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[bioontology-support] [BioPortal] Feedback from brycemecum

John Graybeal jgraybeal at stanford.edu
Fri Aug 2 09:54:54 PDT 2019


Hi Bryce,

We've done a bit more investigation, but it's clear this will take some more time than we have right now. The short answer is that we have some code that attempts to determine the 'origin' ontology in the UI, and organizes things appropriately. Unfortunately the Javascript for this is 'before our time' and the results are of unknown quality, so we aren't in a position to quickly reuse it in other contexts.

If you have a specific use case we would be interested in understanding that better. (One of our teams here has made a similar request to the BioPortal team, so it will be useful to know if you are in a similar situation.)

Based on the lack of questions about this up until now—perhaps people haven't written many applications against the search API?—we can't prioritize it too highly given current resoures. But it seems like a valid question and request, and we hope to be able to pursue it before too long.

John

On Jul 29, 2019, at 4:25 PM, Bryce Mecum <mecum at nceas.ucsb.edu<mailto:mecum at nceas.ucsb.edu>> wrote:

Hi Jennifer, thanks for getting back to me! Ranking ontologies as you
have makes sense.

You mentioned that the result from UO is the one you really want. I’m not sure if you’re aware that you can narrow your search results to a particular ontology using the “ontologies” parameter, e.g.

I was, though my use case doesn't allow me to know the ontology of
origin at the time I look up the class. But that's more a problem on
my end rather than yours. I think I can work with what the API
provides.

Apologies that I don’t have an immediate response to this last part of your message. I’m unclear on why the BioPortal web application (which is built on top of the REST API) is showing the ordering differently. I would need to investigate the code further.

If you could that'd be appreciated.

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


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