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[bioontology-support] [BioPortal] Feedback from marcibowen

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Sep 7 18:14:53 PDT 2017


Hello Marci,

Unfortunately, the screen shot came through very small and is unreadable.

Just to clarify, if I issue this REST call in a browser:

http://data.bioontology.org/search?q=seizure&ontology=SNOMEDCT

The search endpoint returns 925 matches:

[cid:73F808FA-7779-48B3-90C5-BB686411439F at stanford.edu]

I’m guessing you’re referring to the first item in the result set - the term with preferred name “Seizure” and cui “C0036572”? I’m also guessing that you want the list of values for the “Definitional manifestation of” property? I don’t know of a way to get this data via the search endpoint. The only way I’m aware of to retrieve that data is via the classes endpoint. The call looks like this:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000?include=all<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/91175000?include=all>

The portion of the URL after /classes/ is the URL encoded version of the BioPortal class ID for the Seizure class. To follow is a partial screen shot showing that this call will return the list of values for the desired property:

[cid:91B19BDE-55F0-4EEE-BCE0-A4C341080C16 at stanford.edu]



Kind regards,
Jennifer



On Sep 7, 2017, at 3:27 PM, Marci Bowen <marcia.bowen at duke.edu<mailto:marcia.bowen at duke.edu>> wrote:

The rest api is

free_text = 'seizure'
url = 'http://data.bioontology.org/search?q='
headers = {'Authorization': 'apikey token=a9b1cb5e-9729-40ac-bd13-5596f66ca5a8'}

This is a screen shot of what I am trying to do.
<BioPortal Web Search.png>
On Sep 7, 2017, at 6:12 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Apologies Marci, but I’m not sure what you’re asking. Could you send the REST API call that you’re using? Also, what property are you referring to when you say “code”?

Kind regards,
Jennifer


On Sep 7, 2017, at 1:03 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: marcibowen

Email: marcia.bowen at duke.edu<mailto:marcia.bowen at duke.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=_XpVTJrtr0X0leljtIDRlyodLng6oKbmgmLrhWmENRA&m=428p5FlqrR4aafurPbUzonUx6xH0tl4bDJj0I1zcE3w&s=kNWdD6O4doZTMQd4OW8X-8u65NUkAtTMUeLwScFMRIo&e=>%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Droot

Feedback:

When using the api when I submit 'seizure" I only get 50 SNOMED Codes, but when I go to the web portal (http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=root<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioportal.bioontology.org_ontologies_SNOMEDCT-3Fp-3Dclasses-26conceptid-3Droot&d=DwMGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=_XpVTJrtr0X0leljtIDRlyodLng6oKbmgmLrhWmENRA&m=428p5FlqrR4aafurPbUzonUx6xH0tl4bDJj0I1zcE3w&s=9m8TkKKBhityx-fTxZSma3UJZQSgUb5QreOid6st62A&e=>) I get 325 SNOMED codes. How do I fix the api to return 325 SNOMED codes.

Thanks,
Marci Bowen

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