Add Rhea to GO relation and some other domain/range constraints

biopragmatics · Feb 2, 2024 · c62f047 · c62f047
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diff --git a/docs/0000047/index.html b/docs/0000047/index.html
@@ -0,0 +1,74 @@
+
+
+<!DOCTYPE html>
+<html lang="en">
+<head>        <meta charset="utf-8">
+        <meta name="viewport" content="width=device-width, initial-scale=1.0">    <link
+        rel="stylesheet"
+        href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css"
+        integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm"
+        crossorigin="anonymous"
+    />
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/c3/0.6.12/c3.min.css"/>
+    <style>
+        h2 {
+            margin-top: 35px;
+        }
+
+        html, body {
+            height: 100%;
+        }
+
+        body {
+            display: flex;
+            flex-flow: column;
+        }
+
+        .footer {
+            margin-top: auto;
+            padding-top: 1em;
+            background-color: #f5f5f5;
+        }
+    </style>    <title>reaction enabled by molecular function</title></head>
+
+<body>
+<nav class="navbar navbar-expand-lg navbar-light bg-light">
+    <span class="navbar-brand">
+        Decentralized Biomedical Ontology
+    </span>
+</nav>
+
+<div class="container" style="margin-top: 50px; margin-bottom: 50px">
+<div class="card">
+        <h5 class="card-header">
+                <span class="badge badge-info">Relation</span>
+            reaction enabled by molecular function
+        </h5>
+        <div class="card-body">
+                <p>connects a reaction (e.g., from Rhea) to a molecular function (e.g., from GO) that corresponds</p>
+            <dl>
+                <dt>Local Unique Identifier</dt>
+                <dd>
+                    <a href="https://bioregistry.io/debio:0000047">0000047</a>
+                </dd>
+
+
+
+
+            </dl>
+        </div>
+    </div></div>
+
+<footer class="footer">
+    <p class="small text-center text-muted">
+        Generated with PyOBO
+    </p>
+</footer>
+
+<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js"
+        integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN"
+        crossorigin="anonymous"></script>
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"
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+        crossorigin="anonymous"></script></body>
+</html>
diff --git a/docs/index.html b/docs/index.html
@@ -451,6 +451,14 @@ <h5 class="card-header">
                         <td>search results in</td>
                         <td>connects any entity to an article that a search over the entity label or its synonyms produces</td>
                     </tr>
+                    <tr>
+                        <td>
+                                TypeDef
+                        </td>
+                        <td align="right"><a href="0000047">0000047</a></td>
+                        <td>reaction enabled by molecular function</td>
+                        <td>connects a reaction (e.g., from Rhea) to a molecular function (e.g., from GO) that corresponds</td>
+                    </tr>
                 </tbody>
             </table>
         </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" : "10:01:2024 13:52"
+        "val" : "02:02:2024 08:42"
       }, {
         "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
         "val" : "1.2"
@@ -707,6 +707,19 @@
           "val" : "orcid:0000-0001-9439-5346"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/debio_0000047",
+      "lbl" : "reaction enabled by molecular function",
+      "type" : "PROPERTY",
+      "meta" : {
+        "definition" : {
+          "val" : "connects a reaction (e.g., from Rhea) to a molecular function (e.g., from GO) that corresponds"
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "orcid:0000-0001-9439-5346"
+        } ]
+      }
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
       "lbl" : "database_cross_reference",
@@ -716,6 +729,41 @@
       "lbl" : "has_obo_format_version",
       "type" : "PROPERTY"
     } ],
+    "edges" : [ {
+      "sub" : "http://purl.obolibrary.org/obo/DOID_4",
+      "pred" : "is_a",
+      "obj" : "http://www.w3.org/2002/07/owl#Thing"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/GO_0003674",
+      "pred" : "is_a",
+      "obj" : "http://www.w3.org/2002/07/owl#Thing"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1",
+      "pred" : "is_a",
+      "obj" : "http://www.w3.org/2002/07/owl#Thing"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/VO_0000001",
+      "pred" : "is_a",
+      "obj" : "http://www.w3.org/2002/07/owl#Thing"
+    } ],
+    "domainRangeAxioms" : [ {
+      "predicateId" : "http://purl.obolibrary.org/obo/debio_0000033",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/NCBITaxon_1" ],
+      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/NCBITaxon_1" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/debio_0000034",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/VO_0000001" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/debio_0000037",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/VO_0000001" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/debio_0000041",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/VO_0000001" ],
+      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/DOID_4" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/debio_0000047",
+      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GO_0003674" ]
+    } ],
     "propertyChainAxioms" : [ {
       "predicateId" : "http://purl.obolibrary.org/obo/debio_0000001",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002205", "http://purl.obolibrary.org/obo/RO_0002350" ]

