Add xrefs to new RO chemical relations

biopragmatics · Jan 4, 2024 · 6f361e5 · 6f361e5
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diff --git a/docs/0000010/index.html b/docs/0000010/index.html
@@ -56,6 +56,8 @@ <h5 class="card-header">
 
                     <dt><span class="badge badge-primary">Xref</span> Open Biological and Biomedical Ontologies</dt>
                     <dt><a href="https://bioregistry.io/obo:chebi#is_conjugate_base_of"><code>obo:chebi#is_conjugate_base_of</code></a></dt>
+                    <dt><span class="badge badge-primary">Xref</span> Relation Ontology</dt>
+                    <dt><a href="https://bioregistry.io/ro:0018033"><code>ro:0018033</code></a></dt>
 
             </dl>
         </div>

diff --git a/docs/0000011/index.html b/docs/0000011/index.html
@@ -56,6 +56,8 @@ <h5 class="card-header">
 
                     <dt><span class="badge badge-primary">Xref</span> Open Biological and Biomedical Ontologies</dt>
                     <dt><a href="https://bioregistry.io/obo:chebi#is_conjugate_acid_of"><code>obo:chebi#is_conjugate_acid_of</code></a></dt>
+                    <dt><span class="badge badge-primary">Xref</span> Relation Ontology</dt>
+                    <dt><a href="https://bioregistry.io/ro:0018034"><code>ro:0018034</code></a></dt>
 
             </dl>
         </div>

diff --git a/docs/0000012/index.html b/docs/0000012/index.html
@@ -56,6 +56,8 @@ <h5 class="card-header">
 
                     <dt><span class="badge badge-primary">Xref</span> Open Biological and Biomedical Ontologies</dt>
                     <dt><a href="https://bioregistry.io/obo:chebi#is_enantiomer_of"><code>obo:chebi#is_enantiomer_of</code></a></dt>
+                    <dt><span class="badge badge-primary">Xref</span> Relation Ontology</dt>
+                    <dt><a href="https://bioregistry.io/ro:0018039"><code>ro:0018039</code></a></dt>
 
             </dl>
         </div>

diff --git a/docs/0000013/index.html b/docs/0000013/index.html
@@ -56,6 +56,8 @@ <h5 class="card-header">
 
                     <dt><span class="badge badge-primary">Xref</span> Open Biological and Biomedical Ontologies</dt>
                     <dt><a href="https://bioregistry.io/obo:chebi#is_tautomer_of"><code>obo:chebi#is_tautomer_of</code></a></dt>
+                    <dt><span class="badge badge-primary">Xref</span> Relation Ontology</dt>
+                    <dt><a href="https://bioregistry.io/ro:0018036"><code>ro:0018036</code></a></dt>
 
             </dl>
         </div>

diff --git a/docs/0000014/index.html b/docs/0000014/index.html
@@ -56,6 +56,8 @@ <h5 class="card-header">
 
                     <dt><span class="badge badge-primary">Xref</span> Open Biological and Biomedical Ontologies</dt>
                     <dt><a href="https://bioregistry.io/obo:chebi#has_parent_hydride"><code>obo:chebi#has_parent_hydride</code></a></dt>
+                    <dt><span class="badge badge-primary">Xref</span> Relation Ontology</dt>
+                    <dt><a href="https://bioregistry.io/ro:0018040"><code>ro:0018040</code></a></dt>
 
             </dl>
         </div>

diff --git a/docs/0000015/index.html b/docs/0000015/index.html
@@ -56,6 +56,8 @@ <h5 class="card-header">
 
                     <dt><span class="badge badge-primary">Xref</span> Open Biological and Biomedical Ontologies</dt>
                     <dt><a href="https://bioregistry.io/obo:chebi#has_functional_parent"><code>obo:chebi#has_functional_parent</code></a></dt>
+                    <dt><span class="badge badge-primary">Xref</span> Relation Ontology</dt>
+                    <dt><a href="https://bioregistry.io/ro:0000015"><code>ro:0000015</code></a></dt>
 
