID (ZFIN)", + "http://edamontology.org/data_2644": "Reaction ID (Rhea)", + "http://edamontology.org/data_2645": "Pathway ID (Unipathway)", + "http://edamontology.org/data_2646": "Compound ID (ChEMBL)", + "http://edamontology.org/data_2647": "LGICdb identifier", + "http://edamontology.org/data_2648": "Reaction kinetics ID (SABIO-RK)", + "http://edamontology.org/data_2649": "PharmGKB ID", + "http://edamontology.org/data_2650": "Pathway ID (PharmGKB)", + "http://edamontology.org/data_2651": "Disease ID (PharmGKB)", + "http://edamontology.org/data_2652": "Drug ID (PharmGKB)", + "http://edamontology.org/data_2653": "Drug ID (TTD)", + "http://edamontology.org/data_2654": "Target ID (TTD)", + "http://edamontology.org/data_2655": "Cell type identifier", + "http://edamontology.org/data_2656": "NeuronDB ID", + "http://edamontology.org/data_2657": "NeuroMorpho ID", + "http://edamontology.org/data_2658": "Compound ID (ChemIDplus)", + "http://edamontology.org/data_2659": "Pathway ID (SMPDB)", + "http://edamontology.org/data_2660": "BioNumbers ID", + "http://edamontology.org/data_2662": "T3DB ID", + "http://edamontology.org/data_2663": "Carbohydrate identifier", + "http://edamontology.org/data_2664": "GlycomeDB ID", + "http://edamontology.org/data_2665": "LipidBank ID", + "http://edamontology.org/data_2666": "CDD ID", + "http://edamontology.org/data_2667": "MMDB ID", + "http://edamontology.org/data_2668": "iRefIndex ID", + "http://edamontology.org/data_2669": "ModelDB ID", + "http://edamontology.org/data_2670": "Pathway ID (DQCS)", + "http://edamontology.org/data_2671": "Ensembl ID (Homo sapiens)", + "http://edamontology.org/data_2672": "Ensembl ID ('Bos taurus')", + "http://edamontology.org/data_2673": "Ensembl ID ('Canis familiaris')", + "http://edamontology.org/data_2674": "Ensembl ID ('Cavia porcellus')", + "http://edamontology.org/data_2675": "Ensembl ID ('Ciona intestinalis')", + "http://edamontology.org/data_2676": "Ensembl ID ('Ciona savignyi')", + "http://edamontology.org/data_2677": "Ensembl ID ('Danio rerio')", + "http://edamontology.org/data_2678": "Ensembl ID ('Dasypus novemcinctus')", + "http://edamontology.org/data_2679": "Ensembl ID ('Echinops telfairi')", + "http://edamontology.org/data_2680": "Ensembl ID ('Erinaceus europaeus')", + "http://edamontology.org/data_2681": "Ensembl ID ('Felis catus')", + "http://edamontology.org/data_2682": "Ensembl ID ('Gallus gallus')", + "http://edamontology.org/data_2683": "Ensembl ID ('Gasterosteus aculeatus')", + "http://edamontology.org/data_2684": "Ensembl ID ('Homo sapiens')", + "http://edamontology.org/data_2685": "Ensembl ID ('Loxodonta africana')", + "http://edamontology.org/data_2686": "Ensembl ID ('Macaca mulatta')", + "http://edamontology.org/data_2687": "Ensembl ID ('Monodelphis domestica')", + "http://edamontology.org/data_2688": "Ensembl ID ('Mus musculus')", + "http://edamontology.org/data_2689": "Ensembl ID ('Myotis lucifugus')", + "http://edamontology.org/data_2690": "Ensembl ID (\"Ornithorhynchus anatinus\")", + "http://edamontology.org/data_2691": "Ensembl ID ('Oryctolagus cuniculus')", + "http://edamontology.org/data_2692": "Ensembl ID ('Oryzias latipes')", + "http://edamontology.org/data_2693": "Ensembl ID ('Otolemur garnettii')", + "http://edamontology.org/data_2694": "Ensembl ID ('Pan troglodytes')", + "http://edamontology.org/data_2695": "Ensembl ID ('Rattus norvegicus')", + "http://edamontology.org/data_2696": "Ensembl ID ('Spermophilus tridecemlineatus')", + "http://edamontology.org/data_2697": "Ensembl ID ('Takifugu rubripes')", + "http://edamontology.org/data_2698": "Ensembl ID ('Tupaia belangeri')", + "http://edamontology.org/data_2699": "Ensembl ID ('Xenopus tropicalis')", + "http://edamontology.org/data_2700": "CATH identifier", + "http://edamontology.org/data_2701": "CATH node ID (family)", + "http://edamontology.org/data_2702": "Enzyme ID (CAZy)", + "http://edamontology.org/data_2704": "Clone ID (IMAGE)", + "http://edamontology.org/data_2705": "GO concept ID (cellular component)", + "http://edamontology.org/data_2706": "Chromosome name (BioCyc)", + "http://edamontology.org/data_2709": "CleanEx entry name", + "http://edamontology.org/data_2710": "CleanEx dataset code", + "http://edamontology.org/data_2711": "Genome report", + "http://edamontology.org/data_2713": "Protein ID (CORUM)", + "http://edamontology.org/data_2714": "CDD PSSM-ID", + "http://edamontology.org/data_2715": "Protein ID (CuticleDB)", + "http://edamontology.org/data_2716": "DBD ID", + "http://edamontology.org/data_2717": "Oligonucleotide probe annotation", + "http://edamontology.org/data_2718": "Oligonucleotide ID", + "http://edamontology.org/data_2719": "dbProbe ID", + "http://edamontology.org/data_2720": "Dinucleotide property", + "http://edamontology.org/data_2721": "DiProDB ID", + "http://edamontology.org/data_2722": "Protein features report (disordered structure)", + "http://edamontology.org/data_2723": "Protein ID (DisProt)", + "http://edamontology.org/data_2724": "Embryo report", + "http://edamontology.org/data_2725": "Ensembl transcript ID", + "http://edamontology.org/data_2726": "Inhibitor annotation", + "http://edamontology.org/data_2727": "Promoter ID", + "http://edamontology.org/data_2728": "EST accession", + "http://edamontology.org/data_2729": "COGEME EST ID", + "http://edamontology.org/data_2730": "COGEME unisequence ID", + "http://edamontology.org/data_2731": "Protein family ID (GeneFarm)", + "http://edamontology.org/data_2732": "Family name", + "http://edamontology.org/data_2733": "Genus name (virus)", + "http://edamontology.org/data_2734": "Family name (virus)", + "http://edamontology.org/data_2735": "Database name (SwissRegulon)", + "http://edamontology.org/data_2736": "Sequence feature ID (SwissRegulon)", + "http://edamontology.org/data_2737": "FIG ID", + "http://edamontology.org/data_2738": "Gene ID (Xenbase)", + "http://edamontology.org/data_2739": "Gene ID (Genolist)", + "http://edamontology.org/data_2740": "Gene name (Genolist)", + "http://edamontology.org/data_2741": "ABS ID", + "http://edamontology.org/data_2742": "AraC-XylS ID", + "http://edamontology.org/data_2743": "Gene name (HUGO)", + "http://edamontology.org/data_2744": "Locus ID (PseudoCAP)", + "http://edamontology.org/data_2745": "Locus ID (UTR)", + "http://edamontology.org/data_2746": "MonosaccharideDB ID", + "http://edamontology.org/data_2747": "Database name (CMD)", + "http://edamontology.org/data_2748": "Database name (Osteogenesis)", + "http://edamontology.org/data_2749": "Genome identifier", + "http://edamontology.org/data_2751": "GenomeReviews ID", + "http://edamontology.org/data_2752": "GlycoMap ID", + "http://edamontology.org/data_2753": "Carbohydrate conformational map", + "http://edamontology.org/data_2755": "Transcription factor name", + "http://edamontology.org/data_2756": "TCID", + "http://edamontology.org/data_2757": "Pfam domain name", + "http://edamontology.org/data_2758": "Pfam clan ID", + "http://edamontology.org/data_2759": "Gene ID (VectorBase)", + "http://edamontology.org/data_2761": "UTRSite ID", + "http://edamontology.org/data_2762": "Sequence signature report", + "http://edamontology.org/data_2763": "Locus annotation", + "http://edamontology.org/data_2764": "Protein name (UniProt)", + "http://edamontology.org/data_2765": "Term ID list", + "http://edamontology.org/data_2766": "HAMAP ID", + "http://edamontology.org/data_2767": "Identifier with metadata", + "http://edamontology.org/data_2768": "Gene symbol annotation", + "http://edamontology.org/data_2769": "Transcript ID", + "http://edamontology.org/data_2770": "HIT ID", + "http://edamontology.org/data_2771": "HIX ID", + "http://edamontology.org/data_2772": "HPA antibody id", + "http://edamontology.org/data_2773": "IMGT/HLA ID", + "http://edamontology.org/data_2774": "Gene ID (JCVI)", + "http://edamontology.org/data_2775": "Kinase name", + "http://edamontology.org/data_2776": "ConsensusPathDB entity ID", + "http://edamontology.org/data_2777": "ConsensusPathDB entity name", + "http://edamontology.org/data_2778": "CCAP strain number", + "http://edamontology.org/data_2779": "Stock number", + "http://edamontology.org/data_2780": "Stock number (TAIR)", + "http://edamontology.org/data_2781": "REDIdb ID", + "http://edamontology.org/data_2782": "SMART domain name", + "http://edamontology.org/data_2783": "Protein family ID (PANTHER)", + "http://edamontology.org/data_2784": "RNAVirusDB ID", + "http://edamontology.org/data_2785": "Virus ID", + "http://edamontology.org/data_2786": "NCBI Genome Project ID", + "http://edamontology.org/data_2787": "NCBI genome accession", + "http://edamontology.org/data_2788": "Sequence profile data", + "http://edamontology.org/data_2789": "Protein ID (TopDB)", + "http://edamontology.org/data_2790": "Gel ID", + "http://edamontology.org/data_2791": "Reference map name (SWISS-2DPAGE)", + "http://edamontology.org/data_2792": "Protein ID (PeroxiBase)", + "http://edamontology.org/data_2793": "SISYPHUS ID", + "http://edamontology.org/data_2794": "ORF ID", + "http://edamontology.org/data_2795": "ORF identifier", + "http://edamontology.org/data_2796": "Linucs ID", + "http://edamontology.org/data_2797": "Protein ID (LGICdb)", + "http://edamontology.org/data_2798": "MaizeDB ID", + "http://edamontology.org/data_2799": "Gene ID (MfunGD)", + "http://edamontology.org/data_2800": "Orpha number", + "http://edamontology.org/data_2802": "Protein ID (EcID)", + "http://edamontology.org/data_2803": "Clone ID (RefSeq)", + "http://edamontology.org/data_2804": "Protein ID (ConoServer)", + "http://edamontology.org/data_2805": "GeneSNP ID", + "http://edamontology.org/data_2812": "Lipid identifier", + "http://edamontology.org/data_2831": "Databank", + "http://edamontology.org/data_2832": "Web portal", + "http://edamontology.org/data_2835": "Gene ID (VBASE2)", + "http://edamontology.org/data_2836": "DPVweb ID", + "http://edamontology.org/data_2837": "Pathway ID (BioSystems)", + "http://edamontology.org/data_2838": "Experimental data (proteomics)", + "http://edamontology.org/data_2849": "Abstract", + "http://edamontology.org/data_2850": "Lipid structure", + "http://edamontology.org/data_2851": "Drug structure", + "http://edamontology.org/data_2852": "Toxin structure", + "http://edamontology.org/data_2854": "Position-specific scoring matrix", + "http://edamontology.org/data_2855": "Distance matrix", + "http://edamontology.org/data_2856": "Structural distance matrix", + "http://edamontology.org/data_2857": "Article metadata", + "http://edamontology.org/data_2858": "Ontology concept", + "http://edamontology.org/data_2865": "Codon usage bias", + "http://edamontology.org/data_2866": "Northern blot report", + "http://edamontology.org/data_2870": "Radiation hybrid map", + "http://edamontology.org/data_2872": "ID list", + "http://edamontology.org/data_2873": "Phylogenetic gene frequencies data", + "http://edamontology.org/data_2874": "Sequence set (polymorphic)", + "http://edamontology.org/data_2875": "DRCAT resource", + "http://edamontology.org/data_2877": "Protein complex", + "http://edamontology.org/data_2878": "Protein structural motif", + "http://edamontology.org/data_2879": "Lipid report", + "http://edamontology.org/data_2880": "Secondary structure image", + "http://edamontology.org/data_2881": "Secondary structure report", + "http://edamontology.org/data_2882": "DNA features", + "http://edamontology.org/data_2883": "RNA features report", + "http://edamontology.org/data_2884": "Plot", + "http://edamontology.org/data_2886": "Protein sequence record", + "http://edamontology.org/data_2887": "Nucleic acid sequence record", + "http://edamontology.org/data_2888": "Protein sequence record (full)", + "http://edamontology.org/data_2889": "Nucleic acid sequence record (full)", + "http://edamontology.org/data_2891": "Biological model accession", + "http://edamontology.org/data_2892": "Cell type name", + "http://edamontology.org/data_2893": "Cell type accession", + "http://edamontology.org/data_2894": "Compound accession", + "http://edamontology.org/data_2895": "Drug accession", + "http://edamontology.org/data_2896": "Toxin name", + "http://edamontology.org/data_2897": "Toxin accession", + "http://edamontology.org/data_2898": "Monosaccharide accession", + "http://edamontology.org/data_2899": "Drug name", + "http://edamontology.org/data_2900": "Carbohydrate accession", + "http://edamontology.org/data_2901": "Molecule accession", + "http://edamontology.org/data_2902": "Data resource definition accession", + "http://edamontology.org/data_2903": "Genome accession", + "http://edamontology.org/data_2904": "Map accession", + "http://edamontology.org/data_2905": "Lipid accession", + "http://edamontology.org/data_2906": "Peptide ID", + "http://edamontology.org/data_2907": "Protein accession", + "http://edamontology.org/data_2908": "Organism accession", + "http://edamontology.org/data_2909": "Organism name", + "http://edamontology.org/data_2910": "Protein family accession", + "http://edamontology.org/data_2911": "Transcription factor accession", + "http://edamontology.org/data_2912": "Strain accession", + "http://edamontology.org/data_2913": "Virus identifier", + "http://edamontology.org/data_2914": "Sequence features metadata", + "http://edamontology.org/data_2915": "Gramene identifier", + "http://edamontology.org/data_2916": "DDBJ accession", + "http://edamontology.org/data_2917": "ConsensusPathDB identifier", + "http://edamontology.org/data_2925": "Sequence data", + "http://edamontology.org/data_2927": "Codon usage", + "http://edamontology.org/data_2954": "Article report", + "http://edamontology.org/data_2955": "Sequence report", + "http://edamontology.org/data_2956": "Protein secondary structure", + "http://edamontology.org/data_2957": "Hopp and Woods plot", + "http://edamontology.org/data_2958": "Nucleic acid melting curve", + "http://edamontology.org/data_2959": "Nucleic acid probability profile", + "http://edamontology.org/data_2960": "Nucleic acid temperature profile", + "http://edamontology.org/data_2961": "Gene regulatory network report", + "http://edamontology.org/data_2965": "2D PAGE gel report", + "http://edamontology.org/data_2966": "Oligonucleotide probe sets annotation", + "http://edamontology.org/data_2967": "Microarray image", + "http://edamontology.org/data_2968": "Image", + "http://edamontology.org/data_2969": "Sequence image", + "http://edamontology.org/data_2970": "Protein hydropathy data", + "http://edamontology.org/data_2971": "Workflow data", + "http://edamontology.org/data_2972": "Workflow", + "http://edamontology.org/data_2973": "Secondary structure data", + "http://edamontology.org/data_2974": "Protein sequence (raw)", + "http://edamontology.org/data_2975": "Nucleic acid sequence (raw)", + "http://edamontology.org/data_2976": "Protein sequence", + "http://edamontology.org/data_2977": "Nucleic acid sequence", + "http://edamontology.org/data_2978": "Reaction data", + "http://edamontology.org/data_2979": "Peptide property", + "http://edamontology.org/data_2980": "Protein classification", + "http://edamontology.org/data_2981": "Sequence motif data", + "http://edamontology.org/data_2982": "Sequence profile data", + "http://edamontology.org/data_2983": "Pathway or network data", + "http://edamontology.org/data_2984": "Pathway or network report", + "http://edamontology.org/data_2985": "Nucleic acid thermodynamic data", + "http://edamontology.org/data_2986": "Nucleic acid classification", + "http://edamontology.org/data_2987": "Classification report", + "http://edamontology.org/data_2989": "Protein features report (key folding sites)", + "http://edamontology.org/data_2991": "Protein geometry data", + "http://edamontology.org/data_2992": "Protein structure image", + "http://edamontology.org/data_2994": "Phylogenetic character weights", + "http://edamontology.org/data_3002": "Annotation track", + "http://edamontology.org/data_3021": "UniProt accession", + "http://edamontology.org/data_3022": "NCBI genetic code ID", + "http://edamontology.org/data_3025": "Ontology concept identifier", + "http://edamontology.org/data_3026": "GO concept name (biological process)", + "http://edamontology.org/data_3027": "GO concept name (molecular function)", + "http://edamontology.org/data_3028": "Taxonomy", + "http://edamontology.org/data_3029": "Protein ID (EMBL/GenBank/DDBJ)", + "http://edamontology.org/data_3031": "Core data", + "http://edamontology.org/data_3034": "Sequence feature identifier", + "http://edamontology.org/data_3035": "Structure identifier", + "http://edamontology.org/data_3036": "Matrix identifier", + "http://edamontology.org/data_3085": "Protein sequence composition", + "http://edamontology.org/data_3086": "Nucleic acid sequence composition (report)", + "http://edamontology.org/data_3101": "Protein domain classification node", + "http://edamontology.org/data_3102": "CAS number", + "http://edamontology.org/data_3103": "ATC code", + "http://edamontology.org/data_3104": "UNII", + "http://edamontology.org/data_3105": "Geotemporal metadata", + "http://edamontology.org/data_3106": "System metadata", + "http://edamontology.org/data_3107": "Sequence feature name", + "http://edamontology.org/data_3108": "Experimental measurement", + "http://edamontology.org/data_3110": "Raw microarray data", + "http://edamontology.org/data_3111": "Processed microarray data", + "http://edamontology.org/data_3112": "Gene expression matrix", + "http://edamontology.org/data_3113": "Sample annotation", + "http://edamontology.org/data_3115": "Microarray metadata", + "http://edamontology.org/data_3116": "Microarray protocol annotation", + "http://edamontology.org/data_3117": "Microarray hybridisation data", + "http://edamontology.org/data_3119": "Sequence features (compositionally-biased regions)", + "http://edamontology.org/data_3122": "Nucleic acid features (difference and change)", + "http://edamontology.org/data_3128": "Nucleic acid structure report", + "http://edamontology.org/data_3129": "Protein features report (repeats)", + "http://edamontology.org/data_3130": "Sequence motif matches (protein)", + "http://edamontology.org/data_3131": "Sequence motif matches (nucleic acid)", + "http://edamontology.org/data_3132": "Nucleic acid features (d-loop)", + "http://edamontology.org/data_3133": "Nucleic acid features (stem loop)", + "http://edamontology.org/data_3134": "Gene transcript report", + "http://edamontology.org/data_3137": "Non-coding RNA", + "http://edamontology.org/data_3138": "Transcriptional features (report)", + "http://edamontology.org/data_3140": "Nucleic acid features (immunoglobulin gene structure)", + "http://edamontology.org/data_3141": "SCOP class", + "http://edamontology.org/data_3142": "SCOP fold", + "http://edamontology.org/data_3143": "SCOP superfamily", + "http://edamontology.org/data_3144": "SCOP family", + "http://edamontology.org/data_3145": "SCOP protein", + "http://edamontology.org/data_3146": "SCOP species", + "http://edamontology.org/data_3147": "Mass spectrometry experiment", + "http://edamontology.org/data_3148": "Gene family report", + "http://edamontology.org/data_3153": "Protein image", + "http://edamontology.org/data_3154": "Protein alignment", + "http://edamontology.org/data_3165": "NGS experiment", + "http://edamontology.org/data_3181": "Sequence assembly report", + "http://edamontology.org/data_3210": "Genome index", + "http://edamontology.org/data_3231": "GWAS report", + "http://edamontology.org/data_3236": "Cytoband position", + "http://edamontology.org/data_3238": "Cell type ontology ID", + "http://edamontology.org/data_3241": "Kinetic model", + "http://edamontology.org/data_3264": "COSMIC ID", + "http://edamontology.org/data_3265": "HGMD ID", + "http://edamontology.org/data_3266": "Sequence assembly ID", + "http://edamontology.org/data_3268": "Sequence feature type", + "http://edamontology.org/data_3269": "Gene homology (report)", + "http://edamontology.org/data_3270": "Ensembl