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

Irmgard Teschke irmgard.teschke at
Thu May 24 00:55:20 PDT 2018

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<> (Orphanet Rare Disease Ontology) and MP<> (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<>  and MP<>) is given in the 2nd and 3rd column of the table below.

My Query



PREFIX owl: <>

SELECT (count( ?s) as ?no_mappings)


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

13,666 classes

12,795 classes


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<> 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,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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