             </dl>
         </div>

diff --git a/releases/current/debio.json b/releases/current/debio.json
@@ -13,7 +13,7 @@
         "val" : "bio2obo:debio"
       }, {
         "pred" : "http://www.geneontology.org/formats/oboInOwl#date",
-        "val" : "13:12:2023 15:32"
+        "val" : "04:01:2024 15:37"
       }, {
         "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
         "val" : "1.2"
@@ -25,201 +25,213 @@
       "lbl" : "definition",
       "type" : "PROPERTY"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000001",
-      "lbl" : "gene product is a member of",
+      "id" : "http://purl.obolibrary.org/obo/RO_0000015",
+      "lbl" : "has functional parent",
       "type" : "PROPERTY",
       "meta" : {
+        "definition" : {
+          "val" : "X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil"
+        },
+        "xrefs" : [ {
+          "val" : "RO:0000015"
+        }, {
+          "val" : "obo:chebi#has_functional_parent"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000002",
-      "lbl" : "has mature miRNA",
+      "id" : "http://purl.obolibrary.org/obo/RO_0018033",
+      "lbl" : "is conjugate base of",
       "type" : "PROPERTY",
       "meta" : {
+        "definition" : {
+          "val" : "X is conjugate base of Y typically means that X is a deprotonated form of Y"
+        },
+        "xrefs" : [ {
+          "val" : "RO:0018033"
+        }, {
+          "val" : "obo:chebi#is_conjugate_base_of"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000003",
-      "lbl" : "species specific",
+      "id" : "http://purl.obolibrary.org/obo/RO_0018034",
+      "lbl" : "is conjugate acid of",
       "type" : "PROPERTY",
       "meta" : {
         "definition" : {
-          "val" : "X speciesSpecific Y means that Y is a general phenomena, like a pathway, and X is the version that appears in a species. X should state which species with RO:0002162 (in taxon)"
+          "val" : "X is conjugate acid of Y typically means that Y is a protonated form of X"
         },
+        "xrefs" : [ {
+          "val" : "RO:0018034"
+        }, {
+          "val" : "obo:chebi#is_conjugate_acid_of"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000004",
-      "lbl" : "Antibody has target",
+      "id" : "http://purl.obolibrary.org/obo/RO_0018036",
+      "lbl" : "is tautomer of",
       "type" : "PROPERTY",
       "meta" : {
+        "definition" : {
+          "val" : "X and Y are tautomers if they are different realizations of the resonance structure of the same molecule"
+        },
+        "xrefs" : [ {
+          "val" : "RO:0018036"
+        }, {
+          "val" : "obo:chebi#is_tautomer_of"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000005",
-      "lbl" : "locus group",
+      "id" : "http://purl.obolibrary.org/obo/RO_0018039",
+      "lbl" : "is enantiomer of",
       "type" : "PROPERTY",
       "meta" : {
+        "definition" : {
+          "val" : "X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y"
+        },
+        "xrefs" : [ {
+          "val" : "RO:0018039"
+        }, {
+          "val" : "obo:chebi#is_enantiomer_of"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag",
-          "val" : "true"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000006",
-      "lbl" : "has salt",
+      "id" : "http://purl.obolibrary.org/obo/RO_0018040",
+      "lbl" : "has parent hydride",
       "type" : "PROPERTY",
       "meta" : {
+        "definition" : {
+          "val" : "X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3"
+        },
+        "xrefs" : [ {
+          "val" : "RO:0018040"
+        }, {
+          "val" : "obo:chebi#has_parent_hydride"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000007",
-      "lbl" : "has left-to-right reaction",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000001",
+      "lbl" : "gene product is a member of",
       "type" : "PROPERTY",
       "meta" : {
-        "definition" : {
-          "val" : "X ltr Y means reaction X of undetermined direction has a left-to-right reaction Y. Relevant for Rhea."
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000008",
-      "lbl" : "has right-to-left reaction",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000002",
+      "lbl" : "has mature miRNA",
       "type" : "PROPERTY",
       "meta" : {
-        "definition" : {
-          "val" : "X rtl Y means reaction X of undetermined direction has a right-to-left reaction Y. Relevant for Rhea."
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000009",
-      "lbl" : "has bi-directional reaction",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000003",
+      "lbl" : "species specific",
       "type" : "PROPERTY",
       "meta" : {
         "definition" : {
-          "val" : "X bi Y means reaction X of undetermined direction has a bidirectional reaction Y. Relevant for Rhea."
+          "val" : "X speciesSpecific Y means that Y is a general phenomena, like a pathway, and X is the version that appears in a species. X should state which species with RO:0002162 (in taxon)"
         },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000010",
-      "lbl" : "is conjugate base of",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000004",
+      "lbl" : "Antibody has target",
       "type" : "PROPERTY",
       "meta" : {
-        "definition" : {
-          "val" : "X is conjugate base of Y typically means that X is a deprotonated form of Y"
-        },
-        "xrefs" : [ {
-          "val" : "obo:chebi#is_conjugate_base_of"
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000011",
-      "lbl" : "is conjugate acid of",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000005",
+      "lbl" : "locus group",
       "type" : "PROPERTY",
       "meta" : {
-        "definition" : {
-          "val" : "X is conjugate acid of Y typically means that Y is a protonated form of X"
-        },
-        "xrefs" : [ {
-          "val" : "obo:chebi#is_conjugate_acid_of"
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag",
+          "val" : "true"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000012",
-      "lbl" : "is enantiomer of",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000006",
+      "lbl" : "has salt",
       "type" : "PROPERTY",
       "meta" : {
-        "definition" : {
-          "val" : "X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y"
-        },
-        "xrefs" : [ {
-          "val" : "obo:chebi#is_enantiomer_of"
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000013",
-      "lbl" : "is tautomer of",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000007",
+      "lbl" : "has left-to-right reaction",
       "type" : "PROPERTY",
       "meta" : {
         "definition" : {
-          "val" : "X and Y are tautomers if they are different realizations of the resonance structure of the same molecule"
+          "val" : "X ltr Y means reaction X of undetermined direction has a left-to-right reaction Y. Relevant for Rhea."
         },
-        "xrefs" : [ {
-          "val" : "obo:chebi#is_tautomer_of"
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000014",
-      "lbl" : "has parent hydride",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000008",
+      "lbl" : "has right-to-left reaction",
       "type" : "PROPERTY",
       "meta" : {
         "definition" : {
-          "val" : "X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3"
+          "val" : "X rtl Y means reaction X of undetermined direction has a right-to-left reaction Y. Relevant for Rhea."
         },
-        "xrefs" : [ {
-          "val" : "obo:chebi#has_parent_hydride"
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"
         } ]
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/debio_0000015",
-      "lbl" : "has functional parent",
+      "id" : "http://purl.obolibrary.org/obo/debio_0000009",
+      "lbl" : "has bi-directional reaction",
       "type" : "PROPERTY",
       "meta" : {
         "definition" : {
-          "val" : "X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil"
+          "val" : "X bi Y means reaction X of undetermined direction has a bidirectional reaction Y. Relevant for Rhea."
         },
-        "xrefs" : [ {
-          "val" : "obo:chebi#has_functional_parent"
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "orcid:0000-0003-4423-4370"