Thanks very much, Jie! Tim
On Mar 24, 2010, at 9:07 PM, [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]>: > >> 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) 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 >>> >>> >>>> -----Original Message----- >>>> From: [email protected] [mailto:public-semweb- >>>> [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 >>>> >> > > > > > >
