microarray-ontol-digest Monday, July 22 2002 Volume 01 : Number 027 ---------------------------------------------------------------------- Date: Wed, 3 Jul 2002 11:24:32 -0400 From: Chris Stoeckert Subject: [microarray-ontol] revised new classes Sorry, hit the send button before I finished. Here it is again. Hi All, I'm finally getting around to adding some more resources that Susanna has sent and relevant ones from the GOBO site (http://www.geneontology.org/doc/gobo.html). I propose that we create a new class under BioSourceOntologyEntry for histology (see http://histology.nih.gov/ for human, mouse, rat). Rather than call it histology we might generalize it a bit more to include other types of atlases. In fact we could call it "Atlas" Definition: Annotated images of organisms and their parts. Included in this would be a resource like http://www.ita.fhg.de/reni/trimming/TR_F.HTM that illustrates how samples from rats and mice are trimmed. I also propose that we create another new subclass to BioSourceOntologyEntry (NOT IndividualGeneticCharacteristics) for traits and phenotypes (see http://www.gramene.org/plant_ontology/trait.ontology). Let's call it "PhysicalCharacteristics" after GOBO but restrict it to phenotype and traits and not include pathology and disease. Comments? 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: Fri, 05 Jul 2002 16:20:27 +0100 From: Helen Parkinson Subject: Re: [microarray-ontol] revised new classes Hi Chris, I have no problem with histology class in principle, but if we expand the defintion to Atlas, we get some overlap with OrganismPart, so should the histology class be a subclass of it? Histology is just another way of looking at bits of an animal, you can use the same terms to describe what you see as you would for OrganismPart. Histology - the science which treats of the detailed structure of animal or plant tissues, microscopic morphology (from Henderson's dict. biol. terms) I like the microscopic morphology bit of that definition. Histology to me is a technique, not a class in itself. One other problem with using histology is its association to disease and pathology in the minds of biologists. fine for PhysicalCharacteristics, I agree not to include pathology or disease, we already have classes for those, cheers Helen Chris Stoeckert wrote: > > Sorry, hit the send button before I finished. Here it is again. > Hi All, > I'm finally getting around to adding some more resources that Susanna > has sent and relevant ones from the GOBO site > (http://www.geneontology.org/doc/gobo.html). > > I propose that we create a new class under BioSourceOntologyEntry for > histology (see http://histology.nih.gov/ for human, mouse, rat). Rather > than call it histology we might generalize it a bit more to include > other types of atlases. In fact we could call it "Atlas" Definition: > Annotated images of organisms and their parts. Included in this would be > a resource like http://www.ita.fhg.de/reni/trimming/TR_F.HTM that > illustrates how samples from rats and mice are trimmed. > > I also propose that we create another new subclass to > BioSourceOntologyEntry (NOT IndividualGeneticCharacteristics) for traits > and phenotypes (see > http://www.gramene.org/plant_ontology/trait.ontology). Let's call it > "PhysicalCharacteristics" after GOBO but restrict it to phenotype and > traits and not include pathology and disease. > > Comments? > > 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: Mon, 22 Jul 2002 08:57:24 -0400 From: Chris Stoeckert Subject: Re: [microarray-ontol] revised new classes Hi Helen, Finally getting back to this, sorry for the long delay. I agree with your point that histology is another way of describing OrganismPart and have added resources to the web site such as Histobank, WebRENI, and the IUPS Physiome Project. Am going to follow your suggestion and make histology a subclass of OrganismPart. Definition: Microscopic morphology of tissues. Have also added the PhysicalCharacteristics class to the ontology. We still a need a place to put images but this could point to Histology if appropriate. FYI to the group, have added some resources to the web site as indicated above and have added a crude mail archive. Will also post a new version soon of the ontology that includes study design and add more instances. Cheers, Chris On Friday, July 5, 2002, at 11:20 AM, Helen Parkinson wrote: > Hi Chris, > > I have no problem with histology class in principle, but if > we expand the defintion to Atlas, we get some overlap with > OrganismPart, so should the histology class be a subclass of > it? > > Histology is just another way of looking at bits of an > animal, you can use the same terms to describe what you see > as you would for OrganismPart. > > Histology - the science which treats of the detailed > structure of animal or plant tissues, microscopic morphology > (from Henderson's dict. biol. terms) > > I like the microscopic morphology bit of that definition. > Histology to me is a technique, not a class in itself. One > other problem with using histology is its association to > disease and pathology in the minds of biologists. > > fine for PhysicalCharacteristics, I agree not to include > pathology or disease, we already have classes for those, > > cheers > > Helen > > Chris Stoeckert wrote: >> >> Sorry, hit the send button before I finished. Here it is again. >> Hi All, >> I'm finally getting around to adding some more resources that Susanna >> has sent and relevant ones from the GOBO site >> (http://www.geneontology.org/doc/gobo.html). >> >> I propose that we create a new class under BioSourceOntologyEntry for >> histology (see http://histology.nih.gov/ for human, mouse, rat). Rather >> than call it histology we might generalize it a bit more to include >> other types of atlases. In fact we could call it "Atlas" Definition: >> Annotated images of organisms and their parts. Included in this would >> be >> a resource like http://www.ita.fhg.de/reni/trimming/TR_F.HTM that >> illustrates how samples from rats and mice are trimmed. >> >> I also propose that we create another new subclass to >> BioSourceOntologyEntry (NOT IndividualGeneticCharacteristics) for >> traits >> and phenotypes (see >> http://www.gramene.org/plant_ontology/trait.ontology). Let's call it >> "PhysicalCharacteristics" after GOBO but restrict it to phenotype and >> traits and not include pathology and disease. >> >> Comments? >> >> 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 > ------------------------------ End of microarray-ontol-digest V1 #27 *************************************