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[bioontology-support] Fwd: [BioPortal] Feedback from Fabian Goguta

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Mar 18 15:36:43 PDT 2019


Forwarding my reply to the support list in case this information is helpful to the community in general.

Jennifer



Begin forwarded message:

From: Jennifer Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Fabian Goguta
Date: March 18, 2019 at 3:16:50 PM PDT
To: XYZ Metauser <xyzmetauser at gmail.com<mailto:xyzmetauser at gmail.com>>

Hello Fabian,

You could do this programmatically using our REST API. For example, here’s a REST call issued via a browser that retrieves the data for the class you pointed out below:

http://data.bioontology.org/ontologies/CPT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCPT%2F01952?include=all<http://data.bioontology.org/ontologies/CPT/classes/http://purl.bioontology.org/ontology/CPT/01952?include=all>

If you use the “include=all”, or “include=properties” field-value pairs in the query string, BioPortal will return all of the properties and their values in the result set:


[cid:A3C6287A-499F-41FC-93D2-A9524E3FF67F at lan]


Our REST API is documented here:

http://data.bioontology.org/documentation

Kind regards,
Jennifer


On Mar 16, 2019, at 5:23 AM, XYZ Metauser <xyzmetauser at gmail.com<mailto:xyzmetauser at gmail.com>> wrote:

Hey there. Here's an example: http://bioportal.bioontology.org/ontologies/CPT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCPT%2F01952

So we have Anesthesia for second- and third-degree burn excision or debridement with or without skin grafting. There are several alternative labels for the same code (see altLable): anesthesia for treatment of second and third-degree burn, between 4% and 9% total body surface area
ANES 2/3 DGR BRN EXC/DBRDMT W/WO GRFT 4-9 % TBSA
Anesthesia for second and third degree burn debridement with skin graft
Anesthesia for second and third degree burn excision
Anesthesia for second and third degree burn excision with skin graft
Anesthesia for second and third degree burn debridement

I was wondering if there is any way of extracting these altLabels from each code instead of copying them manually for each code (which would take weeks).

Thanks!

On Fri, Mar 15, 2019 at 9:07 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Fabian,

We import CPT into BioPortal from the UMLS Metathesaurus [1]. I looked at a few of the CPT classes in BioPortal and I don’t see this “altlabels” property you’re referring to. Are you able to offer any additional detail about this property that you’re looking for?

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CPT/



On Mar 14, 2019, at 3:58 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Fabian Goguta

Email: xyzmetauser at gmail.com<mailto:xyzmetauser at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Ffeedback%3Flocation%3Dhttp%25253A%25252F%25252Fbioportal.bioontology.org<http://25252fbioportal.bioontology.org/>%25252Fontologies%25252FCPT%25253Fp%25253Dclasses%252526conceptid%25253D90281

Feedback:

Hello. I would like to know whether there is any way of obtaining a complete list of altlabels for each CPT code. Thank you.

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