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[bioontology-support] [BioPortal] Feedback from Nick Felicelli

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Aug 23 16:28:38 PDT 2016


Hi Nick,

The BTO ontology is repaired and reindexed.  I tested the search functionality and it seems to be working well.  Let us know if you encounter any issues.

Apologies for the inconvenience.

Best,
Jennifer



On Aug 17, 2016, at 6:36 AM, Felicelli, Nicholas (Nick) <Nicholas.Felicelli at cchmc.org<mailto:Nicholas.Felicelli at cchmc.org>> wrote:

Thanks for the info.

-Nick

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Monday, August 15, 2016 at 8:41 PM
To: "<support at bioontology.org<mailto:support at bioontology.org>>" <support at bioontology.org<mailto:support at bioontology.org>>, "Felicelli, Nicholas (Nick)" <Nicholas.Felicelli at cchmc.org<mailto:Nicholas.Felicelli at cchmc.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Nick Felicelli

Hello Nick,

The latest BTO ontology failed to parse correctly, and BioPortal is not falling back to the previous submission. I tried opening the most recent BTO submission with Protege, and it failed with a "string out of bounds error". I will contact the ontology owner to see if a new ontology may be available.

This is partly affected by a systematic issue that our development team can diagnose more thoroughly later this week, so rather than attempt a stop-gap solution, I'd like to wait until they can devote some time to it.

Please contact me offline if you have an urgent need for these results, and we can explore options.

John


On Aug 15, 2016, at 12:09 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Nick Felicelli
Location: https://bioportal.bioontology.org/search<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_search&d=CwMFAg&c=P0c35rBvlN7D8BNx7kSJTg&r=pWDnieq-OzyjZChNAbXt8FBGr2Wn-Y79NGiLV0nxfrM&m=3G7uderVF9dw_ozXl8MOZ_ay6A6ibU-AD_jVAU8554Y&s=gzMNB9RrcAwN9dvlokWnGMHmy7onjNrh5YHRoY2-3e4&e=>

Feedback:
It seems that the BTO ontology is not working. For any search I am not able to get any data out of it. Load the following url and click search to see the no results
URL:
https://bioportal.bioontology.org/search?q=skin&ontologies=BTO&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories=<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_search-3Fq-3Dskin-26ontologies-3DBTO-26include-5Fproperties-3Dfalse-26include-5Fviews-3Dfalse-26includeObsolete-3Dfalse-26require-5Fdefinition-3Dfalse-26exact-5Fmatch-3Dfalse-26categories-3D&d=CwMFAg&c=P0c35rBvlN7D8BNx7kSJTg&r=pWDnieq-OzyjZChNAbXt8FBGr2Wn-Y79NGiLV0nxfrM&m=3G7uderVF9dw_ozXl8MOZ_ay6A6ibU-AD_jVAU8554Y&s=U9LXjcAybfQxIHXHEJH0JRO116gcKglSt5sNGO-f0RY&e=>

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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
skype: graybealski

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