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Re: Minutes for Scientific Discourse call

From: Jie Zheng <jiezheng@pcbi.upenn.edu>
Date: Wed, 31 Mar 2010 10:47:32 -0400
Message-ID: <4BB36084.2010302@pcbi.upenn.edu>
To: Jim McCusker <mccusker@gmail.com>
CC: Helen Parkinson <parkinson@ebi.ac.uk>, Michael Miller <mmiller@teranode.com>, "M. Scott Marshall" <marshall@science.uva.nl>, HCLS <public-semweb-lifesci@w3.org>
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, <jiezheng@pcbi.upenn.edu 
> <mailto:jiezheng@pcbi.upenn.edu>> 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 <parkinson@ebi.ac.uk
>     <mailto:parkinson@ebi.ac.uk>>:
>
>         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>) 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>
>
>
>                 -----Original Message-----
>                 From: public-semweb-lifesci-request@w3.org
>                 <mailto:public-semweb-lifesci-request@w3.org>
>                 [mailto:public-semweb- <mailto:public-semweb->
>                 lifesci-request@w3.org
>                 <mailto:lifesci-request@w3.org>] 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
> james.mccusker@yale.edu <mailto:james.mccusker@yale.edu> | (203) 785-6330
> http://krauthammerlab.med.yale.edu
>
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mccusj@cs.rpi.edu <mailto:mccusj@cs.rpi.edu>
> http://tw.rpi.edu
Received on Wednesday, 31 March 2010 14:48:21 GMT

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