species with 2 subClassOf values in NCBITaxon_9460 (species)

[andrecastro0o]

while looking a bit at ncbitaxon I found out that http://purl.obolibrary.org/obo/NCBITaxon_9460 has 2 subClassOf values NCBITaxon_30615 and NCBITaxon_9459

see describe sparl query

<http://purl.obolibrary.org/obo/NCBITaxon_9460>
    rdf:type    owl:Class ;
    rdfs:label  "Cheirogaleus medius"^^xsd:string ;
    rdfs:subClassOf <http://purl.obolibrary.org/obo/NCBITaxon_30615> , <http://purl.obolibrary.org/obo/NCBITaxon_9459> ;

This seemed odd. When a I looked a bit further into the ncbi taxonomy browser (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9460) and node.dmp

cat nodes.dmp |grep "^9460[[:space:]]"

9460 | 9459 | species | CM | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |

and it seems that only has 9459 (genus) is its parent and not 30615.

9459 (genus) has as parent 30615 (family) .

cat nodes.dmp |grep "^9459[[:space:]]" 9459 | 30615 | genus | | 5 | 1 | 1 | 1 | 2 | 1 | 0 | 0 | |

It might be a bug on ncbitaxon side.

[matentzn]

Before getting into debugging:

Did you try querying ncbitaxon.owl directly with SPARQL? The ontobee endpoint is not very reliable for querying the asserted structure of ontologies, as other ontologies may inject reasoned classification into their release..

[andrecastro0o]

@matentzn actually I did not quey the owl. Arq was taking a very long time due to the large size of the owl. Might try it again, and see if I don't have to import it to a triple store. Will report. Thanks

[andrecastro0o]

@matentzn you were right. When querying the owl there is only subClassOf value

Think that settles it. Thank you for pointing that ontobee endpoint is not very reliable for querying the asserted structure of ontologies,wasn't aware of it. Thanks!

<http://purl.obolibrary.org/obo/NCBITaxon_9460> a owl:Class;
  rdfs:subClassOf <http://purl.obolibrary.org/obo/NCBITaxon_9459>;
  rdfs:label "Cheirogaleus medius";
  <http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_species>;
  <http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> "ncbi_taxonomy";
  <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GC_ID:1";
  <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> "Lesser dwarf lemur",
    "fat-tailed dwarf lemur" .

_:node329278 owl:annotatedSource <http://purl.obolibrary.org/obo/NCBITaxon_9460> .

_:node329279 owl:annotatedSource <http://purl.obolibrary.org/obo/NCBITaxon_9460> .