ChEBI Ontology | Add the deprecated compounds (Part I)
As part of the ChEBI Ontology generation process, it is necessary to include the deprecated compounds in the chebi.owl
file. A compound is classified as deprecated if:
- It is a child of another compound: An example is
CHEBI:1
compound, which is deprecated because CHEBI:18357 is its parent. In the chebi.owl these compounds are modelled as follows:
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_1">
<obo:IAO_0000231 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000227"/>
<obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/CHEBI_18357"/> <!-- its parent! -->
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
- It was part of a deleted submission, for example:
CHEBI:53008
. (TableSUBMISSION
, statusD
for the old schema). In the chebi.owl file these compounds are modelled as follows:
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_53008">
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">chebi_ontology</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CHEBI:53008</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inositol phosphoceramide D</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
This task covers the first point because we have not defined the schema for the submission yet.
compounds.source_id = 55
(SUBMITTER) which looks like the compounds meet the requirements for the second point.