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[bioontology-support] FW: BioPortal

Trish Whetzel whetzel at stanford.edu
Mon Dec 15 19:05:52 PST 2008


Hi Eamonn, 

 

To follow-up on the last part of your query, the search includes synonyms. 

 

Cheers, 

Trish

 

 

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Thursday, December 04, 2008 5:35 PM
To: 'Eamonn Maguire'
Cc: 'Natasha Noy'; 'Benjamin Dai'; 'Michael Montegut'
Subject: RE: FW: BioPortal

 

Hi Eamonn, 

 

The format to follow in that case would be:
http://rest.bioontology.org/bioportal/rest/search/concepts/cancer?ontologies
=13578,38312 where the ontologies of interest are listed by their id
separated by a comma without any space in between. The ontology id's can be
found from the REST call:
http://rest.bioontology.org/bioportal/rest/ontologies

 

As for the inclusion of synonyms in the search, a query has been posted to
the developers for the detailed search specs.  

 

Trish

 

 

From: Eamonn Maguire [mailto:eamonnmag at googlemail.com] 
Sent: Wednesday, December 03, 2008 1:36 AM
To: Trish Whetzel
Cc: Natasha Noy; Benjamin Dai; Michael Montegut
Subject: Re: FW: BioPortal

 

No problem. I will let you know if I have any problems :) oh actually, does
the query string have to be of any format, or can i simply include "cancer"
and it will query the ontology of choice (or all ontologies) for terms
including cancer or synonyms of it?

 

Thanks again,

 

Eamonn

 

2008/12/2 Trish Whetzel <whetzel at stanford.edu>

Neat - look forward to seeing the release of ISAcreator. It looks like a
very nicely developed application. If there are any other ontologies that
would be useful to have loaded directly in BioPortal let us know and we can
load those.

 

Cheers,

Trish

  

 

From: Eamonn Maguire [mailto:eamonnmag at googlemail.com] 
Sent: Tuesday, December 02, 2008 4:07 AM
To: Trish Whetzel
Subject: Re: FW: BioPortal

 

Hi Trish,

 

Thanks for the quick response. I do plan to include bioportal into
ISAcreator so as to serve the OBI ontology...should be incorporated for the
first release in January.

 

thanks,

 

Eamonn

2008/12/1 Trish Whetzel <whetzel at stanford.edu>

Hi Eamonn,

 

The proper format for the REST calls are:

URI:  /rest/ontologies

URI:  /rest/ontologies/{ontology_id}

URI:  /rest/ontologies/download/{ontology_id}

URI:  /rest/concepts/{ontology_id}/root

URI:  /rest/concepts/{ontology_id}/{concept_id}

URI:  /rest/path/{ontology_id}/{concept_id}/root

URI:  /rest/search/concepts/{term}?ontologies={ontologies to search in}

 

Therefore to turn these into working URLs, prefix with:
http://rest.bioontology.org/bioportal

For example,
http://rest.bioontology.org/bioportal/rest/concepts/38757/DOID:1909 or
http://rest.bioontology.org/bioportal/rest/ontologies

 

Do you plan to incorporate these calls into ISAcreator? 

 

Trish

 

From: eamonnmag at googlemail.com [mailto:eamonnmag at googlemail.com] On Behalf
Of Eamonn Maguire
Sent: Monday, December 01, 2008 2:52 AM
To: benjamin.dai at stanford.edu
Subject: BioPortal

 

Hello Ben,

 

Just a quick question. For the rest webservices, what is the URL to prepend
to the request? I've been trying different combinations yet still get a not
found error.

 

So say I was querying rest/ontologies, what would the full URL be?

 

Many thanks in advance, 


-- 
Eamonn Maguire

maguire at ebi.ac.uk
eamonnmag at gmail.com

http://www.ebi.ac.uk/~maguire 

 




-- 
Eamonn Maguire

maguire at ebi.ac.uk
eamonnmag at gmail.com

http://www.ebi.ac.uk/~maguire




-- 
Eamonn Maguire

maguire at ebi.ac.uk
eamonnmag at gmail.com

http://www.ebi.ac.uk/~maguire

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