diff --git a/releases/current/debio.obo b/releases/current/debio.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-date: 10:01:2024 13:52
+date: 02:02:2024 08:42
 auto-generated-by: bio2obo:debio
 data-version: 0.1.2-dev
 idspace: RO http://purl.obolibrary.org/obo/RO_
@@ -239,12 +239,15 @@ id: debio:0000033
 name: pathogen has host
 def: "connects a pathogen (NCBITaxon) to a host (NCBITaxon)"
 created_by: orcid:0000-0003-4423-4370
+domain: NCBITaxon:1
+range: NCBITaxon:1
 
 [Typedef]
 id: debio:0000034
 name: vaccine has gene engineering
 def: "connects a vaccine (VO) to a gene that has been engineered. Most applicable to OMVs, Nanosponges, and nanolipoparticles (NLP)."
 created_by: orcid:0000-0003-4423-4370
+domain: VO:0000001
 
 [Typedef]
 id: debio:0000035
@@ -263,6 +266,7 @@ id: debio:0000037
 name: has platform
 def: "connects a vaccine to its platform"
 created_by: orcid:0000-0003-4423-4370
+domain: VO:0000001
 
 [Typedef]
 id: debio:0000038
@@ -287,6 +291,8 @@ id: debio:0000041
 name: prevents infection
 def: "Sibling relationship to vo:0001011 (immunizes against disease)"
 created_by: orcid:0000-0003-4423-4370
+domain: VO:0000001
+range: DOID:4
 
 [Typedef]
 id: debio:0000042
@@ -319,3 +325,10 @@ id: debio:0000046
 name: search results in
 def: "connects any entity to an article that a search over the entity label or its synonyms produces"
 created_by: orcid:0000-0001-9439-5346
+
+[Typedef]
+id: debio:0000047
+name: reaction enabled by molecular function
+def: "connects a reaction (e.g., from Rhea) to a molecular function (e.g., from GO) that corresponds"
+created_by: orcid:0000-0001-9439-5346
+range: GO:0003674
diff --git a/releases/current/debio.owl b/releases/current/debio.owl
@@ -14,7 +14,7 @@
         <dc:description>A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.</dc:description>
         <dc:title>Decentralized Biomedical Ontology</dc:title>
         <oboInOwl:auto-generated-by>bio2obo:debio</oboInOwl:auto-generated-by>
-        <oboInOwl:date>10:01:2024 13:52</oboInOwl:date>
+        <oboInOwl:date>02:02:2024 08:42</oboInOwl:date>
         <oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
     </owl:Ontology>
 
@@ -540,6 +540,8 @@
     <!-- http://purl.obolibrary.org/obo/debio_0000033 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/debio_0000033">
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
         <obo:IAO_0000115>connects a pathogen (NCBITaxon) to a host (NCBITaxon)</obo:IAO_0000115>
         <oboInOwl:created_by>orcid:0000-0003-4423-4370</oboInOwl:created_by>
         <oboInOwl:id>debio:0000033</oboInOwl:id>
@@ -551,6 +553,7 @@
     <!-- http://purl.obolibrary.org/obo/debio_0000034 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/debio_0000034">
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/VO_0000001"/>
         <obo:IAO_0000115>connects a vaccine (VO) to a gene that has been engineered. Most applicable to OMVs, Nanosponges, and nanolipoparticles (NLP).</obo:IAO_0000115>
         <oboInOwl:created_by>orcid:0000-0003-4423-4370</oboInOwl:created_by>
         <oboInOwl:id>debio:0000034</oboInOwl:id>
@@ -584,6 +587,7 @@
     <!-- http://purl.obolibrary.org/obo/debio_0000037 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/debio_0000037">
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/VO_0000001"/>
         <obo:IAO_0000115>connects a vaccine to its platform</obo:IAO_0000115>
         <oboInOwl:created_by>orcid:0000-0003-4423-4370</oboInOwl:created_by>
         <oboInOwl:id>debio:0000037</oboInOwl:id>
@@ -628,6 +632,8 @@
     <!-- http://purl.obolibrary.org/obo/debio_0000041 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/debio_0000041">
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/VO_0000001"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/DOID_4"/>
         <obo:IAO_0000115>Sibling relationship to vo:0001011 (immunizes against disease)</obo:IAO_0000115>
         <oboInOwl:created_by>orcid:0000-0003-4423-4370</oboInOwl:created_by>
         <oboInOwl:id>debio:0000041</oboInOwl:id>
@@ -666,6 +672,53 @@
         <oboInOwl:id>debio:0000046</oboInOwl:id>
         <rdfs:label>search results in</rdfs:label>
     </owl:ObjectProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/debio_0000047 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/debio_0000047">
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
+        <obo:IAO_0000115>connects a reaction (e.g., from Rhea) to a molecular function (e.g., from GO) that corresponds</obo:IAO_0000115>
+        <oboInOwl:created_by>orcid:0000-0001-9439-5346</oboInOwl:created_by>
+        <oboInOwl:id>debio:0000047</oboInOwl:id>
+        <rdfs:label>reaction enabled by molecular function</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/DOID_4 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_4"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/GO_0003674 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003674"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_1 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0000001 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000001"/>
 </rdf:RDF>
 
