Drop the vacuous GO annotations, upgrade the ones that meant something (#182)

docs/communities/AMD_Acidophile_Heterotroph_Network.html

@@ -841,8 +841,8 @@ <h3>Organic Carbon Scavenging and Remineralization</h3>
 
                     <li>
                         nitrogen compound metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071941"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071941</a>)
                     </li>
 
                 </ul>

docs/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.html

@@ -604,8 +604,8 @@ <h3>DNRA Competes with Anammox for Nitrogen Removal</h3>
 
                     <li>
                         nitrogen compound metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071941"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071941</a>)
                     </li>
 
                 </ul>

docs/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.html

@@ -667,8 +667,8 @@ <h3>Non-Sulfate Seawater Ions Drive Community And Emission Responses</h3>
 
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0009056"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0009056</a>)
                     </li>
 
                 </ul>
@@ -813,8 +813,8 @@ <h3>Artificial Seawater Alters Carbon Nitrogen And Phosphorus Gene Response</h3>
 
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0009056"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0009056</a>)
                     </li>
 
                 </ul>

docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html

@@ -751,17 +751,6 @@ <h3>Methylotrophic Formaldehyde Mitigation</h3>
 
 
 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
-                </ul>
-
 
 
 
@@ -1307,10 +1296,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var processes = [];
 
-
-            processes.push("metabolic process");
-
-
             var evidenceCount = 1;
 
             nodes.push({

docs/communities/ORNL_PMI_Populus_PD10_SynCom.html

@@ -918,12 +918,6 @@ <h3>Medium-Dependent Cross-Feeding</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1028,12 +1022,6 @@ <h3>Metabolite Exchange with Pantoea</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1086,12 +1074,6 @@ <h3>Cross-Feeding with Rhizobium</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1144,12 +1126,6 @@ <h3>Cross-Feeding with Bacillus</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1202,12 +1178,6 @@ <h3>Cross-Feeding with Caulobacter</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1260,12 +1230,6 @@ <h3>Cross-Feeding with Duganella</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1318,12 +1282,6 @@ <h3>Cross-Feeding with Streptomyces</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1376,12 +1334,6 @@ <h3>Cross-Feeding with Paraburkholderia</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
 
-                    <li>
-                        metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
-                    </li>
-
                 </ul>
 
 
@@ -1780,8 +1732,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 
@@ -1858,8 +1808,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 
@@ -1898,8 +1846,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 
@@ -1938,8 +1884,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 
@@ -1978,8 +1922,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 
@@ -2018,8 +1960,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 
@@ -2058,8 +1998,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 
@@ -2098,8 +2036,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             processes.push("interspecies interaction between organisms");
 
-            processes.push("metabolic process");
-
 
             var evidenceCount = 1;
 

docs/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.html

@@ -730,8 +730,8 @@ <h3>Diverse Sulfate-Reduction Guild</h3>
 
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0009056"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0009056</a>)
                     </li>
 
                 </ul>

docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html

@@ -766,8 +766,8 @@ <h3>Bacterial Anaerobic Methylotrophy</h3>
 
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0009056"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0009056</a>)
                     </li>
 
                 </ul>

docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html

@@ -853,8 +853,8 @@ <h3>Lactate-Sulfate Carbon And Sulfur Subnetwork</h3>
 
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0009056"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0009056</a>)
                     </li>
 
                 </ul>

kb/communities/AMD_Acidophile_Heterotroph_Network.yaml

@@ -344,8 +344,8 @@ ecological_interactions:
       label: aerobic respiration
   - preferred_term: nitrogen compound metabolic process
     term:
-      id: GO:0008152
-      label: metabolic process
+      id: GO:0071941
+      label: nitrogen cycle metabolic process
   evidence:
   - reference: doi:10.3389/fmicb.2015.00475
     supports: SUPPORT

kb/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.yaml

@@ -164,8 +164,8 @@ ecological_interactions:
   biological_processes:
   - preferred_term: nitrogen compound metabolic process
     term:
-      id: GO:0008152
-      label: metabolic process
+      id: GO:0071941
+      label: nitrogen cycle metabolic process
   evidence:
   - reference: PMID:31980038
     supports: SUPPORT

kb/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.yaml

@@ -129,8 +129,8 @@ ecological_interactions:
       label: methanogenesis
   - preferred_term: organic substance catabolic process
     term:
-      id: GO:0008152
-      label: metabolic process
+      id: GO:0009056
+      label: catabolic process
   evidence:
   - reference: PMID:38628812
     supports: SUPPORT
@@ -198,8 +198,8 @@ ecological_interactions:
   biological_processes:
   - preferred_term: organic substance catabolic process
     term:
-      id: GO:0008152
-      label: metabolic process
+      id: GO:0009056
+      label: catabolic process
   evidence:
   - reference: PMID:38628812
     supports: SUPPORT

kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml

@@ -236,10 +236,6 @@ ecological_interactions:
       id: CHEBI:16842
       label: formaldehyde
   biological_processes:
-  - preferred_term: metabolic process
-    term:
-      id: GO:0008152
-      label: metabolic process
   evidence:
   - reference: doi:10.3390/microorganisms9020321
     supports: SUPPORT