gene tree ID", + "http://edamontology.org/data_3271": "Gene tree", + "http://edamontology.org/data_3272": "Species tree", + "http://edamontology.org/data_3273": "Sample ID", + "http://edamontology.org/data_3274": "MGI accession", + "http://edamontology.org/data_3275": "Phenotype name", + "http://edamontology.org/data_3354": "Transition matrix", + "http://edamontology.org/data_3355": "Emission matrix", + "http://edamontology.org/data_3356": "Hidden Markov model", + "http://edamontology.org/data_3358": "Format identifier", + "http://edamontology.org/data_3424": "Raw image", + "http://edamontology.org/data_3425": "Carbohydrate property", + "http://edamontology.org/data_3426": "Proteomics experiment report", + "http://edamontology.org/data_3427": "RNAi report", + "http://edamontology.org/data_3428": "Simulation experiment report", + "http://edamontology.org/data_3442": "MRI image", + "http://edamontology.org/data_3449": "Cell migration track image", + "http://edamontology.org/data_3451": "Rate of association", + "http://edamontology.org/data_3479": "Gene order", + "http://edamontology.org/data_3483": "Spectrum", + "http://edamontology.org/data_3488": "NMR spectrum", + "http://edamontology.org/data_3490": "Chemical structure sketch", + "http://edamontology.org/data_3492": "Nucleic acid signature", + "http://edamontology.org/data_3494": "DNA sequence", + "http://edamontology.org/data_3495": "RNA sequence", + "http://edamontology.org/data_3496": "RNA sequence (raw)", + "http://edamontology.org/data_3497": "DNA sequence (raw)", + "http://edamontology.org/data_3498": "Sequence variations", + "http://edamontology.org/data_3505": "Bibliography", + "http://edamontology.org/data_3509": "Ontology mapping", + "http://edamontology.org/data_3546": "Image metadata", + "http://edamontology.org/data_3558": "Clinical trial report", + "http://edamontology.org/data_3567": "Reference sample report", + "http://edamontology.org/data_3568": "Gene Expression Atlas Experiment ID", + "http://edamontology.org/data_3667": "Disease identifier", + "http://edamontology.org/data_3668": "Disease name", + "http://edamontology.org/data_3669": "Training material", + "http://edamontology.org/data_3670": "Online course", + "http://edamontology.org/data_3671": "Text", + "http://edamontology.org/data_3707": "Biodiversity data", + "http://edamontology.org/data_3716": "Biosafety report", + "http://edamontology.org/data_3717": "Isolation report", + "http://edamontology.org/data_3718": "Pathogenicity report", + "http://edamontology.org/data_3719": "Biosafety classification", + "http://edamontology.org/data_3720": "Geographic location", + "http://edamontology.org/data_3721": "Isolation source", + "http://edamontology.org/data_3722": "Physiology parameter", + "http://edamontology.org/data_3723": "Morphology parameter", + "http://edamontology.org/data_3724": "Cultivation parameter", + "http://edamontology.org/data_3732": "Sequencing metadata name", + "http://edamontology.org/data_3733": "Flow cell identifier", + "http://edamontology.org/data_3734": "Lane identifier", + "http://edamontology.org/data_3735": "Run number", + "http://edamontology.org/data_3736": "Ecological data", + "http://edamontology.org/data_3737": "Alpha diversity data", + "http://edamontology.org/data_3738": "Beta diversity data", + "http://edamontology.org/data_3739": "Gamma diversity data", + "http://edamontology.org/data_3743": "Ordination plot", + "http://edamontology.org/data_3753": "Over-representation data", + "http://edamontology.org/data_3754": "GO-term enrichment data", + "http://edamontology.org/data_3756": "Localisation score", + "http://edamontology.org/data_3757": "Unimod ID", + "http://edamontology.org/data_3759": "ProteomeXchange ID", + "http://edamontology.org/data_3768": "Clustered expression profiles", + "http://edamontology.org/data_3769": "BRENDA ontology concept ID", + "http://edamontology.org/data_3779": "Annotated text", + "http://edamontology.org/data_3786": "Query script", + "http://edamontology.org/data_3805": "3D EM Map", + "http://edamontology.org/data_3806": "3D EM Mask", + "http://edamontology.org/data_3807": "EM Movie", + "http://edamontology.org/data_3808": "EM Micrograph", + "http://edamontology.org/data_3842": "Molecular simulation data", + "http://edamontology.org/data_3856": "RNA central ID", + "http://edamontology.org/data_3861": "Electronic health record", + "http://edamontology.org/data_3869": "Simulation", + "http://edamontology.org/data_3870": "Trajectory data", + "http://edamontology.org/data_3871": "Forcefield parameters", + "http://edamontology.org/data_3872": "Topology data", + "http://edamontology.org/data_3905": "Histogram", + "http://edamontology.org/data_3914": "Quality control report", + "http://edamontology.org/data_3917": "Count matrix", + "http://edamontology.org/data_3924": "DNA structure alignment", + "http://edamontology.org/data_3932": "Q-value", + "http://edamontology.org/data_3949": "Profile HMM", + "http://edamontology.org/data_3952": "Pathway ID (WikiPathways)", + "http://edamontology.org/data_3953": "Pathway overrepresentation data", + "http://edamontology.org/format_1196": "SMILES", + "http://edamontology.org/format_1197": "InChI", + "http://edamontology.org/format_1198": "mf", + "http://edamontology.org/format_1199": "InChIKey", + "http://edamontology.org/format_1200": "smarts", + "http://edamontology.org/format_1206": "unambiguous pure", + "http://edamontology.org/format_1207": "nucleotide", + "http://edamontology.org/format_1208": "protein", + "http://edamontology.org/format_1209": "consensus", + "http://edamontology.org/format_1210": "pure nucleotide", + "http://edamontology.org/format_1211": "unambiguous pure nucleotide", + "http://edamontology.org/format_1212": "dna", + "http://edamontology.org/format_1213": "rna", + "http://edamontology.org/format_1214": "unambiguous pure dna", + "http://edamontology.org/format_1215": "pure dna", + "http://edamontology.org/format_1216": "unambiguous pure rna sequence", + "http://edamontology.org/format_1217": "pure rna", + "http://edamontology.org/format_1218": "unambiguous pure protein", + "http://edamontology.org/format_1219": "pure protein", + "http://edamontology.org/format_1228": "UniGene entry format", + "http://edamontology.org/format_1247": "COG sequence cluster format", + "http://edamontology.org/format_1248": "EMBL feature location", + "http://edamontology.org/format_1295": "quicktandem", + "http://edamontology.org/format_1296": "Sanger inverted repeats", + "http://edamontology.org/format_1297": "EMBOSS repeat", + "http://edamontology.org/format_1316": "est2genome format", + "http://edamontology.org/format_1318": "restrict format", + "http://edamontology.org/format_1319": "restover format", + "http://edamontology.org/format_1320": "REBASE restriction sites", + "http://edamontology.org/format_1332": "FASTA search results format", + "http://edamontology.org/format_1333": "BLAST results", + "http://edamontology.org/format_1334": "mspcrunch", + "http://edamontology.org/format_1335": "Smith-Waterman format", + "http://edamontology.org/format_1336": "dhf", + "http://edamontology.org/format_1337": "lhf", + "http://edamontology.org/format_1341": "InterPro hits format", + "http://edamontology.org/format_1342": "InterPro protein view report format", + "http://edamontology.org/format_1343": "InterPro match table format", + "http://edamontology.org/format_1349": "HMMER Dirichlet prior", + "http://edamontology.org/format_1350": "MEME Dirichlet prior", + "http://edamontology.org/format_1351": "HMMER emission and transition", + "http://edamontology.org/format_1356": "prosite-pattern", + "http://edamontology.org/format_1357": "EMBOSS sequence pattern", + "http://edamontology.org/format_1360": "meme-motif", + "http://edamontology.org/format_1366": "prosite-profile", + "http://edamontology.org/format_1367": "JASPAR format", + "http://edamontology.org/format_1369": "MEME background Markov model", + "http://edamontology.org/format_1370": "HMMER format", + "http://edamontology.org/format_1391": "HMMER-aln", + "http://edamontology.org/format_1392": "DIALIGN format", + "http://edamontology.org/format_1393": "daf", + "http://edamontology.org/format_1419": "Sequence-MEME profile alignment", + "http://edamontology.org/format_1421": "HMMER profile alignment (sequences versus HMMs)", + "http://edamontology.org/format_1422": "HMMER profile alignment (HMM versus sequences)", + "http://edamontology.org/format_1423": "Phylip distance matrix", + "http://edamontology.org/format_1424": "ClustalW dendrogram", + "http://edamontology.org/format_1425": "Phylip tree raw", + "http://edamontology.org/format_1430": "Phylip continuous quantitative characters", + "http://edamontology.org/format_1431": "Phylogenetic property values format", + "http://edamontology.org/format_1432": "Phylip character frequencies format", + "http://edamontology.org/format_1433": "Phylip discrete states format", + "http://edamontology.org/format_1434": "Phylip cliques format", + "http://edamontology.org/format_1435": "Phylip tree format", + "http://edamontology.org/format_1436": "TreeBASE format", + "http://edamontology.org/format_1437": "TreeFam format", + "http://edamontology.org/format_1445": "Phylip tree distance format", + "http://edamontology.org/format_1454": "dssp", + "http://edamontology.org/format_1455": "hssp", + "http://edamontology.org/format_1457": "Dot-bracket format", + "http://edamontology.org/format_1458": "Vienna local RNA secondary structure format", + "http://edamontology.org/format_1475": "PDB database entry format", + "http://edamontology.org/format_1476": "PDB", + "http://edamontology.org/format_1477": "mmCIF", + "http://edamontology.org/format_1478": "PDBML", + "http://edamontology.org/format_1500": "Domainatrix 3D-1D scoring matrix format", + "http://edamontology.org/format_1504": "aaindex", + "http://edamontology.org/format_1511": "IntEnz enzyme report