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[bioontology-support] questions regarding our importation tests in stage.bioontology.org

Ray Fergerson ray.fergerson at stanford.edu
Mon Jul 8 15:44:46 PDT 2013


Bernard,



I can’t set up the purl on staging and still have it working in
production. After you submit to production I can fix it if it is broken.
(We don’t have a separate staging purl server).



We are trying to get people to use shorter acronyms. Can I suggest instead
something like “ONL-MSA”.



As for the duplicate information, we need to improve the UI a bit to make
it clear what is going on. The first section of the details panel for a
term shows our “standard bioportal” properties. These are often mapped to
user defined properties with different names. (Hence standard
“Definitions” is mapped to “definition” for your ontology. After the
standard set (but currently indistinguishable) are the user defined
properties. Some people who know an ontology really want to see the names
of the properties from the ontology rather than our “standard set”. Thus
we put all user-defined properties in this second list. This results in
duplicate properties but it seems to be the lesser of the two evils.



Ray



From: bernard gibaud [mailto:bernard.gibaud at univ-rennes1.fr]
Sent: Monday, July 08, 2013 12:21 AM
To: ray.fergerson at stanford.edu; support at bioontology.org
Cc: Bénédicte Batrancourt
Subject: questions regarding our importation tests in
stage.bioontology.org



Hi Ray,

Benedicte Batrancourt and I made a number of importation tests during the
last week using stage.bioontology.org.

We are almost ready for importing our ontology modules into
bioontology.org, but we'd like to fix a number of remaining imperfections.

1. When we go on one of the ontologies we have imported, e.g. 'Mental
State Assessment', we cannot access the taxonomy using the 'BIOPORTAL
PURL' field: actually clicking the link
http://purl.bioontology.org/ontology/OntoNeuroLOG-MSA   leads to the
following message :  'We're sorry but something has gone wrong. Wehave
been notified of this error'

In fact, when we click on the 'version' filed, everything looks fine, and
the tree is shown normally.

How to fix that ?

2. Besides, we note that definitions are shown twice : for example if you
go on entity called  'instrument variable', you can see two definition
items, one called 'Definitions' and the other called 'Definition', with
the same content (which is encoded in our ontology using the
'http://www.w3.org/2004/02/skos/core#definition' annotation).

Same question: is it possible to fix that ?

Many thanks for your help. If you note any other things that you believe
we should change, don't hesitate to tell us.

Best regards,

Bernard Gibaud




--
Bernard Gibaud
Equipe INSERM MediCIS
Unite U1099 LTSI, Universite de Rennes 1
Faculte de Medecine
2, Avenue du Pr. Leon Bernard
CS 34317
35043 Rennes Cedex, France
France
Tel +33 (0) 2 23 23 45 90 ou +33 (0) 2 23 23 47 18 (secr)
email: bernard.gibaud at univ-rennes1.fr
page web: https://medicis.univ-rennes1.fr/members/bernard.gibaud/index

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