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[bioontology-support] Missing broade/narrowerr mappings?

Ray Fergerson ray.fergerson at
Fri Apr 4 15:52:34 PDT 2014


First, you are correct that our mapping counts are inconsistent between
the metrics and the actual mappings. I have filed a tracker issue so that
we look into this. Thanks for reporting it. The difference is huge but I
don’t really know the source of this problem.

The documentation lists types of mappings that can be created in
bioportal. For any given ontology these mappings may or may not exist. It
would not surprise me if we had no broader or narrower mappings at all
because no one has created them. We do have xref mappings but these
mappings are specific to OBO format ontologies.  In all I think that we
have about 9 million mappings. Most of these (99%) are loom mappings
(lexical matches on class names and synonyms) and are identified as


From: bioontology-support
[mailto:bioontology-support-bounces at] On Behalf Of
Ernesto Jimenez-Ruiz
Sent: Thursday, April 3, 2014 10:48 AM
To: bioontology-support at
Subject: [bioontology-support] Missing broade/narrowerr mappings?


I'm interested in extracting mappings from bioportal from a few pairs of

I checked the mappings pages to have an idea about the number of mappings
between each pair of ontologies. For example, between MA and FMA
ontologies one may expect to get more than 5,000 mappings according to

However only 961 were extracted using the new BioPortal REST API

In any case MA has only 3205 classes according to

So 961 seems reasonable, as equivalence mappings.

Furthermore, I have also noticed that the source of the mappings are in
the most of the cases loom, umls, or same_uri;  and a few of them do not
have an associated source.
Unfortunately, for all 19 pairs of ontologies I checked,  I could not find
many "xref" mappings and none "broader/narrower" matches as indicated in:

I wonder if I'm missing something and/or I'm not searching the source in
the proper data field. So far I was looking at the field ""
for each mapping in the returned collections (e.g.

Many thanks in advance


Ernesto Jiménez-Ruiz
Research Assistant
Department of Computer Science
University of Oxford
Wolfson Building, Parks Road, Oxford OX1 3QD, UK

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