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[bioontology-support] EDAM Ontology Classes

Ray Fergerson ray.fergerson at stanford.edu
Fri Dec 5 16:28:14 PST 2014


Thanks for pointing this out. We think that this is a probably with the
EDAM ontology itself. We are contacting the author to fix it. It is not
only a syntactic problem, it is semantically incorrect as well. The link
to documentation about a concept should a "seeAlso" and not a synonym. 

You are correct that synonyms should just be strings.

Ray

-----Original Message-----
From: bioontology-support
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Aaron
Baker
Sent: Monday, December 1, 2014 1:14 PM
To: support at bioontology.org
Subject: [bioontology-support] EDAM Ontology Classes

Hi Bioportal Team,

I had a question regarding the EDAM ontology and perhaps other ontologies.
When I retrieve results using the /classes endpoint, I noticed there are
some endpoints that have a JSON object (instead of the usual String) as a
synonym. For example, making a request at

http://data.bioontology.org/ontologies/EDAM/classes/http%3A%2F%2Fedamontol
ogy.org%2Fformat_2331?apikey={apikey}

gives the following object as a synonym

{"uri": "http://filext.com/file-extension/HTML"}

I had previously thought that synonyms were only Strings. Are there other
types of objects that may show up in the synonym area? Can the prefLabel
contain these sorts of objects as well?

Thanks for your help.

Best,
Aaron
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