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[bioontology-support] [BioPortal] Feedback from superraptor2

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Sep 19 11:32:30 PDT 2019


Hi Clair,

Yes - there is a way to do this. You can specify the “also_search_properties” parameter for API calls to the /search endpoint. That syntax looks like the following:

http://data.bioontology.org/search?q=RC571&ontologies=GSSO&also_search_properties=true

… and returns the desired “Down syndrome” class:


[cid:42D9B5B0-17F0-4874-82F8-A73E99AC652F at stanford.edu]


The /search endpoint is documented here: http://data.bioontology.org/documentation#nav_search.

Hope that helps.

Kind regards,
Jennifer


On Sep 19, 2019, at 9:45 AM, Clair Kronk <clair.kronk at gmail.com<mailto:clair.kronk at gmail.com>> wrote:

Jennifer,

Sorry to bother again, but I've been looking through and API docs and I'm not sure if this functionality is currently supported:

So I have a property for Library of Congress Subject Headings in my ontology (GSSO). Is there any way to query my ontology for a match to a subject heading and return the entry to the user without downloading all classes?

For instance, if a user queries for the subject heading "RC571" it should return the entry for Down Syndrome.

Thanks so much!

 Best wishes,

Clair Kronk

On Thu, Sep 19, 2019 at 12:13 PM Clair Kronk <clair.kronk at gmail.com<mailto:clair.kronk at gmail.com>> wrote:
Jennifer,

Thanks so much for your help! Sorry this got buried a bit in my email! Thanks so much for the instances endpoint, it helps a ton!

Best,

Clair Kronk

On Fri, Sep 13, 2019 at 8:42 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Clair,


On Sep 13, 2019, at 4:59 PM, Clair Kronk <clair.kronk at gmail.com<mailto:clair.kronk at gmail.com>> wrote:

Jennifer,

I figured it out! I put the wrong GitHub link (you have to link to the raw file, not just the file link itself). I saved one as the Manchester OWL format and it seems to be working now (1.0.1e).


Great! Glad you were able to get your ontology successfully loaded.



I'm still trying to figure out how to link things in the best way (my ontology has quite a few instances in it which don't seem to be able to be explored as of now).


Currently we don’t have anything in the BioPortal user interface for browsing instances. Instance data is available via our REST API however:

http://data.bioontology.org/ontologies/GSSO/instances

Not sure if that helps.

Kind regards,
Jennifer



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