format", + "http://edamontology.org/format_1512": "BRENDA enzyme report format", + "http://edamontology.org/format_1513": "KEGG REACTION enzyme report format", + "http://edamontology.org/format_1514": "KEGG ENZYME enzyme report format", + "http://edamontology.org/format_1515": "REBASE proto enzyme report format", + "http://edamontology.org/format_1516": "REBASE withrefm enzyme report format", + "http://edamontology.org/format_1551": "Pcons report format", + "http://edamontology.org/format_1552": "ProQ report format", + "http://edamontology.org/format_1563": "SMART domain assignment report format", + "http://edamontology.org/format_1568": "BIND entry format", + "http://edamontology.org/format_1569": "IntAct entry format", + "http://edamontology.org/format_1570": "InterPro entry format", + "http://edamontology.org/format_1571": "InterPro entry abstract format", + "http://edamontology.org/format_1572": "Gene3D entry format", + "http://edamontology.org/format_1573": "PIRSF entry format", + "http://edamontology.org/format_1574": "PRINTS entry format", + "http://edamontology.org/format_1575": "Panther Families and HMMs entry format", + "http://edamontology.org/format_1576": "Pfam entry format", + "http://edamontology.org/format_1577": "SMART entry format", + "http://edamontology.org/format_1578": "Superfamily entry format", + "http://edamontology.org/format_1579": "TIGRFam entry format", + "http://edamontology.org/format_1580": "ProDom entry format", + "http://edamontology.org/format_1581": "FSSP entry format", + "http://edamontology.org/format_1582": "findkm", + "http://edamontology.org/format_1603": "Ensembl gene report format", + "http://edamontology.org/format_1604": "DictyBase gene report format", + "http://edamontology.org/format_1605": "CGD gene report format", + "http://edamontology.org/format_1606": "DragonDB gene report format", + "http://edamontology.org/format_1607": "EcoCyc gene report format", + "http://edamontology.org/format_1608": "FlyBase gene report format", + "http://edamontology.org/format_1609": "Gramene gene report format", + "http://edamontology.org/format_1610": "KEGG GENES gene report format", + "http://edamontology.org/format_1611": "MaizeGDB gene report format", + "http://edamontology.org/format_1612": "MGD gene report format", + "http://edamontology.org/format_1613": "RGD gene report format", + "http://edamontology.org/format_1614": "SGD gene report format", + "http://edamontology.org/format_1615": "GeneDB gene report format", + "http://edamontology.org/format_1616": "TAIR gene report format", + "http://edamontology.org/format_1617": "WormBase gene report format", + "http://edamontology.org/format_1618": "ZFIN gene report format", + "http://edamontology.org/format_1619": "TIGR gene report format", + "http://edamontology.org/format_1620": "dbSNP polymorphism report format", + "http://edamontology.org/format_1623": "OMIM entry format", + "http://edamontology.org/format_1624": "HGVbase entry format", + "http://edamontology.org/format_1625": "HIVDB entry format", + "http://edamontology.org/format_1626": "KEGG DISEASE entry format", + "http://edamontology.org/format_1627": "Primer3 primer", + "http://edamontology.org/format_1628": "ABI", + "http://edamontology.org/format_1629": "mira", + "http://edamontology.org/format_1630": "CAF", + "http://edamontology.org/format_1631": "EXP", + "http://edamontology.org/format_1632": "SCF", + "http://edamontology.org/format_1633": "PHD", + "http://edamontology.org/format_1637": "dat", + "http://edamontology.org/format_1638": "cel", + "http://edamontology.org/format_1639": "affymetrix", + "http://edamontology.org/format_1640": "ArrayExpress entry format", + "http://edamontology.org/format_1641": "affymetrix-exp", + "http://edamontology.org/format_1644": "CHP", + "http://edamontology.org/format_1645": "EMDB entry format", + "http://edamontology.org/format_1647": "KEGG PATHWAY entry format", + "http://edamontology.org/format_1648": "MetaCyc entry format", + "http://edamontology.org/format_1649": "HumanCyc entry format", + "http://edamontology.org/format_1650": "INOH entry format", + 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dynamics", + "http://edamontology.org/operation_3893": "Forcefield parameterisation", + "http://edamontology.org/operation_3894": "DNA profiling", + "http://edamontology.org/operation_3896": "Active site prediction", + "http://edamontology.org/operation_3897": "Ligand-binding site prediction", + "http://edamontology.org/operation_3898": "Metal-binding site prediction", + "http://edamontology.org/operation_3899": "Protein-protein docking", + "http://edamontology.org/operation_3900": "DNA-binding protein prediction", + "http://edamontology.org/operation_3901": "RNA-binding protein prediction", + "http://edamontology.org/operation_3902": "RNA binding site prediction", + "http://edamontology.org/operation_3903": "DNA binding site prediction", + "http://edamontology.org/operation_3904": "Protein disorder prediction", + "http://edamontology.org/operation_3907": "Information extraction", + "http://edamontology.org/operation_3908": "Information retrieval", + 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"http://edamontology.org/operation_3938": "Virtual screening", + "http://edamontology.org/operation_3939": "Metabolic engineering", + "http://edamontology.org/operation_3942": "Tree dating", + "http://edamontology.org/operation_3946": "Ecological modelling", + "http://edamontology.org/operation_3947": "Phylogenetic tree reconciliation", + "http://edamontology.org/operation_3950": "Selection detection", + "http://edamontology.org/operation_3960": "Principal component analysis", + "http://edamontology.org/operation_3961": "Copy number variation detection", + "http://edamontology.org/operation_3962": "Deletion detection", + "http://edamontology.org/operation_3963": "Duplication detection", + "http://edamontology.org/operation_3964": "Complex CNV detection", + "http://edamontology.org/operation_3965": "Amplification detection", + "http://edamontology.org/operation_3968": "Adhesin prediction", + "http://edamontology.org/operation_4008": "Protein design", + "http://edamontology.org/operation_4009": "Small molecule design", + "http://edamontology.org/topic_0003": "Topic", + "http://edamontology.org/topic_0077": "Nucleic acids", + "http://edamontology.org/topic_0078": "Proteins", + "http://edamontology.org/topic_0079": "Metabolites", + "http://edamontology.org/topic_0080": "Sequence analysis", + "http://edamontology.org/topic_0081": "Structure analysis", + "http://edamontology.org/topic_0082": "Structure prediction", + "http://edamontology.org/topic_0083": "Alignment", + "http://edamontology.org/topic_0084": "Phylogeny", + "http://edamontology.org/topic_0085": "Functional genomics", + "http://edamontology.org/topic_0089": "Ontology and terminology", + "http://edamontology.org/topic_0090": "Information retrieval", + "http://edamontology.org/topic_0091": "Bioinformatics", + "http://edamontology.org/topic_0092": "Data visualisation", + "http://edamontology.org/topic_0094": "Nucleic acid thermodynamics", + "http://edamontology.org/topic_0097": "Nucleic acid structure analysis", + "http://edamontology.org/topic_0099": "RNA", + "http://edamontology.org/topic_0100": "Nucleic acid restriction", + "http://edamontology.org/topic_0102": "Mapping", + "http://edamontology.org/topic_0107": "Genetic codes and codon usage", + "http://edamontology.org/topic_0108": "Protein expression", + "http://edamontology.org/topic_0109": "Gene finding", + "http://edamontology.org/topic_0110": "Transcription", + "http://edamontology.org/topic_0111": "Promoters", + "http://edamontology.org/topic_0112": "Nucleic acid folding", + "http://edamontology.org/topic_0114": "Gene structure", + "http://edamontology.org/topic_0121": "Proteomics", + "http://edamontology.org/topic_0122": "Structural genomics", + "http://edamontology.org/topic_0123": "Protein properties", + "http://edamontology.org/topic_0128": "Protein interactions", + "http://edamontology.org/topic_0130": "Protein folding, stability and design", + "http://edamontology.org/topic_0133": "Two-dimensional gel electrophoresis", + "http://edamontology.org/topic_0134": "Mass spectrometry", + "http://edamontology.org/topic_0135": "Protein microarrays", + "http://edamontology.org/topic_0137": "Protein hydropathy", + "http://edamontology.org/topic_0140": "Protein targeting and localisation", + "http://edamontology.org/topic_0141": "Protein cleavage sites and proteolysis", + "http://edamontology.org/topic_0143": "Protein structure comparison", + "http://edamontology.org/topic_0144": "Protein residue interactions", + "http://edamontology.org/topic_0147": "Protein-protein interactions", + "http://edamontology.org/topic_0148": "Protein-ligand interactions", + "http://edamontology.org/topic_0149": "Protein-nucleic acid interactions", + "http://edamontology.org/topic_0150": "Protein design", + "http://edamontology.org/topic_0151": "G protein-coupled receptors (GPCR)", + "http://edamontology.org/topic_0152": "Carbohydrates", + "http://edamontology.org/topic_0153": "Lipids", + "http://edamontology.org/topic_0154": "Small molecules", + "http://edamontology.org/topic_0156": "Sequence editing", + "http://edamontology.org/topic_0157": "Sequence composition, complexity and repeats", + "http://edamontology.org/topic_0158": "Sequence motifs", + "http://edamontology.org/topic_0159": "Sequence comparison", + "http://edamontology.org/topic_0160": "Sequence sites, features and motifs", + "http://edamontology.org/topic_0163": "Sequence database search", + "http://edamontology.org/topic_0164": "Sequence clustering", + "http://edamontology.org/topic_0166": "Protein structural motifs and surfaces", + "http://edamontology.org/topic_0167": "Structural (3D) profiles", + "http://edamontology.org/topic_0172": "Protein structure prediction", + "http://edamontology.org/topic_0173": "Nucleic acid structure