Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Gap in term services?

Colin Morris colin at sciencescape.org
Tue Apr 2 07:56:13 PDT 2013


Thanks Trish!

Two things:

1) The wiki seems to be a bit out of date in this respect. It gives
examples for the alt virtual signature like:

http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey

Which I think should be:

http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=http%3A//bioontology.org/ontologies/BiomedicalResourceOntology.owl%23Software&apikey=YourAPIKey

(I would edit it myself, but I was denied a user account for the wiki, so I
hope you guys don't mind me bugging you about these things)

2) The new urls are working some of the time, but I'm still getting some
funny 404's. For example, given the following results:

8 47638/Field Data Field
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Field Field [...]

I construct a URL like

http://rest.bioontology.org/bioportal/virtual/ontology/1032?conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23Field&apikey=
<apikey>

Which gives a 'concept not found' error. When I searched for the term
through the web interface, I found it living at:

http://bioportal.bioontology.org/ontologies/1032?p=terms&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25507

I'm not sure what the 23C70773 is, but it doesn't seem to be anywhere in
the tab-delimited results I get back for that concept.

Thanks,
Colin


On Mon, Apr 1, 2013 at 3:08 PM, Trish Whetzel <whetzel at stanford.edu> wrote:

> In this case, the ontology abbreviation is included as part of the
> "conceptid", therefore either the abbreviation also needs to be included as
> part of the conceptid:
> http://rest.bioontology.org/bioportal/virtual/ontology
> /1086?conceptid=ODGI%3ACharacterized&apikey=<apikey>
> OR
> the preferred method is to use the full Id of the term (URL encoded) in
> the call formatted as:
> http://rest.bioontology.org/bioportal/virtual/ontology
> /1086?conceptid=http%3A%2F%2Fpurl.obolibrary.org
> %2Fobo%2FODGI.owl%23Characterized&apikey=<apikey>
>
> Trish
>
>
> On Mar 27, 2013, at 2:32 PM, Colin Morris wrote:
>
> Hi,
>
> One of the concepts I got as output from the NCBO annotator was term
> 'Characterized' in ontology 39579 (ODGI - virtual ontology id 1086).
>
> But using the 'alt virtual signature' described in the documentation (
> http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Term_services)
> to build a url for this concept gives me a 404:
>
>
> http://rest.bioontology.org/bioportal/virtual/ontology/1086?conceptid=Characterized&apikey=
> <apikey>
>
> Can you think of any reason why this would be?
>
> Thanks,
> Colin
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20130402/ef433221/attachment-0001.html>


More information about the bioontology-support mailing list