Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Irmgard Teschke irmgard.teschke at osthus.com
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<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
________________________________________________
OSTHUS GmbH
Eisenbahnweg 9 - 11
Eingang TH 6
52068 Aachen
T    +49 241-94314-xxx
F    +49 241-94314-19
irmgard.teschke at osthus.com<mailto:irmgard.teschke at osthus.com>
www.osthus.com<http://www.osthus.com/>
LinkedIn<https://www.linkedin.com/company/osthus>          Twitter<https://twitter.com/OSTHUS>            Youtube<https://www.youtube.com/user/OsthusCompany>


Handelsniederlassung: 52068 Aachen
Register: Amtsgericht Aachen, HRB 6398
Geschäftsführer: Dr. Torsten Osthus, Wolfgang Colsman, Andreas Mohr
________________________________________________
Der Inhalt dieser E-Mail ist ausschließlich für den bezeichneten Adressaten bestimmt. Wenn Sie nicht der vorgesehene Adressat dieser E-Mail oder dessen Vertreter sein sollten, so beachten Sie bitte, dass jede Form der Kenntnisnahme, Veröffentlichung, Vervielfältigung oder Weitergabe des Inhalts dieser E-Mail unzulässig ist. Wir bitten Sie, sich in diesem Fall mit dem Absender der E-Mail in Verbindung zu setzen.
________________________________________________
The information contained in this email is intended solely for the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20180524/08834001/attachment-0001.html>


More information about the bioontology-support mailing list