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[bioontology-support] [BioPortal] Feedback from marcibowen

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Aug 17 11:28:01 PDT 2017


Hello Marci,


On Aug 16, 2017, at 4:12 PM, Marci Bowen <marcia.bowen at duke.edu<mailto:marcia.bowen at duke.edu>> wrote:

I use Firefox. I cleared the cache and that corrected the problem.

Now, how I can I download the SNOMED code and description of all the decedents that result from searching.


Due to licensing restrictions, we’re unable to provide the SNOMED ontology as a file download. You can however, access SNOMED data via our REST API.  For example, to retrieve the descendants of the “Seizure” term, you can use this call:

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

I don’t know what property you’re referring to when you say “code”. You can use the BioPortal user interface to look at the properties and their associated values for any class:


[cid:4B1C4D28-57CB-49BD-87DC-713F36DFCF9A at stanford.edu]


I don’t see any properties on the right-hand side that are called code or definition. If you can’t find what you’re looking for in BioPortal, you might consider getting a UMLS license (free and easy), and try out the web-based browser that they offer for the set of UMLS ontologies (SNOMEDCT is one of them).


[cid:CA44E871-4794-4B2B-9549-178F9086A91F at stanford.edu]



Can I also download the hierarchy? In this case, I searched seizure.


Yes, this is possible from the REST endpoint. You may want to look at the tree and/or paths_to_root calls:

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

The REST API documentation is here:

http://data.bioontology.org/documentation#nav_home

Kind regards,
Jennifer






Thanks,
Marci
On Aug 16, 2017, at 19:01, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Marci,

I’m wondering if you could try clearing your browser cache? I’m not sure what browser you’re using. To clear the cache in Chrome, you’d select the menu item “Chrome” -> “Clear Browsing Data…” and follow the instructions in the resulting dialog.

Kind regards,
Jennifer



On Aug 16, 2017, at 1:27 PM, Marci Bowen <marcia.bowen at duke.edu<mailto:marcia.bowen at duke.edu>> wrote:

This is what I am doing:
after I log in, under tools, I select "Ontology Browser”. then I select blue highlighted "SNOMED CT”, I get this error:
We're sorry but something has gone wrong. We have been notified of this error.
So I then have to go back and select classes. I type in Seziure in the jump to: box.
Then I get :
We're sorry but something has gone wrong. We have been notified of this error.

I just want to get a report of all the SNOMED codes and descriptions that a search for seizure gets.

Thanks,
Marci

PS My phone number is 828.408.2434 if you would prefer to call.

Hi Marcia,

Could you give me an example of the term you’re searching for? Are you using any of the advanced search options? Which browser are you using?

Also, do you mean that search is only working for you when you’re logged out?

Kind regards,
Jennifer


On Aug 16, 2017, at 1:09 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: https%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=tljDhJ_diA57oSMHRCNdxMYjIdUGsv8R7MxBMW0SJ4g&s=zfnSclPJVkTpgFBaRPSgf6oRmLB2h1Q1M7zotZd7TR0&e=>%2F500

Feedback:

I desperately need your help. I keep getting :
We're sorry but something has gone wrong. We have been notified of this error.

When I try to search after I log in. What do I need to do?

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