[bioontology-support] Question about reproducing Bioportal mapping and class metrics

[Irmgard Teschke]

Dear Bioontology Support,

I have downloaded some ontologies and a few mappings from the Bioportal REST API and have been trying (unsuccessfully) to reproduce the class and mappings metrics for these ontologies and mapping pairs. I must be missing something and was hoping that someone might be able to point me in the right direction.

I will try to explain my problem with the example of the ontologies ORDO<https://bioportal.bioontology.org/ontologies/ORDO?p=summary> (Orphanet Rare Disease Ontology) and MP<https://bioportal.bioontology.org/ontologies/MP?p=summary> (Mammalian Phenotype Ontology).

To count number of classes in the ontology I used a sparql query (Table below, lefthand column), the result of which (no. classes) is given on the right for the ontologies ORDO and MP. The Bioportal result (see ORDO<https://bioportal.bioontology.org/ontologies/ORDO?p=summary>  and MP<https://bioportal.bioontology.org/ontologies/MP?p=summary>) is given in the 2nd and 3rd column of the table below.

My Query

ORDO

MP

PREFIX owl: <http://www.w3.org/2002/07/owl#>

SELECT (count( ?s) as ?no_mappings)

FROM <http://xyzmapping.com/ORDO>

WHERE {?s a owl:Class .
Filter (! isblank(?s))
}

13,666 classes

12,795 classes

Bioportal

13,666 classes

13,556 classes



As you can see, my number is the same as the bioportal no. classes for ORDO, but not for MP. I wonder why?

Furthermore, here<https://bioportal.bioontology.org/ontologies/ORDO?p=mappings> I checked the number of mappings from ORDO to MP and found that there should be 128 mappings. However, when I download/parse the json through the rest API, I only get 69 mappings. I have confirmed my number (69) also by actually counting the number of mapping pairs given in the REST API for this pair (the REST API source for the mapping I downloaded and also counted by hand is http://data.bioontology.org/mappings?ontologies=ORDO,MP&apikey=xyz). I have similar discrepancies for all ontologies and mappings that I have downloaded to date. Any ideas about why this could be?

Any help would be much appreciated!!!


Mit freundlichen Grüßen / Kind Regards

Irmgard Teschke
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