From: William B. <William.Bug@DrexelMed.edu> - 2007-04-19 19:17:01
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This is an extremely important issue. Thanks for starting the ball rolling on this, Trish. This issue will become increasingly important as more ontologies start to build out complexity guided by the OBO Foundry principles of community involvement and ontology re-use. OBI is certainly going to need to do this for biochemicals, cells, and tissues. I believe this may have been what Trish was referring to by "a case requesting this 'linking' for OBI". I have a specific follow-up regarding what Barry refers to as "linking" - as distinct from using "owl:import"**. By linking, do you mean referencing an entity from an existing ontology (or other artifact) in such as way that no additional semantic entailments are explicitly stated in an algorithmically accessible manner? If yes, I assume the reference (e.g., "link" from a CARO anatomy class to a MeSH term) is simply meant to provide a lexical variant from a defined, existing CV for that ontology class where all the assertions about that class derive solely from the referencing ontology and are not in any way altered by the link. If no, then I don't really understand the distinction - EXCEPT the software systems available now for processing semantic entailments as they are specified in OWL will not be able to explicitly make use of the semantic entailments declared via the link. In this case, any additional semantic entailments added by the link must be interpreted manually by an expert user or via some custom software constructed specifically for that purpose, though they should still be considered explicit, as opposed to implicit (i.e., not to be used for reasoning purposes). Here's an example of "linking" that will come up in OBI. When describing the Polymerase Chain Reaction (PCR) technique, we will need to explicitly specify continuants playing a "reagent" role in the context of that procedure. Some of these will currently come either from a resources such as the Enzyme Commission nomenclature (EC), UniProt, UniGene, etc. and/or be represented NOT as continuants but as molecular functions as characterized in GO-MF. Other reagents are best specified using the entities described in ChEBI. Some of these are - or will eventually be - OBO Foundry compliant - others won't. In either case, "links" to such entities in the context of fully describing PCR will need to be interpreted along with their semantic entailments. This is clearly not an issue limited to OBI. We have the same issues in BIRNLex, as will many other ontologies that - though specified to cover restricted domains - will NEED to reference elements from other ontologies and artifacts, the latter of which may turn out to take a LONG time to become fully OBO Foundry compliant and/or may not be even planning at this time to make that leap. Cheers, Bill ** There is a thorough model-theoretic treatment of the ontological entailments written by Ian Horrocks & Peter Patel-Schneider available here: http://www.w3.org/TR/2003/WD-owl-semantics-20030331/ direct.html#owl_imports_closure). On Apr 19, 2007, at 11:50 AM, Smith, Barry wrote: > There are no restrictions on linking to external ontologies or other > artifacts (some OBO Foundry ontologies are planning links to MeSH for > example); there are restrictions only when external ontologies are > imported into OBO Foundry ontologies in such a way that they become > part of the latter. Then, the imported parts need to satisfy the same > rules as all the other parts of Foundry ontologies. > BS > > > > At 05:13 PM 4/19/2007, you wrote: >> Are there any constraints from the OBO Foundry on active reference >> ontologies on what resources (ontology or controlled vocabulary) an >> OBO Foundry ontology can link or point to? >> >> For example, if ontology A is developed as an OBO Foundry >> reference ontology and then points to/imports ontology B, which is >> not an >> OBO Foundry ontology and therefore may follow a different design >> pattern, >> set of rules for the subsumption hierarchy etc., is this >> acceptable in the >> view of the OBO Foundry? Is ontology A still an OBO Foundry >> ontology if >> it includes a link to non-OBO Foundry ontologies? >> >> I ask becuase one there may be a case requesting this 'linking' >> for OBI >> and secondly it seems as though if this is allowable it breaks the >> idea >> of semantic interoperability, unless it is the knowledge that >> ontology B >> is not an OBO Foundry ontology that serves as the 'marker' that >> semantic >> interoperability is then not guarenteed with terms from ontology B >> extending from ontology A. >> >> Trish >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss Bill Bug Senior Research Analyst/Ontological Engineer Laboratory for Bioimaging & Anatomical Informatics www.neuroterrain.org Department of Neurobiology & Anatomy Drexel University College of Medicine 2900 Queen Lane Philadelphia, PA 19129 215 991 8430 (ph) 610 457 0443 (mobile) 215 843 9367 (fax) Please Note: I now have a new email - William.Bug@DrexelMed.edu |