microarray-ontol-digest Friday, November 2 2001 Volume 01 : Number 013 ---------------------------------------------------------------------- Date: Sun, 7 Oct 2001 11:13:42 -0400 From: Chris Stoeckert Subject: [microarray-ontol] ontology update Dear Group, I've updated the hand-crafted ontology and associated RDFS file. A really nice feature of the OILed tool I've been using is the ability to export in different formats including DAML and html. I've posted these and encourage you to look at the html because it lays all the relationships out nicely. http://www.cbil.upenn.edu/Ontology/biomaterial.html OILed also has a "fact reasoner" to check for logical consistencies that I've applied. Changes: I was never happy about biosource, biosample, and labeled_extract as instances of BiomaterialState. Finally convinced myself that these should be subclasses because you can have a class of Biosamples each of which has been manipulated by a different treatment. Also eliminated unit_name as a slot (attribute) for Unit. Decided that these (e.g., years, months, etc) were instances (of TimeUnit). Next steps: There are 3 areas I'd like to make progress on. 1) continue to flesh out the ontology (instances, documentation). 2) review ontology constraints (class type, axioms, etc.) 3) generate example annotation based on ontology. As always, I appreciate any help, feedback, questions. Is anyone else trying this with another tool? 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: Thu, 11 Oct 2001 18:00:53 -0400 From: Chris Stoeckert Subject: [microarray-ontol] more changes/ addition to the ontology Dear Group, Have switched URI from a slot (attribute) to a class so that I can add individual URIs to the ontology. e.g. start with http://www.cbil.upenn.edu/Ontology/biomaterial11.html#NCBI_taxonomy NCBI_taxonomy has_database_entry NCBI_taxon_id and NCBI_taxon_id has_URI www.ncbi.nlm.nih.gov/htbin- post/Taxonomy/wgetorg?id= Cheers, Chris ------------------------------ Date: Fri, 2 Nov 2001 11:09:29 -0500 From: Chris Stoeckert Subject: [microarray-ontol] feedback on ontology development Dear Group, Some things I've been thinking about regarding the MGED Ontology that I would appreciate your thoughts on. First let me point you at the html page: http://www.cbil.upenn.edu/Ontology/biomaterial11.html ClinicalHistory subclasses: Right now the only attributes for ClinicTreatmentHistory, CurrentDiseaseHistory, and PastMedicalHistory are those inherited from ClinialHistory (i.e., lab values and clinical information). This doesn't strike me as sufficient but I'm not sure what else to add. Any suggestions? Compund: Compound is "A drug, solvent, chemical, etc., that can be measured. " I'm changing this class to be a subclass of OntologyEntry so that people can point to the Merck Index or catalogs. Any objections? OntologyEntry: Not all ontologies are on-line and can be specified as a DatabaseEntry. I'm thinking of adding attributes: has_citation, resource_name. OK with you? BehavioralStimulus: Currently this has no attributes except has_protocol inherited from Treatment. I'm thinking of expanding the attributes to include stimulus_type. Instances (individuals) for stimulus_type would be avoidance, reward, deprivation (others?). stimulus_name could also be an attribute but I' m not sure how to describe instances like "shock" or "sleep" and also use a class like Compound. thoughts? 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 ------------------------------ End of microarray-ontol-digest V1 #13 *************************************