- From: zucker <zucker@research.dfci.harvard.edu>
- Date: Mon, 26 Sep 2005 22:45:50 -0400
- To: public-semweb-lifesci@w3.org
Hello Xiaoshu, One semantic web-enabled ontology that several on this mailing list have been involved with is BioPAX. The primary goal is to integrate the overlapping schemas of all the metabolic, molecular interaction, and signaling pathway databases into one merged upper level ontology, specified in OWL. The secondary goal is to make the data from all these databases available in BioPAX format. Check out www.biopax.org and www.biopaxwiki.org Sincerely, Jeremy >> >> Dear Luca, >> >> Thank you for the input. I know of (but not KNOW in the matter of >> detail) about the ontologies you mentioned. But a few reasons that >> "push" me off about these ontologies for the use in the context of >> Semantic Web are: (1) They do not comply to SW technology >> specifications. >> If you go to OBO and check those developed ontology, most of them are >> not coded in RDF/OWL. Even for a few that have the "OWL-version", they >> are not coded corrected. For instance, GO has a presumed namespace >> "http://www.geneontology.org/owl/", but access that URI leads to a 404. >> Coding an ontology in RDF or OWL doesn't mean they are using the >> semantic web ontology. >> (2) Many of them are overlapping, for instance, GALEN and MSH, etc. >> IMHO, ontology merging is no easier than schema integration. It is a >> transformation of the old problem but not the solution. >> (3) All these ontologies are still developed in a monolithic manner. No >> consideration about the granuality and practicality has been emphasized. >> An encyclopedic-like ontology is only useful as referece but not for >> other "reasoning task". I have used Jena before to play around the >> w3c's example Wine Ontology. Reasoning with subClass etc., is O.K. but >> once all other axioms are considered, my computer always run of memory. >> >> So, when I made the suggestion, I meant more from the technical >> perspective than content. Particularly, I meant the application of >> ontology in the context of semantic web. If an ontology is designed in >> such that it can not be executed in the context of SW, what good it does >> to us - at least in this group? My own personal interest in ontologies >> are about experimental data, like how to model gel, MS data etc. Maybe, >> as a group, we can start from this, I already have some prelimiary work >> done like a trivial top ontology about scientific research - BOSS >> (http://www.charlestoncore.org/ontology/boss), which I don't think >> overlap with any of the ontologies you recommend? >> >> Xiaoshu Wang >> > > >>>> However I would like to prompt your attention on the work >>>> which has already been done. >>>> The goal of creating biological and meaningful ontologies for >>>> biology and for chemistry or medicine has a very long >>>> history, thus by learning from "the past" one could save some >>>> considerable time and also avoid repeating the same "design >>>> flaws" (let's not call them mistakes). >>>> >>>> If you have not yet done so, I would strongly suggest you to >>>> add depth to your knowledge in the field of biomedical >>>> ontologies before starting coding yourself "yet-another-ontology" if >>>> you want to have your effort being well rewarded (by >>>> spread use of the ontology itself). >>>> >>>> Few examples are: >>>> Open Biological Ontologies (obo.sourceforge.net >>>> Unified Medical Language System >>>> GALEN Ontology >>>> Medical Subject Headings >>>> SWISS-PROT Keywords the SWISS-PROT keyword list now has >>>> definitions >>>> (in nat. lang.) associated with each keyword. >>>> Edinburgh Anatomies Have whole or partial anatomy ontologies for >>>> adult and developmental stages for several model organisms. The >>>> Ingenuity company has a large knowledge base of experimental >>>> findings in biology. Currently, their ontology is not viewable. >>>> The MGED ontology working group aim to develop ontologies for >>>> describing gene expression experiments and data. >>>> Semiotes >>>> Regulatory Networks Model >>>> PharmGKB: Pharmacogenetics Knowledge Base. >>>> the TAMBIS ontology (TaO) an ontology of bioinformatics >>>> and molecular >>>> biology. >>>> RiboWeb an ontology describing ribosomal components, >>>> associated data >>>> and computations for processing those data. >>>> EcoCyc an ontology describing the genes, gene product function, >>>> metabolism and regulation within E. coli. >>>> Molecular Biology Ontology (MBO)A general, reference >>>> ontology for >>>> molecular biology. >>>> Gene Ontology (GO) an ontology describing the function, >>>> the process >>>> and cellular location of gene products from eukaryotes. >>>> Mouse Genome Informatics GO browser >>>> Mouse Anatomical Dictionary >>>> ImMunoGeneTics (IMGT) Ontology >>>> STAR/mmCIF Macromolecule structure ontology. >>>> STAR/mmCIF Signal Transduction Knowledge #Environment (STKE). >>>> GENAROM Ontology of gene product interactions. >>>> GeneX Ontologies for comparing gene expression across species. >>>> EpoDB Controlled Vocabulary function, cell and tissue type, >>>> developmental stage and experimental type. >>>> CBIL Controlled Vocabulary Terms for human anatomy. >>>> Japan Bio-Ontology Committee including Signal >>>> Transduction Ontology >>>> flybase controlled vocabulary for fly anatomy used for >>>> describing >>>> phenotypes. >>>> >>>> and certainly is a good idea to involve those which are >>>> already 10+ years in the field: >>>> http://anil.cchmc.org/Bio-Ontologies.html >>>> http://www.cs.man.ac.uk/~stevensr/ontology.html >>>> >>>> Good luck ! >>>> luca >>>> >>>> This message and any attachment are confidential and may be >>>> privileged or otherwise protected from disclosure. If you are >>>> not the intended recipient, you must not copy this message or >>>> attachment or disclose the contents to any other person. If >>>> you have received this transmission in error, please notify >>>> the sender immediately and delete the message and any >>>> attachment from your system. Merck does not accept liability >>>> for any omissions or errors in this message which may arise >>>> as a result of E-Mail-transmission or for damages resulting >>>> from any unauthorized changes of the content of this message >>>> and any attachment thereto. Merck does not guarantee that >>>> this message is free of viruses and does not accept liability >>>> for any damages caused by any virus transmitted therewith. >>>> >>>> >>>> >> >>
Received on Tuesday, 27 September 2005 02:45:58 UTC