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[bioontology-support] Missing broade/narrowerr mappings?

Ernesto Jimenez-Ruiz ernesto.jimenez.ruiz at gmail.com
Thu Apr 3 10:48:11 PDT 2014


Hi

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

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
http://data.bioontology.org/mappings/statistics/ontologies/MA

However only 961 were extracted using the new BioPortal REST API
http://data.bioontology.org/documentation#Mapping

In any case MA has only 3205 classes according to
http://data.bioontology.org/ontologies/MA/metrics
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:
http://www.bioontology.org/wiki/index.php/BioPortal_Mappings

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 "process.name" for
each mapping in the returned collections (e.g.
http://data.bioontology.org/ontologies/MA/mappings).

Many thanks in advance
Ernesto



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

http://krono.act.uji.es/people/Ernesto
http://www.cs.ox.ac.uk/people/ernesto.jimenez-ruiz/
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