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:

1. 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>

2. It was part of a deleted submission, for example: CHEBI:53008. (Table SUBMISSION, status D 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.

✏ [Update]: There are compounds with compounds.source_id = 55 (SUBMITTER) which looks like the compounds meet the requirements for the second point.