- From: Jie Zheng <jiezheng@pcbi.upenn.edu>
- Date: Wed, 31 Mar 2010 21:12:25 -0400
- 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>
Hi Jim, I have updated the MO to OBI mapping file and check in soureforge.net. However, I got trouble to update the MGED ontology website hosted by sourceforge.net. Will try it later and send email if I made it. Sorry about it since I will take 2 week vacations from tomorrow. If you like, you can send me the terms you used and I can check whether they are in OBI. Thanks, Jie Jim McCusker wrote: > The terms I use (as opposed to classes, like BioSource, Experiment, > Hybridization, etc.) are picked up through the Term Sources listed in > the MAGE-TAB files. > > Jim > > On Wed, Mar 31, 2010 at 12:12 PM, Jie Zheng <jiezheng@pcbi.upenn.edu > <mailto:jiezheng@pcbi.upenn.edu>> wrote: > > 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 > <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> > <mailto: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>> > <mailto: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>> > <mailto: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> > <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> > <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-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->> > <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>> > <mailto: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>> > <mailto: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>> > <mailto: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> > <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 Thursday, 1 April 2010 01:13:15 UTC