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[bioontology-support] Fwd: mappings

Amir Ghazvinian amirg at stanford.edu
Tue Nov 24 12:43:45 PST 2009


---------- Forwarded message ----------
From: Amir Ghazvinian <amirg at stanford.edu>
Date: Mon, Nov 23, 2009 at 11:34 AM
Subject: Re:mappings
To: juliadmtr at gmail.com


Hi Julia,

In order to use LOOM, the ontologies must be in OWL format, but you should
create a .pprj file for each ontology by opening and saving the ontology
with Protege (http://protege.stanford.edu).  You also need to ensure that
the name of the class shows up in the browser text.  This is confusing but
important for finding the mappings, and instructions are given in the
documentation (http://www.bioontology.org/wiki/index.php/LOOM).

The SynonymSlotURI for an OBO ontology that has been converted to OWL
generally looks something like
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym.  It is the
full URI to the property storing synonym values for the concepts.

I hope that this helps, and please feel free to contact me if you have any
questions.

Amir



Begin forwarded message:

*From: *Julia Dmitrieva <juliadmtr at gmail.com>
*Date: *November 21, 2009 9:10:27 AM PST
*To: *support at bioontology.org
*Subject: **[bioontology-support] mappings*

Dear BioPortal community.

I would like to create mappings in different ontologies with LOOM.
Is it possible to use OBO or OWL format (in description is written,
that I have to use .pprj file format).

My second question is:
In the case of OBO ontology what will be the TargetSynonymSlotURI:

for example,  what will be the TargetSynonymSlotURI in the following case:

format-version: 1.0
date: 27:04:2009 14:30
saved-by: VPetri
auto-generated-by: OBO-Edit 1.101
default-namespace: pathway
.
.
.
.
[Term]
id: PW:0000416
name: sentrinization pathway
def: "A pathway of protein modification via conjugation with sentrin - a
family of ubiquitin-like protein. Sentrinization does not target proteins to
the proteasome, rather it targets proteins to particular cellular
compartments." [PubMed:PMID\: 10806345; 15808504 "Review articles in
PubMed"]
related_synonym: "SUMO modification pathway" []
related_synonym: "sumoylation pathway" []
is_a: PW:0000433 ! protein modification pathway via conjugation with
ubiquitin and ubiqutin-like molecules

Is it pathway#related_synonym?

Thank you for your help,
with best regards,

Julia
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