prediction", + "http://edamontology.org/topic_0174": "Ab initio structure prediction", + "http://edamontology.org/topic_0175": "Homology modelling", + "http://edamontology.org/topic_0176": "Molecular dynamics", + "http://edamontology.org/topic_0177": "Molecular docking", + "http://edamontology.org/topic_0178": "Protein secondary structure prediction", + "http://edamontology.org/topic_0179": "Protein tertiary structure prediction", + "http://edamontology.org/topic_0180": "Protein fold recognition", + "http://edamontology.org/topic_0182": "Sequence alignment", + "http://edamontology.org/topic_0183": "Structure alignment", + "http://edamontology.org/topic_0184": "Threading", + "http://edamontology.org/topic_0188": "Sequence profiles and HMMs", + "http://edamontology.org/topic_0191": "Phylogeny reconstruction", + "http://edamontology.org/topic_0194": "Phylogenomics", + "http://edamontology.org/topic_0195": "Virtual PCR", + "http://edamontology.org/topic_0196": "Sequence assembly", + "http://edamontology.org/topic_0199": "Genetic variation", + "http://edamontology.org/topic_0200": "Microarrays", + "http://edamontology.org/topic_0202": "Pharmacology", + "http://edamontology.org/topic_0203": "Gene expression", + "http://edamontology.org/topic_0204": "Gene regulation", + "http://edamontology.org/topic_0208": "Pharmacogenomics", + "http://edamontology.org/topic_0209": "Medicinal chemistry", + "http://edamontology.org/topic_0210": "Fish", + "http://edamontology.org/topic_0211": "Flies", + "http://edamontology.org/topic_0213": "Mice or rats", + "http://edamontology.org/topic_0215": "Worms", + "http://edamontology.org/topic_0217": "Literature analysis", + "http://edamontology.org/topic_0218": "Natural language processing", + "http://edamontology.org/topic_0219": "Data submission, annotation and curation", + "http://edamontology.org/topic_0220": "Document, record and content management", + "http://edamontology.org/topic_0221": "Sequence annotation", + "http://edamontology.org/topic_0222": "Genome annotation", + "http://edamontology.org/topic_0593": "NMR", + "http://edamontology.org/topic_0594": "Sequence classification", + "http://edamontology.org/topic_0595": "Protein classification", + "http://edamontology.org/topic_0598": "Sequence motif or profile", + "http://edamontology.org/topic_0601": "Protein modifications", + "http://edamontology.org/topic_0602": "Molecular interactions, pathways and networks", + "http://edamontology.org/topic_0605": "Informatics", + "http://edamontology.org/topic_0606": "Literature data resources", + "http://edamontology.org/topic_0607": "Laboratory information management", + "http://edamontology.org/topic_0608": "Cell and tissue culture", + "http://edamontology.org/topic_0610": "Ecology", + "http://edamontology.org/topic_0611": "Electron microscopy", + "http://edamontology.org/topic_0612": "Cell cycle", + "http://edamontology.org/topic_0613": "Peptides and amino acids", + "http://edamontology.org/topic_0616": "Organelles", + "http://edamontology.org/topic_0617": "Ribosomes", + "http://edamontology.org/topic_0618": "Scents", + "http://edamontology.org/topic_0620": "Drugs and target structures", + "http://edamontology.org/topic_0621": "Model organisms", + "http://edamontology.org/topic_0622": "Genomics", + "http://edamontology.org/topic_0623": "Gene and protein families", + "http://edamontology.org/topic_0624": "Chromosomes", + "http://edamontology.org/topic_0625": "Genotype and phenotype", + "http://edamontology.org/topic_0629": "Gene expression and microarray", + "http://edamontology.org/topic_0632": "Probes and primers", + "http://edamontology.org/topic_0634": "Pathology", + "http://edamontology.org/topic_0635": "Specific protein resources", + "http://edamontology.org/topic_0637": "Taxonomy", + "http://edamontology.org/topic_0639": "Protein sequence analysis", + "http://edamontology.org/topic_0640": "Nucleic acid sequence analysis", + "http://edamontology.org/topic_0641": "Repeat sequences", + "http://edamontology.org/topic_0642": "Low complexity sequences", + "http://edamontology.org/topic_0644": "Proteome", + "http://edamontology.org/topic_0654": "DNA", + "http://edamontology.org/topic_0655": "Coding RNA", + "http://edamontology.org/topic_0659": "Functional, regulatory and non-coding RNA", + "http://edamontology.org/topic_0660": "rRNA", + "http://edamontology.org/topic_0663": "tRNA", + "http://edamontology.org/topic_0694": "Protein secondary structure", + "http://edamontology.org/topic_0697": "RNA structure", + "http://edamontology.org/topic_0698": "Protein tertiary structure", + "http://edamontology.org/topic_0722": "Nucleic acid classification", + "http://edamontology.org/topic_0724": "Protein families", + "http://edamontology.org/topic_0736": "Protein folds and structural domains", + "http://edamontology.org/topic_0740": "Nucleic acid sequence alignment", + "http://edamontology.org/topic_0741": "Protein sequence alignment", + "http://edamontology.org/topic_0747": "Nucleic acid sites and features", + "http://edamontology.org/topic_0748": "Protein sites and features", + "http://edamontology.org/topic_0749": "Transcription factors and regulatory sites", + "http://edamontology.org/topic_0751": "Phosphorylation sites", + "http://edamontology.org/topic_0753": "Metabolic pathways", + "http://edamontology.org/topic_0754": "Signaling pathways", + "http://edamontology.org/topic_0767": "Protein and peptide identification", + "http://edamontology.org/topic_0769": "Workflows", + "http://edamontology.org/topic_0770": "Data types and objects", + "http://edamontology.org/topic_0771": "Theoretical biology", + "http://edamontology.org/topic_0779": "Mitochondria", + "http://edamontology.org/topic_0780": "Plant biology", + "http://edamontology.org/topic_0781": "Virology", + "http://edamontology.org/topic_0782": "Fungi", + "http://edamontology.org/topic_0783": "Pathogens", + "http://edamontology.org/topic_0786": "Arabidopsis", + "http://edamontology.org/topic_0787": "Rice", + "http://edamontology.org/topic_0796": "Genetic mapping and linkage", + "http://edamontology.org/topic_0797": "Comparative genomics", + "http://edamontology.org/topic_0798": "Mobile genetic elements", + "http://edamontology.org/topic_0803": "Human disease", + "http://edamontology.org/topic_0804": "Immunology", + "http://edamontology.org/topic_0820": "Membrane and lipoproteins", + "http://edamontology.org/topic_0821": "Enzymes", + "http://edamontology.org/topic_0922": "Primers", + "http://edamontology.org/topic_1302": "PolyA signal or sites", + "http://edamontology.org/topic_1304": "CpG island and isochores", + "http://edamontology.org/topic_1305": "Restriction sites", + "http://edamontology.org/topic_1307": "Splice sites", + "http://edamontology.org/topic_1308": "Matrix/scaffold attachment sites", + "http://edamontology.org/topic_1311": "Operon", + "http://edamontology.org/topic_1312": "Promoters", + "http://edamontology.org/topic_1317": "Structural biology", + "http://edamontology.org/topic_1456": "Protein membrane regions", + "http://edamontology.org/topic_1770": "Structure comparison", + "http://edamontology.org/topic_1775": "Function analysis", + "http://edamontology.org/topic_1811": "Prokaryotes and Archaea", + "http://edamontology.org/topic_2225": "Protein databases", + "http://edamontology.org/topic_2226": "Structure determination", + "http://edamontology.org/topic_2229": "Cell biology", + "http://edamontology.org/topic_2230": "Classification", + "http://edamontology.org/topic_2232": "Lipoproteins", + "http://edamontology.org/topic_2257": "Phylogeny visualisation", + "http://edamontology.org/topic_2258": "Cheminformatics", + "http://edamontology.org/topic_2259": "Systems biology", + "http://edamontology.org/topic_2269": "Statistics and probability", + "http://edamontology.org/topic_2271": "Structure database search", + "http://edamontology.org/topic_2275": "Molecular modelling", + "http://edamontology.org/topic_2276": "Protein function prediction", + "http://edamontology.org/topic_2277": "SNP", + "http://edamontology.org/topic_2278": "Transmembrane protein prediction", + "http://edamontology.org/topic_2280": "Nucleic acid structure comparison", + "http://edamontology.org/topic_2397": "Exons", + "http://edamontology.org/topic_2399": "Gene transcription", + "http://edamontology.org/topic_2533": "DNA mutation", + "http://edamontology.org/topic_2640": "Oncology", + "http://edamontology.org/topic_2661": "Toxins and targets", + "http://edamontology.org/topic_2754": "Introns", + "http://edamontology.org/topic_2807": "Tool topic", + "http://edamontology.org/topic_2809": "Study topic", + "http://edamontology.org/topic_2811": "Nomenclature", + "http://edamontology.org/topic_2813": "Disease genes and proteins", + "http://edamontology.org/topic_2814": "Protein structure analysis", + "http://edamontology.org/topic_2815": "Human biology", + "http://edamontology.org/topic_2816": "Gene resources", + "http://edamontology.org/topic_2817": "Yeast", + "http://edamontology.org/topic_2818": "Eukaryotes", + "http://edamontology.org/topic_2819": "Invertebrates", + "http://edamontology.org/topic_2820": "Vertebrates", + "http://edamontology.org/topic_2821": "Unicellular eukaryotes", + "http://edamontology.org/topic_2826": "Protein structure alignment", + "http://edamontology.org/topic_2828": "X-ray diffraction", + "http://edamontology.org/topic_2829": "Ontologies, nomenclature and classification", + "http://edamontology.org/topic_2830": "Immunoproteins and antigens", + "http://edamontology.org/topic_2839": "Molecules", + "http://edamontology.org/topic_2840": "Toxicology", + "http://edamontology.org/topic_2842": "High-throughput sequencing", + "http://edamontology.org/topic_2846": "Gene regulatory networks", + "http://edamontology.org/topic_2847": "Disease (specific)", + "http://edamontology.org/topic_2867": "VNTR", + "http://edamontology.org/topic_2868": "Microsatellites", + "http://edamontology.org/topic_2869": "RFLP", + "http://edamontology.org/topic_2885": "DNA