Thanks. I will check your use case later. Now Dr. Chris Stoeckert (my
supervisor) and I are working on MO terms that were used in the
microarray experiments which stored in ArrayExpress. Most of the terms
used in those studies have been added into OBI. If you have other terms
needed including those out of scope of MGED ontology, you can either
provide the list to me or check OBI first and submit needed terms to OBI
tracker items directly
(http://sourceforge.net/tracker/?group_id=177891&atid=886178).
I will post latest mapping file later today and let you know the link.
Thanks,
Jie
Jim McCusker wrote:
Thanks. I have been using classes and properties from MGED Ontology in
magetab2magerdf (http://magetab2magerdf.googlecode.com), and was
hoping to move to an OBI-based mapping sooner rather than later. You
can see an example at
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986.rdf
You will note that I am using an extension of MO which includes
classes and properties for things like Comments, ProtocolApplications,
and other items that are missing from MO. Any advice on if those items
exist in OBI would be helpful.
Thanks,
Jim
On Wed, Mar 31, 2010 at 10:47 AM, Jie Zheng <[email protected]
<mailto:[email protected]>> wrote:
Hi Jim,
We are only working on classes and instances but properties now.
Most of mapped classes have logical definition (use OBI
properties) in OBI. We will map properties when classes/instances
mapping are done. If you have any use cases that used MO
properties, please let me know. I can check whether it can map to
any OBI one.
Thanks,
Jie
Jim McCusker wrote:
Is this just classes, or are properties mapped as well?
Jim
On Wed, Mar 24, 2010 at 9:07 PM, <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
Hi All,
I have made the mapping between MO and OBI/OBO ontologies and
posted the mapping
files on MGED ontology page. You can find the links in the
mapping
section of
page
http://mged.sourceforge.net/ontologies/MGEDontology.php
The mapping were made based on the definition. We found it
should
be more
accurate to map the terms based on how they were used in the
MAGE-TAB files.
This work is in progress. I will update the MO to OBI
mapping file
soon and
distribute the link.
Thanks,
Jie
Quoting Helen Parkinson <[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>:
Hi all,
let me clarify. OBI is at release 1.0
1. EFO imports parts of OBI that we need for
ArrayExpress, we
will continue to use EFO in ArrayExpress, as it has added
terms and relations between terms that exist nowhere else -
cell types, to cell lines for example. And it has some
terms
that are imported from e.g. the cell type ontologu EFO
is an
application ontology and will persist as we need it in our
GUIs. You can see our paper on this here:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq099
2. Where we import terms from OBI - or any other
ontology we
retain their namespace as recommended by OBI foundry.
As more
terms are in OBI we will import them.
3. My colleague Jie Zheng is in the process of mapping
MO to
OBI and when this is complete we will import more terms
from
OBI into EFO, but EFO will still be used for the
foreseeable
future by ArrayExpress. You can think of EFO as an
application
ontology, or view on OBI and many other ontologies.
4. Where ontology terms imported into EFO have an
authoritative source e.g. Chebi we use their namespace and
where they are from non authoritative sources, for example
there is no obo foundry ontology and many competing
ontologies
we assign our own ids and will continue to do so
Happy to answer any questions.
best regards
Helen
Michael Miller wrote:
hi all,
some comments on the minutes.
"Possible overlaps with EFO ontology from EBI and OBI"
if i understand correctly, EFO was created because
OBI was
not finalized
yet and ArrayExpress at EBI is a live gene
expression data
repository and
the curators needed an ontology they could use. i
believe
their plan is
to move to OBI or update EFO to reflect the
relationship
of terms in EFO
to terms in OBI.
"MGED may be part of OBI now"
MGED (www.mged.org <http://www.mged.org>
<http://www.mged.org>) is a non-profit
organization. What is being referred
to as MGED on the HCLS web site is a predecessor to OBI
which should be
called the MGED Ontology, also referred to as MO, that
came out of an MGED
effort. OBI is to replace MO.
cheers,
michael
Michael Miller
Principal Software Developer
www.teranode.com <http://www.teranode.com>
<http://www.teranode.com>
-----Original Message-----
From: [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
[mailto:public-semweb- <mailto:public-semweb->
<mailto:public-semweb- <mailto:public-semweb->>
[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>] On Behalf Of M. Scott
Marshall
Sent: Wednesday, March 24, 2010 12:31 PM
To: HCLS
Subject: Minutes for Scientific Discourse call
Minutes for the Scientific Discourse call last
Monday
can be found at:
http://www.w3.org/2010/03/22-hcls-minutes.html
Sudeshna has distilled them nicely onto the wiki:
http://esw.w3.org/HCLSIG/SWANSIOC/Meetings/2010-3-22_Conference_Call
Cheers,
Scott
--
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
http://tw.rpi.edu
--
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
[email protected] <mailto:[email protected]> | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
[email protected] <mailto:[email protected]>
http://tw.rpi.edu
