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 brycemecum

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Jul 29 15:49:03 PDT 2019


Hello,

On Jul 26, 2019, at 7:17 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

I'm using the term lookup API to find information such as prefLabels for URIs I have. This has mostly worked perfectly (thank you!) but I noticed one oddity:

When searching with the URI "http://purl.obolibrary.org/obo/UO_0000301", which is a term from the UO ontology, the first result from the API is for what appears to be an import of the term into the EFO ontology. The second result is for an instance of the term in the CHEAR ontology and finally, the third result is for the instance of it in UO which is the one I really want.


We have an internal script that runs once per week to calculate an ontology ranking list:

https://github.com/ncbo/ncbo_cron/blob/master/lib/ncbo_cron/ontology_rank.rb

Here’s an example snapshot of what the ranking file looks like:

https://gist.github.com/mdorf/cea96433cf4bf7dd94d109c8e06e29c0

 The BioPortal REST API will order the search results according to ontology rank, which is why EFO and CHEAR appear above UO.

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.:

http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000301&ontologies=UO<http://data.bioontology.org/search?q=http://purl.obolibrary.org/obo/UO_0000301&ontologies=UO>

A complete list of the parameters you can use with the search endpoint is available in the documentation:

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


It'd be really great if the API had listed the result from UO first. The web-based seach does this: http://bioportal.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000301&ontologies=&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories=.


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.

Kind regards,
Jennifer


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20190729/bd5b14e9/attachment.html>


More information about the bioontology-support mailing list