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Re: Minutes for Scientific Discourse call

From: Jie Zheng <jiezheng@pcbi.upenn.edu>
Date: Wed, 31 Mar 2010 12:12:24 -0400
Message-ID: <4BB37468.2000703@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>, Chris Stoeckert <stoeckrt@pcbi.upenn.edu>
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 <jiezheng@pcbi.upenn.edu 
> <mailto:jiezheng@pcbi.upenn.edu>> 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, <jiezheng@pcbi.upenn.edu
>         <mailto:jiezheng@pcbi.upenn.edu>
>         <mailto: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>
>            <mailto: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>
>         <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: public-semweb-lifesci-request@w3.org
>         <mailto:public-semweb-lifesci-request@w3.org>
>                        <mailto:public-semweb-lifesci-request@w3.org
>         <mailto:public-semweb-lifesci-request@w3.org>>
>                        [mailto:public-semweb- <mailto:public-semweb->
>         <mailto:public-semweb- <mailto:public-semweb->>
>                        lifesci-request@w3.org
>         <mailto:lifesci-request@w3.org>
>                        <mailto: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>
>         <mailto: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>
>         <mailto:mccusj@cs.rpi.edu <mailto:mccusj@cs.rpi.edu>>
>         http://tw.rpi.edu
>
>
>
>
>
> -- 
> 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 16:13:15 GMT

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