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[bioontology-support] [BioPortal] Feedback from Sougato Das

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue May 1 12:33:11 PDT 2018


Hello Sougato

Here’s an example of a call you can use to retrieve the properties and their values for the “melanoma” class in MEDDRA:

http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10053571?include=all<http://data.bioontology.org/ontologies/MEDDRA/classes/http://purl.bioontology.org/ontology/MEDDRA/10053571?include=all>

Their will be a properties entry in the JSON results, which you’d need to iterate over to get the value of the “classified_as” property.

Similarly, you can use this call to retrieve the value of “classifies” on the “headache” class:

http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10019211?include=all<http://data.bioontology.org/ontologies/MEDDRA/classes/http://purl.bioontology.org/ontology/MEDDRA/10019211?include=all>

Kind regards,
Jennifer



On May 1, 2018, at 12:21 PM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

The ontology is MEDDRA and the first term is "melanoma" and the second term is "headache"


________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Tuesday, May 1, 2018 2:24 PM
To: Sougato Das
Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

Hello Sougato,

Could you please include what ontology you are working with, as well as the name of a term that you are trying to retrieve these properties for?

Jennifer


On May 1, 2018, at 7:32 AM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

I have read through the API documentation and I am sorry to say that I cannot figure out how to get the "classifies" and "Classified as" values of a given term through the API. I would be grateful if you could show me a sample API call that pulls the "classifies" and "Classified as" value of a given term.

Kind regards,
Sougato

________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Monday, April 16, 2018 5:51 PM
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Sougato Das
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

Hello Sougato,

Apologies that we don’t currently offer mappings as a file download. They're only accessible programmatically via our REST API, e.g.:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA

This is more performant version of the REST call if you’re not interested in seeing the hypermedia links:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA&display_links=false

Kind regards,
Jennifer



On Apr 16, 2018, at 10:17 AM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

Hello Samson,

Is there anyway to download the mappings, particularly the one between MeSH and MedDRA? I can see how to access it in the user interface, but there does not appear to be anyway to export it. Perhaps this is available in the API?

Kind regards
Sougato

________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Tuesday, December 12, 2017 2:57 PM
To: Jennifer Vendetti
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

“SIB” is a UMLS abbreviation for "has sibling relationship in a Metathesaurus source vocabulary” [1].

With best regards,
Samson

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nlm.nih.gov%2Fresearch%2Fumls%2Fknowledge_sources%2Fmetathesaurus%2Frelease%2Fabbreviations.html&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=PgT6RqR8HpKztRXJmXSOCQbnRMidKTmPqO%2BmoBgX30Q%3D&reserved=0>

On Dec 11, 2017, at 9:04 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sougato,

Could you please be more specific about what class, in which ontology you’re looking at? The URL you sent results in a 404 error (http://bioportal.bioontology.org/404?p=classes&conceptid=SIB<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioportal.bioontology.org%2F404%3Fp%3Dclasses%26conceptid%3DSIB&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=bQgTRXD1MlpCl82yJN10fOPvdQ2SIYxDxawJJY%2FQHmE%3D&reserved=0>).

Jennifer



On Dec 10, 2017, at 9:14 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Sougato Das
Email: sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=h%2B%2BzuX4xvYMQRn6XeUqiPXPy1Bw1bD8z75chnLaAMAU%3D&reserved=0>%2F404%3Fp%3Dclasses%26conceptid%3DSIB

Feedback:
What does "Inverse of SIB" mean? I've googled extensively for the definition of this term and have not had any luck. Thanks.

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