From: Chris M. <cj...@fr...> - 2005-02-08 22:30:30
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On Wed, 2 Feb 2005, Mikel Egana Aranguren wrote: > Yes, I did my MSc dissertation on summer using the workflow written by > Chris Wroe and now I'm writting my own one using GO MySQL and Protege > OWL API via the protege ScriptTab (programing in JYTHON). > > The thing is that I build new OWL ontologies from GO 'dissecting' the > terms and adding restrictions on properties based on the dissection > criteria, then importing an external ontology related to those criteria > to reason over both (detailed explanation can be found at: > http://www.sindominio.net/~pik/thesis.pdf). In any case I will have a > look, is this related to OBOL? (http://www.fruitfly.org/~cjm/obol/) > Where can I obtain the GO OWL exports? The OWL exports can be found at the URL you provide above (just look under 'latest results'). These exports are distinct from the OWL exports on the godatabase.org site, which are purely format conversions. Your thesis is very interesting & well written. Your approach is indeed similar to Obol. Here's a few of the differences: - You use a regular grammar for decomposing term strings, Obol uses a context free grammar - You use Racer as a reasoner, Obol uses a native prolog reasoner; this reasoner is only capable of reasoning over aristotelian definitions which are less expressive than DL definitions, but appear to be expressive enough for most GO or OBO terms (although 5.8 in your thesis suggests otherwise). The Obol reasoner also seems to catch a few cases that racer doesn't. - You use the MESH chemical ontology, whereas Obol uses the OBO-ChEBI ontology. This means Obol misses some of the cases you catch, such as "somatostatin binding is_a neuropeptide binding". You seem to suggest that some of the rejected is_as you create may be a result of errors in the MESH subsumption hierarchy. Obol could easily use MESH, I haven't yet done a comparison of the two for the purposes of reasoning. > Chris did some work in extending the GO MySQL schema to add some results > of the workflow (OWL restrictions, for example), and I think I will try > to add it to my workflow once it is finished, I will inform you about > the results. You can ask Chris to send you the little report he wrote on > that (cw...@cs...). OK. We should try and synchronise the schema since the GO MySQL schema will have optional extensions for some DL expressions (in line with the extensions to the obo format), and these may be different from ChrisW's. > Cheers > > Mikel > > > On Tue, 1 Feb 2005 15:53:21 -0800 (PST) > Chris Mungall <cj...@fr...> wrote: > > > > > Hi Mikel > > > > Is this based on the work that Chris Wroe did extending the GO > database to > > allow some OWL features? > > > > You may be interested in the experimental OWL exports we're making > > available from GO - we should check our respective mappings are > > consistent. The current OWL exports don't attempt to model any of the > > metadata (such as synonyms), just the structure of the ontology. > > > > I'm also considering optional extensions to the GO MySQL schema for > some > > OWL features, in particular defining classes via intersection_of > > > > Cheers > > Chris > > > > On Mon, 31 Jan 2005, Mikel Egana Aranguren wrote: > > > > > That sound really good but I will first try with go-db-perl, as it > is > > > more apropriate for my level of knowledge. In any case perhaps in > the > > > later I go for redland and RDF (and ask you fot those python > > > scripts!!!). > > > > > > What I'm planing to do with the ontology is just query the database > and > > > build an OWL ontology (after some changes) using the OWL API in the > > > protege script tab. I have already setup a system that does it for > GO > > > MySQL, so I just wanted to save up some time. > > > > > > Thank you > > > > > > Mikel > > > > > > On Fri, 28 Jan 2005 16:39:32 +0200 > > > Simon Cross <si...@sa...> wrote: > > > > > > > Hi Mikel, > > > > > > > > > Has anyone put an OBO ontology in MySQL before?Any pointers? > > > > > I'm interested in doing it for the Drosophila anatomy: > > > > > http://obo.sourceforge.net/cgi-bin/detail.cgi?drosanat > > > > > > > > I'm not sure what you're planning to do with the ontologies once > > > they're > > > > in the database but I've recently being using Redland [1] to store > the > > > > eVOC ontologies as RDF [2] in a MySQL database. > > > > > > > > If you think this is appropriate for you I'm happy to chat about > my > > > > experiences. I could probably also share some Python scripts I > have > > > for > > > > importing OBO files into Redland (I'll have to check that they're > > > > suitably generic - I might have built-in some eVOCisms without > > > realising > > > > it). > > > > > > > > [1] http://librdf.org/ > > > > [2] http://www.w3.org/TR/rdf-primer/ > > > > > > > > Schiavo > > > > Simon > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > > > Reporting > > > > Tool for open source databases. Create drag-&-drop reports. Save > time > > > > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, > etc. > > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > > > > _______________________________________________ > > > > Obo-discuss mailing list > > > > Obo...@li... > > > > https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > > > > > > > ------------------------------------------------------- > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > Reporting > > > Tool for open source databases. Create drag-&-drop reports. Save > time > > > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, > etc. > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > > > _______________________________________________ > > > Obo-discuss mailing list > > > Obo...@li... > > > https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > Reporting > > Tool for open source databases. Create drag-&-drop reports. Save time > > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > > _______________________________________________ > > Obo-discuss mailing list > > Obo...@li... > > https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > |