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[bioontology-support] ontology mappings

John Graybeal jgraybeal at stanford.edu
Tue Feb 13 14:11:03 PST 2018


On the perhaps-broader subject of how to put mappings for an ontology into BioPortal, the answer is 'via the API'. (If you have just a few, you can do so via the UI at https://bioportal.bioontology.org/help#Viewing_and_editing_mappings .)

Example code for creating API mappings is at
  https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java

A past thread on how to do this is at
  http://ncbo-support.2288202.n4.nabble.com/Uploading-a-Mapping-td4653220.html#a4653222
It mentions the general info on running the above sample code:
  https://github.com/ncbo/ncbo_rest_sample_code/tree/master/java

Links that might be useful:
  https://www.bioontology.org/wiki/index.php/BioPortal_Mappings
  http://data.bioontology.org/documentation#Mapping    -- the actual API documentation

Sorry we do not have more better documentation!

John


On Feb 13, 2018, at 11:00 AM, Clement Jonquet <jonquet.lirmm at gmail.com<mailto:jonquet.lirmm at gmail.com>> wrote:

Hi Michel,

NCBO and us do not have a lot of documentation about mappings. A small technical explanation is here:
https://github.com/agroportal/documentation/wiki/Mappings

On the "recognized’’ point:
BioPortal does not automatically extract/recognize mappings that would be in described inside the ontologies. Except if the class explicitly uses the same URI or has a CUI property described properly (as documented in the link).

If an ontology file contains "mappings" represented with SKOS matching properties or owl:sameAs or any other specific property (e.g., OBO-XREF), those mappings will not be extracted by AgroPortal.

It sounds weird, but there are multiple historical reasons for this including the fact that at the beginning of the NCBO project, one would not always expect the mapped ontologies to be « already » in BioPortal. This situation is not always true, but now there is a strong chance  the mapped ontologies are already on BioPortal.
Within AgroPortal we removed that constraint a couple of years ago (external mappings) and will start soon working (again) on mappings with Elcio (CC) who just join us at LIRMM.

As of now, I would recommend to use SKOS properties inside you SIO file to represent mappings. Those would be considered by the new parser for sure.

Bye
Clement


Le 13 févr. 2018 à 00:59, Michel Dumontier <michel.dumontier at gmail.com<mailto:michel.dumontier at gmail.com>> a écrit :

Hi!
  Can you point me to public documentation that describes how my ontology (SIO) can be annotated with mappings that can be recognized by the BioPortal system?
  thanks!
m.

--
Michel Dumontier
Distinguished Professor of Data Science
Maastricht University
http://dumontierlab.com<http://dumontierlab.com/>
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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