 

diff --git a/src/debio/api.py b/src/debio/api.py
@@ -52,6 +52,13 @@ def _reference_list(references) -> List[Reference]:
     ]
 
 
+def _reference(d, k) -> Optional[Reference]:
+    v = d.get(k)
+    if not v:
+        return None
+    return Reference.from_curie(v)
+
+
 def _get_typedef(typedef, is_metadata_tag: Optional[bool] = None) -> TypeDef:
     return TypeDef(
         reference=Reference(
@@ -65,7 +72,9 @@ def _get_typedef(typedef, is_metadata_tag: Optional[bool] = None) -> TypeDef:
         xrefs=_reference_list(typedef.get("xrefs", [])),
         created_by=f"orcid:{typedef['creator']}",
         parents=_reference_list(typedef.get("parents", [])),
-        inverse=Reference.from_curie(typedef["inverse"]) if "inverse" in typedef else None,
+        inverse=_reference(typedef, "inverse"),
+        domain=_reference(typedef, "domain"),
+        range=_reference(typedef, "range"),
     )
 
 

diff --git a/src/debio/resources/typedefs.json b/src/debio/resources/typedefs.json
@@ -201,13 +201,17 @@
     "identifier": "0000033",
     "name": "pathogen has host",
     "creator": "0000-0003-4423-4370",
-    "description": "connects a pathogen (NCBITaxon) to a host (NCBITaxon)"
+    "description": "connects a pathogen (NCBITaxon) to a host (NCBITaxon)",
+    "domain": "NCBITaxon:1",
+    "range": "NCBITaxon:1"
+
   },
   {
     "identifier": "0000034",
     "name": "vaccine has gene engineering",
     "creator": "0000-0003-4423-4370",
-    "description": "connects a vaccine (VO) to a gene that has been engineered. Most applicable to OMVs, Nanosponges, and nanolipoparticles (NLP)."
+    "description": "connects a vaccine (VO) to a gene that has been engineered. Most applicable to OMVs, Nanosponges, and nanolipoparticles (NLP).",
+    "domain": "vo:0000001"
   },
   {
     "identifier": "0000035",
@@ -225,7 +229,8 @@
     "identifier": "0000037",
     "name": "has platform",
     "creator": "0000-0003-4423-4370",
-    "description": "connects a vaccine to its platform"
+    "description": "connects a vaccine to its platform",
+    "domain": "vo:0000001"
   },
   {
     "identifier": "0000038",
@@ -249,7 +254,9 @@
     "identifier": "0000041",
     "name": "prevents infection",
     "creator": "0000-0003-4423-4370",
-    "description": "Sibling relationship to vo:0001011 (immunizes against disease)"
+    "description": "Sibling relationship to vo:0001011 (immunizes against disease)",
+    "domain": "vo:0000001",
+    "range": "doid:4"
   },
   {
     "identifier": "0000044",
@@ -268,5 +275,12 @@
     "name": "search results in",
     "creator": "0000-0001-9439-5346",
     "description": "connects any entity to an article that a search over the entity label or its synonyms produces"
+  },
+  {
+    "identifier": "0000047",
+    "name": "reaction enabled by molecular function",
+    "creator": "0000-0001-9439-5346",
+    "description": "connects a reaction (e.g., from Rhea) to a molecular function (e.g., from GO) that corresponds",
+    "range": "GO:0003674"
   }
 ]