Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [BioPortal] Feedback from Jim Van Dyke

John Graybeal jgraybeal at stanford.edu
Fri May 19 09:57:39 PDT 2017


Hello Jim,

Sorry to jump in here, but I need to clarify the question to make sure we can help.

It seems you are trying to construct an inference chain, using the API to follow the class relations. If there is a specific question about how to to use the API to retrieve a particular piece of information, we can try to offer insight. Please let us know the specific API query you are having trouble with, in order that we can be responsive.

On the other hand, if the question is "what is the best way to connect the different parts of the graph?", I have to say that's outside our scope to assess, and would depend on the graph model for the particular ontology(ies). In that case, you will be best served querying experts in those ontologies to determine the best query strategy. (Failing that, a graph query tool may be helpful in exploring the model and paths through it.)

Sorry we can't be more help in the normal run of work.

John



On May 19, 2017, at 9:36 AM, Jim Van Dyke <jvandyke1113 at gmail.com<mailto:jvandyke1113 at gmail.com>> wrote:

Hello Jennifer - Thank you again for your prompt response to our question earlier in the week.  I am at a point where we need to ask for some assistance again with the API generation, as our developer is having problems getting the results we are looking for.


Here is what we are trying to accomplish:

We have a series of NDC codes.  The end result we are looking for is to be able to obtain the CUIs for  May-Treat/May-Prevent data, via NDF-RT, and the ATC Class Level and Notation.

The we had been working through was patterned roughly on the web-site UI flow:

>  Use NDC in RxNORM to navigate via the link to “consists of”

>  Navigate via the Consists of to get to Has_Ingredient CUI

>  Using the “Has_Ingredient” CUI, query ATC to get ATC LEVEL and NOTATION.

>  Using NDC code, query NDF-RT to navigate to ingredient level, and obtain May-Treat and May-prevent CUIs.


Could you please let me know of the API terms or parameters we need to pass and If there is a more direct path to get from NDC to both May-Treat and ATC LEVEL.

Thank you for your assistance.

Kind Regards,
Jim

On Wed, May 17, 2017 at 4:52 PM, Jim Van Dyke <jvandyke1113 at gmail.com<mailto:jvandyke1113 at gmail.com>> wrote:
Hello Jennifer - Thank you for the quick response.  I am totally embarrassed with my typo - should have been NDF-RT (National Drug File - Reference Terminology).

You are correct with what we are trying to do.  We have NDC codes for which we need to look up certain properties such as, for example, Ingredient, and May-Treat/May-Prevent, as well as navigating to other ontologies such as ATC to retrieve ATC Level.

I will try your recommendation above, as I think that will get us on the correct path.

Thank you again.

Jim

On Wed, May 17, 2017 at 4:09 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Jim,

I’m not sure I understood exactly what you want to do.  I’m also not familiar with NRF_RT (I couldn’t find an ontology with that acronym in BioPortal).

With regard to NDDF, are you trying to find classes that have an NDC property with a particular value?  If so, you could do something like this:

http://data.bioontology.org/search?q=66336058120&also_search_properties=true&include=prefLabel,properties

The “/search” portion refers to our term search endpoint.  I used an NDC code for the search term, and I added the “also_search_properties” parameter, which means that both classes and property values will be searched.  The “include” parameter at the end just specifies what data you want as part of the return value.

This portion of our API is documented here:

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

Kind regards,
Jennifer



On May 17, 2017, at 9:31 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jim Van Dyke

Email: jvandyke1113 at gmail.com<mailto:jvandyke1113 at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2F

Feedback:

I am trying to use the API to query NDDF and NRF_RT data based on an NDC code, but I could not find a parameter to submit the NDC code.

Is there a paramater for passing NDC code?

Thank you
Jim

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support



_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170519/ece41a21/attachment-0001.html>


More information about the bioontology-support mailing list