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[bioontology-support] Search by code from REST API

Koray Atalag k.atalag at auckland.ac.nz
Tue Feb 28 17:37:04 PST 2017


Thanks for prompt reply,

An important issue: I’ve sent a previous support request without logging on to bioportal and immediately I started receiving SPAM email with explicit porn content! I’ve sent to the support email.

Back to my problem – I’m actually quite surprised that you don’t support this as pretty much all the biomedical research community is using identifiers.org IRIs and that only points to the original organisation’s website usually; however the key to reach a particular term in a given ontology is given in the original URL. For example OLS from EBI supports this but they don’t have all the ontologies I need (e.g. OPB)

This does raise the question whether a lot of serious projects are actually making use of bioportal?? I think most dev users will want to query by code than just do text searching…Am I missing something here?

Cheers,

-koray

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: Wednesday, 1 March 2017 2:22 p.m.
To: Koray Atalag
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Search by code from REST API

Hi Koray,

Thank you for contacting us. I’m not sure whether I understood you entirely, but BioPortal allows searching by the full term id, and you can always limit the search by the ontology acronym (to eliminate instances of the same term in other ontologies:

http://bioportal.bioontology.org/search?q=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_00340&ontologies=OPB<http://bioportal.bioontology.org/search?q=http://bhi.washington.edu/OPB#OPB_00340&ontologies=OPB>

The equivalent API search is (you’ll need to add your apikey parameter):

http://data.bioontology.org/search?q=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_00340&ontologies=OPB<http://data.bioontology.org/search?q=http://bhi.washington.edu/OPB#OPB_00340&ontologies=OPB>

At the moment we don’t allow searches by the short IDs (i.e. OPB_00340).

Thanks!

Michael


On Feb 27, 2017, at 7:21 PM, Koray Atalag <k.atalag at auckland.ac.nz<mailto:k.atalag at auckland.ac.nz>> wrote:

Hi,

I’m trying to get prefLabel based on ontology identifier (e.g. in the form of identifier.org<http://identifier.org/> URIs)
I reckon you allow for searching by terms but not ontology codes – is there a way to do this?

Let’s say I have this URI: http://identifiers.org/opb/OPB_00340
So given I know I’m looking into OPB and code: 00340 I want to access the bioportal record and get prefLabel

For example using web interface I can get: http://bioportal.bioontology.org/ontologies/OPB?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_00340


Many thanks in advance

Cheers,

-koray

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