polymorphism", + "http://edamontology.org/topic_2953": "Nucleic acid design", + "http://edamontology.org/topic_3032": "Primer or probe design", + "http://edamontology.org/topic_3038": "Structure databases", + "http://edamontology.org/topic_3039": "Nucleic acid structure", + "http://edamontology.org/topic_3041": "Sequence databases", + "http://edamontology.org/topic_3042": "Nucleic acid sequences", + "http://edamontology.org/topic_3043": "Protein sequences", + "http://edamontology.org/topic_3044": "Protein interaction networks", + "http://edamontology.org/topic_3047": "Molecular biology", + "http://edamontology.org/topic_3048": "Mammals", + "http://edamontology.org/topic_3050": "Biodiversity", + "http://edamontology.org/topic_3052": "Sequence clusters and classification", + "http://edamontology.org/topic_3053": "Genetics", + "http://edamontology.org/topic_3055": "Quantitative genetics", + "http://edamontology.org/topic_3056": "Population genetics", + "http://edamontology.org/topic_3060": "Regulatory RNA", + "http://edamontology.org/topic_3061": "Documentation and help", + "http://edamontology.org/topic_3062": "Genetic organisation", + "http://edamontology.org/topic_3063": "Medical informatics", + "http://edamontology.org/topic_3064": "Developmental biology", + "http://edamontology.org/topic_3065": "Embryology", + "http://edamontology.org/topic_3067": "Anatomy", + "http://edamontology.org/topic_3068": "Literature and language", + "http://edamontology.org/topic_3070": "Biology", + "http://edamontology.org/topic_3071": "Biological databases", + "http://edamontology.org/topic_3072": "Sequence feature detection", + "http://edamontology.org/topic_3073": "Nucleic acid feature detection", + "http://edamontology.org/topic_3074": "Protein feature detection", + "http://edamontology.org/topic_3075": "Biological system modelling", + "http://edamontology.org/topic_3077": "Data acquisition", + "http://edamontology.org/topic_3078": "Genes and proteins resources", + "http://edamontology.org/topic_3118": "Protein topological domains", + "http://edamontology.org/topic_3120": "Protein variants", + "http://edamontology.org/topic_3123": "Expression signals", + "http://edamontology.org/topic_3125": "DNA binding sites", + "http://edamontology.org/topic_3126": "Nucleic acid repeats", + "http://edamontology.org/topic_3127": "DNA replication and recombination", + "http://edamontology.org/topic_3135": "Signal or transit peptide", + "http://edamontology.org/topic_3139": "Sequence tagged sites", + "http://edamontology.org/topic_3168": "Sequencing", + "http://edamontology.org/topic_3169": "ChIP-seq", + "http://edamontology.org/topic_3170": "RNA-Seq", + "http://edamontology.org/topic_3171": "DNA methylation", + "http://edamontology.org/topic_3172": "Metabolomics", + "http://edamontology.org/topic_3173": "Epigenomics", + "http://edamontology.org/topic_3174": "Metagenomics", + "http://edamontology.org/topic_3175": "Structural variation", + "http://edamontology.org/topic_3176": "DNA packaging", + "http://edamontology.org/topic_3177": "DNA-Seq", + "http://edamontology.org/topic_3178": "RNA-Seq alignment", + "http://edamontology.org/topic_3179": "ChIP-on-chip", + "http://edamontology.org/topic_3263": "Data security", + "http://edamontology.org/topic_3277": "Sample collections", + "http://edamontology.org/topic_3292": "Biochemistry", + "http://edamontology.org/topic_3293": "Phylogenetics", + "http://edamontology.org/topic_3295": "Epigenetics", + "http://edamontology.org/topic_3297": "Biotechnology", + "http://edamontology.org/topic_3298": "Phenomics", + "http://edamontology.org/topic_3299": "Evolutionary biology", + "http://edamontology.org/topic_3300": "Physiology", + "http://edamontology.org/topic_3301": "Microbiology", + "http://edamontology.org/topic_3302": "Parasitology", + "http://edamontology.org/topic_3303": "Medicine", + "http://edamontology.org/topic_3304": "Neurobiology", + "http://edamontology.org/topic_3305": "Public health and epidemiology", + "http://edamontology.org/topic_3306": "Biophysics", + "http://edamontology.org/topic_3307": "Computational biology", + "http://edamontology.org/topic_3308": "Transcriptomics", + "http://edamontology.org/topic_3314": "Chemistry", + "http://edamontology.org/topic_3315": "Mathematics", + "http://edamontology.org/topic_3316": "Computer science", + "http://edamontology.org/topic_3318": "Physics", + "http://edamontology.org/topic_3320": "RNA splicing", + "http://edamontology.org/topic_3321": "Molecular genetics", + "http://edamontology.org/topic_3322": "Respiratory medicine", + "http://edamontology.org/topic_3323": "Metabolic disease", + "http://edamontology.org/topic_3324": "Infectious disease", + "http://edamontology.org/topic_3325": "Rare diseases", + "http://edamontology.org/topic_3332": "Computational chemistry", + "http://edamontology.org/topic_3334": "Neurology", + "http://edamontology.org/topic_3335": "Cardiology", + "http://edamontology.org/topic_3336": "Drug discovery", + "http://edamontology.org/topic_3337": "Biobank", + "http://edamontology.org/topic_3338": "Mouse clinic", + "http://edamontology.org/topic_3339": "Microbial collection", + "http://edamontology.org/topic_3340": "Cell culture collection", + "http://edamontology.org/topic_3341": "Clone library", + "http://edamontology.org/topic_3342": "Translational medicine", + "http://edamontology.org/topic_3343": "Compound libraries and screening", + "http://edamontology.org/topic_3344": "Biomedical science", + "http://edamontology.org/topic_3345": "Data identity and mapping", + "http://edamontology.org/topic_3346": "Sequence search", + "http://edamontology.org/topic_3360": "Biomarkers", + "http://edamontology.org/topic_3361": "Laboratory techniques", + "http://edamontology.org/topic_3365": "Data architecture, analysis and design", + "http://edamontology.org/topic_3366": "Data integration and warehousing", + "http://edamontology.org/topic_3368": "Biomaterials", + "http://edamontology.org/topic_3369": "Chemical biology", + "http://edamontology.org/topic_3370": "Analytical chemistry", + "http://edamontology.org/topic_3371": "Synthetic chemistry", + "http://edamontology.org/topic_3372": "Software engineering", + "http://edamontology.org/topic_3373": "Drug development", + "http://edamontology.org/topic_3374": "Biotherapeutics", + "http://edamontology.org/topic_3375": "Drug metabolism", + "http://edamontology.org/topic_3376": "Medicines research and development", + "http://edamontology.org/topic_3377": "Safety sciences", + "http://edamontology.org/topic_3378": "Pharmacovigilance", + "http://edamontology.org/topic_3379": "Preclinical and clinical studies", + "http://edamontology.org/topic_3382": "Imaging", + "http://edamontology.org/topic_3383": "Bioimaging", + "http://edamontology.org/topic_3384": "Medical imaging", + "http://edamontology.org/topic_3385": "Light microscopy", + "http://edamontology.org/topic_3386": "Laboratory animal science", + "http://edamontology.org/topic_3387": "Marine biology", + "http://edamontology.org/topic_3388": "Molecular medicine", + "http://edamontology.org/topic_3390": "Nutritional science", + "http://edamontology.org/topic_3391": "Omics", + "http://edamontology.org/topic_3393": "Quality affairs", + "http://edamontology.org/topic_3394": "Regulatory affairs", + "http://edamontology.org/topic_3395": "Regenerative medicine", + "http://edamontology.org/topic_3396": "Systems medicine", + "http://edamontology.org/topic_3397": "Veterinary medicine", + "http://edamontology.org/topic_3398": "Bioengineering", + "http://edamontology.org/topic_3399": "Geriatric medicine", + "http://edamontology.org/topic_3400": "Allergy, clinical immunology and immunotherapeutics", + "http://edamontology.org/topic_3401": "Pain medicine", + "http://edamontology.org/topic_3402": "Anaesthesiology", + "http://edamontology.org/topic_3403": "Critical care medicine", + "http://edamontology.org/topic_3404": "Dermatology", + "http://edamontology.org/topic_3405": "Dentistry", + "http://edamontology.org/topic_3406": "Ear, nose and throat medicine", + "http://edamontology.org/topic_3407": "Endocrinology and metabolism", + "http://edamontology.org/topic_3408": "Haematology", + "http://edamontology.org/topic_3409": "Gastroenterology", + "http://edamontology.org/topic_3410": "Gender medicine", + "http://edamontology.org/topic_3411": "Gynaecology and obstetrics", + "http://edamontology.org/topic_3412": "Hepatic and biliary medicine", + "http://edamontology.org/topic_3413": "Infectious tropical disease", + "http://edamontology.org/topic_3414": "Trauma medicine", + "http://edamontology.org/topic_3415": "Medical toxicology", + "http://edamontology.org/topic_3416": "Musculoskeletal medicine", + "http://edamontology.org/topic_3417": "Opthalmology", + "http://edamontology.org/topic_3418": "Paediatrics", + "http://edamontology.org/topic_3419": "Psychiatry", + "http://edamontology.org/topic_3420": "Reproductive health", + "http://edamontology.org/topic_3421": "Surgery", + "http://edamontology.org/topic_3422": "Urology and nephrology", + "http://edamontology.org/topic_3423": "Complementary medicine", + "http://edamontology.org/topic_3444": "MRI", + "http://edamontology.org/topic_3448": "Neutron diffraction", + "http://edamontology.org/topic_3452": "Tomography", + "http://edamontology.org/topic_3473": "Data mining", + "http://edamontology.org/topic_3474": "Machine learning", + "http://edamontology.org/topic_3489": "Database management", + "http://edamontology.org/topic_3500": "Zoology", + "http://edamontology.org/topic_3510": "Protein sites, features and motifs", + "http://edamontology.org/topic_3511": "Nucleic acid sites, features and motifs", + "http://edamontology.org/topic_3512": "Gene transcripts", + "http://edamontology.org/topic_3514": "Protein-ligand interactions", + "http://edamontology.org/topic_3515": "Protein-drug interactions", + "http://edamontology.org/topic_3516": "Genotyping