microarray-ontol-digest Wednesday, February 6 2002 Volume 01 : Number 019 ---------------------------------------------------------------------- Date: Fri, 25 Jan 2002 22:47:53 -0500 From: Chris Stoeckert Subject: [microarray-ontol] update and MGED4 Dear Group, I've added a couple things to the site (http://www.cbil.upenn.edu/Ontology) including Jason Stewart's html page listing all the ontology entries needed for MAGE. These are in addition to the sample/biomaterial descriptions. I've also updated the MGED ontology to reflect work done with Helen Parkinson (http://www.cbil.upenn.edu/Ontology/Build_Ontology2.html). I've sent the rdfs and DAML files to Jason who has kindly set up MGED site at Sourceforge to host these files for CVS (http://mged.sf.net). Looking forward to seeing you at the MGED4 meeting in a couple weeks in Boston (http://php.aaas.org/mged/agenda.php). On Friday the 15th, we will have an Ontology Working Group meeting from 1:30 -3PM. The agenda I have planned so far is: Overview of ontologies Status of MGED Ontology Incorporating ontologies into microarray database annotation form - Helen Parkinson Discussion of issues: e.g., Relationship between MAGE and MGED ontology, Discussion of Use Cases: needs besides retrieving experiments? Thoughts? Other suggestions? What I'd like to hear about is people's current experience with annotating their experiments. What are you using in terms of c.v.s and ontologies? Has the ontology resource page been helpful? What's missing? Is anyone trying to make use of the MGED ontology in any way? What would make that useful? Cheers, Chris Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics Center for Bioinformatics, University of Pennsylvania 418 Guardian Dr., Philadelphia, PA 19104 Ph:215-573-4409 FAX:215-573-3111 ------------------------------ Date: Sun, 27 Jan 2002 11:30:24 -0800 From: "Miller, Michael (Rosetta)" Subject: RE: [microarray-ontol] update and MGED4 + OMG Dear Group, My apologies for anyone who might get this twice. > What I'd like to hear about is people's current experience with > annotating their experiments. What are you using in terms of > c.v.s and ontologies? Has the ontology resource page been helpful? > What's missing? > Is anyone trying to make use of the MGED ontology in any way? > What would make that useful? I think this is an excellent topic to also raise at the OMG, to get input from the lifesci DTC members. It might be a good subject for a followup RFP to the Gene Expression submission. One other issue that Angel Pizarro raised is how an identifier is specified so that it can be recognized within a community (Please see Angel's e-mail in the mged-mage archive for a much more eloquent statement of this). To this I would add a corollary issue, what formal mechanism could be defined to provide equivalence of identifiers. That is, if I base my identifers for sequences on an in-house identifier and another organization bases it on GenBank accessions how do we agree on what are equivalent sequences? This might also apply to Ontologies. Also look forward to seeing everyone at MGED, Michael Michael Miller Senior Application Developer Rosetta Biosoftware michael_miller@rosettabio.com > -----Original Message----- > From: Chris Stoeckert [mailto:stoeckrt@SNOWBALL.pcbi.upenn.edu] > Sent: Friday, January 25, 2002 7:48 PM > To: microarray-ontol@ebi.ac.uk > Subject: [microarray-ontol] update and MGED4 > > > Dear Group, > ------------------------------ Date: Wed, 06 Feb 2002 10:34:32 +0000 From: Helen Parkinson Subject: [microarray-ontol] [Fwd: Genotype to Pheotype Workshop] Forwarded on behalf of Robert Stevens. Extended call for abstracts: Abstracts for this one day meeting, which is part of Manchester Bioinformatics Week, can now be submitted until 11 February 2002. A one-day workshop on "From Genotype to Phenotype Linking Bioinformatics and Medical Informatics Ontologies" (Chaired by Alan Rector and Robert Stevens) is being held as part of Manchester Bioinformatics Week - Easter 2002. The details on the workshop may be found at http://www.biomed2.man.ac.uk/bioinfconferen/default.htm. The medical informatics community has had an interest and a wealth of experience in developing and using ontologies, that stretches back over many decades. The younger Bioinformatics community has also indicated a growing interest in the subject area. There is both a common interest and a diversity in these fields, that together, we hope can be of mutual interest and benefit to both communities. Bioinformatics ontologies have described knowledge of the genotype of organisms: Their molecular biology, function, pathways, molecular structures and general classifications. Medical informatics ontologies have described knowledge about phenotype: Appearance, anatomy, disease, etc. of mainly one organism -- Human, but occaisionally others. the genotype is the genes and genetics, together with associated cellular machinery, that gives rise to those phenotypes. As Bioinformatics gears up to manage, store and analyse data and knowledge from new experimental techniques, such as micro array gene expression, the discipline is becoming more interested in linking knowledge of genotype to the phenotype governed by that gene expression -- or more broadly in linking molecular - genetic, genomic and proteomic - mechanisms to their consequences for physiology and pathology and ultimately clinical medicine - i.e. the health and disease of organs and organisms. Making this linkage is a key step in understanding the mechanisms of known drugs and discovering new ones. The linking of genotype and phenotype ontologies offers interesting opportunities for collaboration between Medical Informatics and Bioinformatics. I hope that you will be able to attend and I also hope that you can submit an abstract to the workshop. Registration and Submission of Abstracts is possible via the web site. The deadline for receipt of abstracts is 25th January 2002. There are reduced fees for payments received before this date. Dr. Robert StevensDepartment of Computer ScienceKilburn BuildingUniversity of ManchesterManchesterM13 9PLTelephone: +44 (0)161 275 6251Web: http://img.cs.man.a.uk/stevensemail: robert.stevens@cs.man.ac.uk ------------------------------ End of microarray-ontol-digest V1 #19 *************************************