Add HTML documentation for PGxO

practikpharma · Sep 17, 2018 · b5e09f8 · b5e09f8
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diff --git a/README.md b/README.md
@@ -8,6 +8,7 @@ PGxO is also available on the [NCBO BioPortal](https://bioportal.bioontology.org
 
 Documentation is available in the ``doc/`` folder:
 
+* [pgxo.html](doc/pgxo.html): HTML documentation of PGxO
 * [pgxo-overview.pdf](doc/pgxo-overview.pdf): Figure presenting PGxO main concepts and relations.
 * [mapp1.owl](doc/mapp1.owl): Mappings from PGxO to four ontologies related to PGx (SO-PHARM, PO, PHARE and Genomic CDS).
 * [mapp2.owl](doc/mapp2.owl): Mappings from PGxO to three large spectrum ontologies (MeSH, NCIt and SNOMED CT).

diff --git a/doc/pgxo.html b/doc/pgxo.html
@@ -0,0 +1,98 @@
+<!DOCTYPE html>
+<html>
+	<head>
+		<meta charset="utf-8" />
+		<meta name="description" content="PGxO">
+		<title>PGxO</title>
+	</head>
+
+    <body>
+        <h1>PGxO</h1>
+        <h2>Introduction</h2>
+
+        <p>
+            This document describes the namespace <a href="http://pgxo.loria.fr">http://pgxo.loria.fr/</a>.
+            The preferred prefix for this namespace is pgxo.
+        </p>
+
+        <p>Content negotiation is supported for HTML and RDF/XML.</p>
+
+        <p>The OWL ontology file can be accessed directly from <a href="http://pgxo.loria.fr/data/pgxo.owl">http://pgxo.loria.fr/data/pgxo.owl</a>.</p>
+
+        <h2>Index</h2>
+
+        <h3 id="causes">causes</h3>
+        <p>Object property</p>
+        <p>URI: <a href="http://pgxo.loria.fr/causes">http://pgxo.loria.fr/causes</a></p>
+        <p>Inverse of: <a href="http://pgxo.loria.fr/isCausedBy">isCausedBy</a></p>
+
+        <h3 id="Disease">Disease</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/Disease">http://pgxo.loria.fr/Disease</a></p>
+        <p>Subclass of: <a href="http://pgxo.loria.fr/Phenotype">Phenotype</a></p>
+
+        <h3 id="Drug">Drug</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/Drug">http://pgxo.loria.fr/Drug</a></p>
+
+        <h3 id="Gene">Gene</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/Gene">http://pgxo.loria.fr/Gene</a></p>
+        <p>Subclass of: <a href="http://pgxo.loria.fr/GeneticFactor">Genetic factor</a></p>
+
+        <h3 id="GenomicVariation">Genomic variation</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/GenomicVariation">http://pgxo.loria.fr/GenomicVariation</a></p>
+        <p>Subclass of: <a href="http://pgxo.loria.fr/GeneticFactor">Genetic factor</a></p>
+
+        <h3 id="GeneticFactor">Genetic factor</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/GeneticFactor">http://pgxo.loria.fr/GeneticFactor</a></p>
+
+        <h3 id="Haplotype">Haplotype</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/Haplotype">http://pgxo.loria.fr/Haplotype</a></p>
+        <p>Subclass of: <a href="http://pgxo.loria.fr/GenomicVariation">Genomic variation</a></p>
+
+        <h3 id="isCausedBy">isCausedBy</h3>
+        <p>Object property</p>
+        <p>URI: <a href="http://pgxo.loria.fr/isCausedBy">http://pgxo.loria.fr/isCausedBy</a></p>
+        <p>Inverse of: <a href="http://pgxo.loria.fr/causes">causes</a></p>
+
+        <h3 id="PharmacodynamicPhenotype">Pharmacodynamic phenotype</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/PharmacodynamicPhenotype">http://pgxo.loria.fr/PharmacodynamicPhenotype</a></p>
+        <p>Subclass of: <a href="http://pgxo.loria.fr/Phenotype">Phenotype</a></p>
+
+        <h3 id="PharmacogenomicRelationship">Pharmacogenomic relationship</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/PharmacogenomicRelationship">http://pgxo.loria.fr/PharmacogenomicRelationship</a></p>
+        <p>Subclass of: <a href="http://www.w3.org/ns/prov#Entity">prov:Entity</a></p>
+        <p>
+            Additional subclass axiom in Description Logics defining which ``components'' are allowed in a Pharmacogenomic relationship
+            (see OWL file or <a href="https://doi.org/10.1101/390971">paper</a>)
+        </p>
+
+        <h3 id="PharmacokineticPhenotype">Pharmacokinetic phenotype</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/PharmacokineticPhenotype">http://pgxo.loria.fr/PharmacokineticPhenotype</a></p>
+        <p>Subclass of: <a href="http://pgxo.loria.fr/Phenotype">Phenotype</a></p>
+
+        <h3 id="Phenotype">Phenotype</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/Phenotype">http://pgxo.loria.fr/Phenotype</a></p>
+
+        <h3 id="qualifiedProxy">qualifiedProxy</h3>
+        <p>Object property</p>
+        <p>URI: <a href="http://pgxo.loria.fr/qualifiedProxy">http://pgxo.loria.fr/qualifiedProxy</a></p>
+
+        <h3 id="qualifiedVariation">qualifiedVariation</h3>
+        <p>Object property</p>
+        <p>URI: <a href="http://pgxo.loria.fr/qualifiedVariation">http://pgxo.loria.fr/qualifiedVariation</a></p>
+
+        <h3 id="Variant">Variant</h3>
+        <p>Class</p>
+        <p>URI: <a href="http://pgxo.loria.fr/Variant">http://pgxo.loria.fr/Variant</a></p>
+        <p>Subclass of: <a href="http://pgxo.loria.fr/GenomicVariation">Genomic variation</a></p>
+    </body>
+</html>