experiment", + "http://edamontology.org/topic_3517": "GWAS study", + "http://edamontology.org/topic_3518": "Microarray experiment", + "http://edamontology.org/topic_3519": "PCR experiment", + "http://edamontology.org/topic_3520": "Proteomics experiment", + "http://edamontology.org/topic_3521": "2D PAGE experiment", + "http://edamontology.org/topic_3522": "Northern blot experiment", + "http://edamontology.org/topic_3523": "RNAi experiment", + "http://edamontology.org/topic_3524": "Simulation experiment", + "http://edamontology.org/topic_3525": "Protein-nucleic acid interactions", + "http://edamontology.org/topic_3526": "Protein-protein interactions", + "http://edamontology.org/topic_3527": "Cellular process pathways", + "http://edamontology.org/topic_3528": "Disease pathways", + "http://edamontology.org/topic_3529": "Environmental information processing pathways", + "http://edamontology.org/topic_3530": "Genetic information processing pathways", + "http://edamontology.org/topic_3531": "Protein super-secondary structure", + "http://edamontology.org/topic_3533": "Protein active sites", + "http://edamontology.org/topic_3534": "Protein binding sites", + "http://edamontology.org/topic_3535": "Protein-nucleic acid binding sites", + "http://edamontology.org/topic_3536": "Protein cleavage sites", + "http://edamontology.org/topic_3537": "Protein chemical modifications", + "http://edamontology.org/topic_3538": "Protein disordered structure", + "http://edamontology.org/topic_3539": "Protein domains", + "http://edamontology.org/topic_3540": "Protein key folding sites", + "http://edamontology.org/topic_3541": "Protein post-translational modifications", + "http://edamontology.org/topic_3542": "Protein secondary structure", + "http://edamontology.org/topic_3543": "Protein sequence repeats", + "http://edamontology.org/topic_3544": "Protein signal peptides", + "http://edamontology.org/topic_3569": "Applied mathematics", + "http://edamontology.org/topic_3570": "Pure mathematics", + "http://edamontology.org/topic_3571": "Data governance", + "http://edamontology.org/topic_3572": "Data quality management", + "http://edamontology.org/topic_3573": "Freshwater biology", + "http://edamontology.org/topic_3574": "Human genetics", + "http://edamontology.org/topic_3575": "Tropical medicine", + "http://edamontology.org/topic_3576": "Medical biotechnology", + "http://edamontology.org/topic_3577": "Personalised medicine", + "http://edamontology.org/topic_3656": "Immunoprecipitation experiment", + "http://edamontology.org/topic_3673": "Whole genome sequencing", + "http://edamontology.org/topic_3674": "Methylated DNA immunoprecipitation", + "http://edamontology.org/topic_3676": "Exome sequencing", + "http://edamontology.org/topic_3678": "Experimental design and studies", + "http://edamontology.org/topic_3679": "Animal study", + "http://edamontology.org/topic_3697": "Microbial ecology", + "http://edamontology.org/topic_3794": "RNA immunoprecipitation", + "http://edamontology.org/topic_3796": "Population genomics", + "http://edamontology.org/topic_3810": "Agricultural science", + "http://edamontology.org/topic_3837": "Metagenomic sequencing", + "http://edamontology.org/topic_3855": "Environmental science", + "http://edamontology.org/topic_3892": "Biomolecular simulation", + "http://edamontology.org/topic_3895": "Synthetic biology", + "http://edamontology.org/topic_3912": "Genetic engineering", + "http://edamontology.org/topic_3922": "Proteogenomics", + "http://edamontology.org/topic_3930": "Immunogenetics", + "http://edamontology.org/topic_3934": "Cytometry", + "http://edamontology.org/topic_3940": "Chromosome conformation capture", + "http://edamontology.org/topic_3941": "Metatranscriptomics", + "http://edamontology.org/topic_3943": "Paleogenomics", + "http://edamontology.org/topic_3944": "Cladistics", + "http://edamontology.org/topic_3945": "Molecular evolution", + "http://edamontology.org/topic_3948": "Immunoinformatics", + "http://edamontology.org/topic_3954": "Echography", + "http://edamontology.org/topic_3955": "Fluxomics", + "http://edamontology.org/topic_3957": "Protein interaction experiment", + "http://edamontology.org/topic_3958": "Copy number variation", + "http://edamontology.org/topic_3959": "Cytogenetics", + "http://edamontology.org/topic_3966": "Vaccinology", + "http://edamontology.org/topic_3967": "Immunomics", + "http://edamontology.org/topic_3974": "Epistasis", + "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass": "Obsolete concept (EDAM)" +} \ No newline at end of file diff --git a/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java index 7691eb4..6178d57 100644 --- a/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java +++ b/src/test/java/nl/esciencecenter/restape/EdamLabelsTest.java @@ -12,9 +12,9 @@ /** * Verifikation der O(1)-URI-Auflösung nach Initialisierung. * - * Das Laden der OWL-Ontologie wird per Reflection umgangen, um die Tests - * netzwerkunabhängig zu halten. Getestet wird die Map-Lookup-Logik und der - * shortForm-Fallback. + * Das Laden von edam_labels.json wird per Reflection umgangen, um die Tests + * von Classpath-Ressourcen unabhängig zu halten. Getestet wird die + * Map-Lookup-Logik und der shortForm-Fallback. */ @SpringBootTest class EdamLabelsTest { @@ -30,7 +30,7 @@ void setUp() throws Exception { )); } - /** Injects a pre-built map to bypass OWL loading. */ + /** Injects a pre-built map to bypass JSON file loading. */ private void injectLabels(Map map) throws Exception { Field field = EdamLabels.class.getDeclaredField("labels"); field.setAccessible(true); From 53640f45401937e51ccc9e61cc0d9a30c0fbbe1f Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Wed, 24 Jun 2026 17:24:37 +0200 Subject: [PATCH 16/18] refactor: remove unnecessary references --- .../nl/esciencecenter/controller/AlternativesController.java | 2 +- src/main/java/nl/esciencecenter/restape/CwlParser.java | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/main/java/nl/esciencecenter/controller/AlternativesController.java b/src/main/java/nl/esciencecenter/controller/AlternativesController.java index c7138f0..1c7d052 100644 --- a/src/main/java/nl/esciencecenter/controller/AlternativesController.java +++ b/src/main/java/nl/esciencecenter/controller/AlternativesController.java @@ -29,7 +29,7 @@ public class AlternativesController { /** * Parses a CWL v1.2 workflow and returns its DAG representation plus - * workflow-level I/O terms for use as APE synthesis constraints (concept §2.3, §3.2). + * workflow-level I/O terms for use as APE synthesis constraints. */ @PostMapping(value = "/parse", consumes = MediaType.MULTIPART_FORM_DATA_VALUE) @Operation( diff --git a/src/main/java/nl/esciencecenter/restape/CwlParser.java b/src/main/java/nl/esciencecenter/restape/CwlParser.java index 144e347..7fe0d22 100644 --- a/src/main/java/nl/esciencecenter/restape/CwlParser.java +++ b/src/main/java/nl/esciencecenter/restape/CwlParser.java @@ -20,8 +20,7 @@ import nl.esciencecenter.controller.dto.ParseResponse; /** - * Transforms a CWL v1.2 Workflow document into the graph-optimised ParseResponse - * following the extraction algorithm defined in concept chapter 3.2. + * Transforms a CWL v1.2 Workflow document into the graph-optimised ParseResponse. */ public class CwlParser { From b0ce21acb5451bb4fbd18e506292254e52c5f3b7 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Mon, 29 Jun 2026 17:44:45 +0200 Subject: [PATCH 17/18] refactor: replace ApeTaxTuple.java with the existing TaxonomyElem.java as suggested in the review --- .../esciencecenter/controller/dto/ApeTaxTuple.java | 14 -------------- .../controller/dto/ParseResponse.java | 10 +++++----- .../controller/dto/TaxonomyElem.java | 8 +++++--- .../java/nl/esciencecenter/restape/CwlParser.java | 12 ++++++------ .../nl/esciencecenter/restape/CwlParserTest.java | 4 ++-- 5 files changed, 18 insertions(+), 30 deletions(-) delete mode 100644 src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java diff --git a/src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java b/src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java deleted file mode 100644 index 19473df..0000000 --- a/src/main/java/nl/esciencecenter/controller/dto/ApeTaxTuple.java +++ /dev/null @@ -1,14 +0,0 @@ -package nl.esciencecenter.controller.dto; - -public class ApeTaxTuple { - private final String id; - private final String label; - - public ApeTaxTuple(String id, String label) { - this.id = id; - this.label = label; - } - - public String getId() { return id; } - public String getLabel() { return label; } -} diff --git a/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java b/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java index 2128ff2..bd8169a 100644 --- a/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java +++ b/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java @@ -5,11 +5,11 @@ public class ParseResponse { private final List nodes; private final List edges; - private final List inputs; - private final List outputs; + private final List inputs; + private final List outputs; public ParseResponse(List nodes, List edges, - List inputs, List outputs) { + List inputs, List outputs) { this.nodes = nodes; this.edges = edges; this.inputs = inputs; @@ -18,6 +18,6 @@ public ParseResponse(List nodes, List edges, public List getNodes() { return nodes; } public List getEdges() { return edges; } - public List getInputs() { return inputs; } - public List getOutputs() { return outputs; } + public List getInputs() { return inputs; } + public List getOutputs() { return outputs; } } diff --git a/src/main/java/nl/esciencecenter/controller/dto/TaxonomyElem.java b/src/main/java/nl/esciencecenter/controller/dto/TaxonomyElem.java index 009cfa7..1521c7b 100644 --- a/src/main/java/nl/esciencecenter/controller/dto/TaxonomyElem.java +++ b/src/main/java/nl/esciencecenter/controller/dto/TaxonomyElem.java @@ -1,16 +1,18 @@ package nl.esciencecenter.controller.dto; +import