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] Excluding some ontologies.

John Graybeal jgraybeal at stanford.edu
Wed Jun 21 08:25:00 PDT 2017


Vincent,

Great feedback, thanks!

I had forgotten option 2 (Custom Ontology Set), good reminder of that feature!

Unfortunately, numbers one through three all suffer from the problem that a new ontology will not automatically be included in the selected ontologies. Maybe someday we can add an "exclude ontologies" alternative there, to make this capability lower maintenance.

Also, just as a note to the list, in BioPortal users can't create or manage a slice's ontologies at this time, they must ask the BioPortal team to do so. The same for the 'ontologies group' feature.  I'll be writing a post about these features soon.

And as we consider and move toward mutlidisciplinary and internationalized portal software, I think it would not be crazy-hard to index each of the languages represented in the portal separately. Another thought for a future day!

John

On Jun 21, 2017, at 1:37 AM, Vincent Emonet <vincent.emonet at lirmm.fr<mailto:vincent.emonet at lirmm.fr>> wrote:


Hi Sara,

There are multiple options to do this:

  *   You can use the search ontology filter ( Advanced options > Ontologies ). The "Select from list" interface helps you filter the ontologies you want to use (by selecting a whole group or category)

  *   If you are always using the same ontologies, you can filter them in the portal by setting a "Custom Ontology Set" on your account: the portal will only use the ontologies you selected and hide all others

  *   You also can create a slice, a subdomain of the BioPortal services where only a specific set of ontologies are used (i.e.: http://umls.bioportal.bioontology.org<http://umls.bioportal.bioontology.org/> )

  *   On our side we recently made some changes to better handle language in BioPortal. We only index properties from selected languages (so if the portal is set as "french", then it will not index properties that have the english language tag)


Have a nice day,

Vincent

On 20/06/2017 19:12, John Graybeal wrote:
Sara,

Thank you for asking. I'm sorry, the only way I know to do this right now is to explicitly name the ontologies you do want to search.

Our colleagues in France have considered this question for their BioPortal-based servers, which track the language of each ontology. But I don't know if they have implemented the necessary software to search by ontology language. If they have, it might provide an upgrade path for BioPortal, though not one in our immediate plans given available resources.

I'll ask them to respond to this thread if they have anything to add.

John


On Jun 20, 2017, at 10:03 AM, Sara ArabYarmohammadi <s.yarmohammadi at icloud.com<mailto:s.yarmohammadi at icloud.com>> wrote:

Hi,
I know that I can consider some specific ontologies while performing term search but is there a way to exclude some ontologies while searching? Some ontologies are not in English and I don’t want to have their result in my output. Would you please help me with possible options?
Thank you,
Sara
_______________________________________________
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





_______________________________________________
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/20170621/bbbe8dab/attachment-0001.html>


More information about the bioontology-support mailing list