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

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu May 24 15:53:38 PDT 2018


Hello Irmgard,


On May 24, 2018, at 12:55 AM, Irmgard Teschke <irmgard.teschke at osthus.com<mailto:irmgard.teschke at osthus.com>> wrote:

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.


What are you executing the SPARQL query against? At the moment, we don’t have an open SPARQL endpoint that serves current ontology data. Is this something you’ve set up locally?




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?


We don’t use SPARQL to generate class, property, or individual metrics. When end users submit ontologies to BioPortal, we first consume the ontology source files with the OWL API [1]. We use OWL API functions to calculate metrics for classes, properties, and individuals. You can see that code here:

https://github.com/ncbo/owlapi_wrapper/blob/master/src/main/java/org/stanford/ncbo/oapiwrapper/OntologyMetrics.java#L45




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?


There’s a known issue in the BioPortal user interface with displaying duplicate mappings. We have an issue in our tracker here:

https://github.com/ncbo/bioportal-project/issues/69

Apologies that we haven’t had an opportunity to troubleshoot this yet.

Kind regards,
Jennifer


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