com.fasterxml.jackson.annotation.JsonInclude; + import lombok.AllArgsConstructor; import lombok.NoArgsConstructor; /** * This class represents a single element of the taxonomy. - * TODO: This class is not used at the moment, but it is a good idea to use it - * in the future. - * + * Used for taxonomy tree responses as well as for the flat input/output EDAM + * terms of a parsed workflow, where only {@code id} and {@code label} are set. */ @NoArgsConstructor @AllArgsConstructor +@JsonInclude(JsonInclude.Include.NON_NULL) public class TaxonomyElem { public String id; public String label; diff --git a/src/main/java/nl/esciencecenter/restape/CwlParser.java b/src/main/java/nl/esciencecenter/restape/CwlParser.java index 7fe0d22..5b5e6e7 100644 --- a/src/main/java/nl/esciencecenter/restape/CwlParser.java +++ b/src/main/java/nl/esciencecenter/restape/CwlParser.java @@ -14,10 +14,10 @@ import org.yaml.snakeyaml.Yaml; import org.yaml.snakeyaml.constructor.SafeConstructor; -import nl.esciencecenter.controller.dto.ApeTaxTuple; import nl.esciencecenter.controller.dto.GraphEdge; import nl.esciencecenter.controller.dto.GraphNode; import nl.esciencecenter.controller.dto.ParseResponse; +import nl.esciencecenter.controller.dto.TaxonomyElem; /** * Transforms a CWL v1.2 Workflow document into the graph-optimised ParseResponse. @@ -124,8 +124,8 @@ public static ParseResponse parse(InputStream inputStream, UnaryOperator edges.add(new GraphEdge(sourceId, outputId))); // Step 4 – EDAM tuples for APE synthesis constraints - List inputs = extractTuples(inputsSection, labelResolver); - List outputs = extractTuples(outputsSection, labelResolver); + List inputs = extractTuples(inputsSection, labelResolver); + List outputs = extractTuples(outputsSection, labelResolver); return new ParseResponse(nodes, edges, inputs, outputs); } @@ -164,14 +164,14 @@ private static String formatLabel(Object entry, String fallbackId, UnaryOperator } @SuppressWarnings("unchecked") - private static List extractTuples(Map section, UnaryOperator resolver) { - List tuples = new ArrayList<>(); + private static List extractTuples(Map section, UnaryOperator resolver) { + List tuples = new ArrayList<>(); if (section == null) return tuples; for (Map.Entry entry : section.entrySet()) { if (!(entry.getValue() instanceof Map def)) continue; String uri = (String) ((Map) def).get("format"); if (uri == null) continue; - tuples.add(new ApeTaxTuple(uri, resolver.apply(uri))); + tuples.add(new TaxonomyElem(uri, resolver.apply(uri), null, null)); } return tuples; } diff --git a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java index 5b7df37..9c61134 100644 --- a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java +++ b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java @@ -67,8 +67,8 @@ void testParseInputOutputTuples() throws Exception { ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); assertEquals(1, result.getInputs().size()); assertEquals(1, result.getOutputs().size()); - assertEquals("http://edamontology.org/format_3728", result.getInputs().get(0).getId()); - assertEquals("http://edamontology.org/format_3244", result.getOutputs().get(0).getId()); + assertEquals("http://edamontology.org/format_3728", result.getInputs().get(0).id); + assertEquals("http://edamontology.org/format_3244", result.getOutputs().get(0).id); } // ── Robustheit ─────────────────────────────────────────────────────────── From 1ad50ecc4a34d4c80fbd17ea846fe7bae6123856 Mon Sep 17 00:00:00 2001 From: Aaron Strachardt Date: Mon, 29 Jun 2026 18:00:11 +0200 Subject: [PATCH 18/18] refactor: Use @Getter/@AllArgsConstructor on GraphEdge.java, GraphNode.java and ParseResponse.java and replace GraphNode's string type with a enum, as suggested in review. --- .../controller/dto/GraphEdge.java | 13 +++++------ .../controller/dto/GraphNode.java | 22 +++++++++++-------- .../controller/dto/ParseResponse.java | 18 +++++---------- .../nl/esciencecenter/restape/CwlParser.java | 6 ++--- .../esciencecenter/restape/CwlParserTest.java | 7 +++--- 5 files changed, 30 insertions(+), 36 deletions(-) diff --git a/src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java b/src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java index 251f158..c177f8d 100644 --- a/src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java +++ b/src/main/java/nl/esciencecenter/controller/dto/GraphEdge.java @@ -1,14 +1,11 @@ package nl.esciencecenter.controller.dto; +import lombok.AllArgsConstructor; +import lombok.Getter; + +@Getter +@AllArgsConstructor public class GraphEdge { private final String source; private final String target; - - public GraphEdge(String source, String target) { - this.source = source; - this.target = target; - } - - public String getSource() { return source; } - public String getTarget() { return target; } } diff --git a/src/main/java/nl/esciencecenter/controller/dto/GraphNode.java b/src/main/java/nl/esciencecenter/controller/dto/GraphNode.java index a632d4f..a826440 100644 --- a/src/main/java/nl/esciencecenter/controller/dto/GraphNode.java +++ b/src/main/java/nl/esciencecenter/controller/dto/GraphNode.java @@ -1,17 +1,21 @@ package nl.esciencecenter.controller.dto; +import lombok.AllArgsConstructor; +import lombok.Getter; + +@Getter +@AllArgsConstructor public class GraphNode { private final String id; private final String label; - private final String type; // "tool" | "input" | "output" + private final NodeType type; - public GraphNode(String id, String label, String type) { - this.id = id; - this.label = label; - this.type = type; + /** + * Kind of node in the workflow graph. Constants are lowercase so Jackson + * serialises them as {@code "input"}/{@code "tool"}/{@code "output"} for the + * frontend (matching the existing {@code ImageFormat} enum convention). + */ + public enum NodeType { + input, tool, output } - - public String getId() { return id; } - public String getLabel() { return label; } - public String getType() { return type; } } diff --git a/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java b/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java index bd8169a..7f05eef 100644 --- a/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java +++ b/src/main/java/nl/esciencecenter/controller/dto/ParseResponse.java @@ -2,22 +2,14 @@ import java.util.List; +import lombok.AllArgsConstructor; +import lombok.Getter; + +@Getter +@AllArgsConstructor public class ParseResponse { private final List nodes; private final List edges; private final List inputs; private final List outputs; - - public ParseResponse(List nodes, List edges, - List inputs, List outputs) { - this.nodes = nodes; - this.edges = edges; - this.inputs = inputs; - this.outputs = outputs; - } - - public List getNodes() { return nodes; } - public List getEdges() { return edges; } - public List getInputs() { return inputs; } - public List getOutputs() { return outputs; } } diff --git a/src/main/java/nl/esciencecenter/restape/CwlParser.java b/src/main/java/nl/esciencecenter/restape/CwlParser.java index 5b5e6e7..8afebd2 100644 --- a/src/main/java/nl/esciencecenter/restape/CwlParser.java +++ b/src/main/java/nl/esciencecenter/restape/CwlParser.java @@ -67,7 +67,7 @@ public static ParseResponse parse(InputStream inputStream, UnaryOperator for (Map.Entry entry : inputsSection.entrySet()) { String id = entry.getKey(); String label = formatLabel(entry.getValue(), id, labelResolver); - nodes.add(new GraphNode(id, label, "input")); + nodes.add(new GraphNode(id, label, GraphNode.NodeType.input)); inputIds.add(id); } } @@ -75,7 +75,7 @@ public static ParseResponse parse(InputStream inputStream, UnaryOperator // Step 2b – Tool nodes Set stepIds = stepsSection.keySet(); for (String stepId : stepIds) { - nodes.add(new GraphNode(stepId, toolLabel(stepId), "tool")); + nodes.add(new GraphNode(stepId, toolLabel(stepId), GraphNode.NodeType.tool)); } // Step 2c – Output nodes + remember which step feeds each output @@ -84,7 +84,7 @@ public static ParseResponse parse(InputStream inputStream, UnaryOperator for (Map.Entry entry : outputsSection.entrySet()) { String id = entry.getKey(); String label = formatLabel(entry.getValue(), id, labelResolver); - nodes.add(new GraphNode(id, label, "output")); + nodes.add(new GraphNode(id, label, GraphNode.NodeType.output)); if (entry.getValue() instanceof Map def) { String src = (String) ((Map) def).get("outputSource"); diff --git a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java index 9c61134..e1e72d6 100644 --- a/src/test/java/nl/esciencecenter/restape/CwlParserTest.java +++ b/src/test/java/nl/esciencecenter/restape/CwlParserTest.java @@ -1,5 +1,6 @@ package nl.esciencecenter.restape; +import nl.esciencecenter.controller.dto.GraphNode; import nl.esciencecenter.controller.dto.ParseResponse; import org.junit.jupiter.api.Test; import org.springframework.boot.test.context.SpringBootTest; @@ -37,11 +38,11 @@ void testParseCorrectNodeCount() throws Exception { void testParseToolLabelsNoSuffix() throws Exception { ParseResponse result = CwlParser.parse(fixture("test_workflow.cwl"), IDENTITY); long toolCount = result.getNodes().stream() - .filter(n -> "tool".equals(n.getType())) + .filter(n -> n.getType() == GraphNode.NodeType.tool) .count(); assertEquals(3, toolCount); result.getNodes().stream() - .filter(n -> "tool".equals(n.getType())) + .filter(n -> n.getType() == GraphNode.NodeType.tool) .forEach(n -> assertFalse(n.getLabel().matches(".*_\\d+$"), "Tool label should not contain APE suffix: " + n.getLabel())); } @@ -114,7 +115,7 @@ void testParseMissingEdamAnnotations() throws Exception { out: [output_1] """; ParseResponse result = CwlParser.parse(cwl(doc), IDENTITY); - assertEquals(1, result.getNodes().stream().filter(n -> "tool".equals(n.getType())).count()); + assertEquals(1, result.getNodes().stream().filter(n -> n.getType() == GraphNode.NodeType.tool).count()); assertTrue(result.getInputs().isEmpty(), "No EDAM tuples without format annotations"); }