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[bioontology-support] [BioPortal] Feedback from sean.guerrero

Guerrero, Sean Sean.Guerrero at Hoag.org
Mon May 20 09:57:17 PDT 2019


This is perfect, Jennifer. Thank you so much!

Sean A. Guerrero, MHA
Manager of Business Intelligence, Strategic Analytics and Reporting
Hoag Orthopedic Institute
949/727-5066
 Sean.Guerrero at hoag.org<mailto:Sean.Guerrero at hoag.org> | www.HoagOrthopedicInstitute.com<http://www.hoagorthopedicinstitute.com/>

[cid:image001.png at 01D27580.6E6F5760]

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Friday, May 17, 2019 5:40 PM
To: Guerrero, Sean <Sean.Guerrero at Hoag.org>
Cc: support at bioontology.org
Subject: [EXTERNAL] Re: [bioontology-support] [BioPortal] Feedback from sean.guerrero

Hi Sean,

The web-based BioPortal application doesn’t have a table that lists CPT codes and preferred names. We just display the ontology classes as a navigable tree structure.

I’m not sure if using the REST API is a possibility for you. You can pass multiple terms to the search endpoint, e.g., the following URL uses all the CPT codes you listed below (see the q={…} portion):

http://data.bioontology.org/search?q={24546%2024565%2024566%2024575%2024579%2024586}&ontologies=CPT&include=prefLabel&display_links=false&display_context=false<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_search-3Fq-3D-257B24546-252024565-252024566-252024575-252024579-252024586-257D-26ontologies-3DCPT-26include-3DprefLabel-26display-5Flinks-3Dfalse-26display-5Fcontext-3Dfalse&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=qLz4M2PWtVGbWSWWOHNUj_7e00eXYLhVtH6Qos7r4fQ&e=>

If you enter that URL in a browser window, you can see a list of the preferred names for those codes. Screen shot below. FYI - you need an API key to use the REST API (instructions for getting one are here: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FHelp-23Getting-5Fan-5FAPI-5Fkey&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=B0vvK3Hsz2YaG8dnowJARtKwMGNG49yRpddV-dc01yw&e=>).

We also provide examples in a GitHub repository for using the API programmatically: https://github.com/ncbo/ncbo_rest_sample_code<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=USW8G7Nf1SQZHPX23pslXxFgtBA_HaK9TjbAQcCgNJI&e=>. It’s possible to write a short script that would retrieve this data.

Hope that information helps.

Kind regards,
Jennifer

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On May 16, 2019, at 5:31 PM, Guerrero, Sean <Sean.Guerrero at Hoag.org<mailto:Sean.Guerrero at Hoag.org>> wrote:

Hi Jennifer,

Thanks for the quick response!
I have a batch of CPT codes and would like to pull the descriptions under the Preferred Name field. Example below:

It doesn’t look like there’s a way to pull a batch of these and the only way to do it would be to copy and paste the CPT codes, one by one. Is this correct? Is their a table of some sort on your website with all CPT codes and preferred names?

<image001.png>

24546
24565
24566
24575
24579
24586


Sean A. Guerrero, MHA
Manager of Business Intelligence, Strategic Analytics and Reporting
Hoag Orthopedic Institute
949/727-5066
 Sean.Guerrero at hoag.org<mailto:Sean.Guerrero at hoag.org> | www.HoagOrthopedicInstitute.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.hoagorthopedicinstitute.com_&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=3z7yXcEbTLnShYj-xaJqpfiZonoON0IzRX9IrJQoZPQ&e=>

<image002.png>


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