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Re: [GUSDEV] Gene Association data load (GFUS 3.0)
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From: Jonathan S. <js...@pc...> - 2005-09-08 14:57:25
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Mark: If I recall correctly, the with/from annotation indicates another sequence or database entry of some kind that supports the association. It appears that this will still be the approach as there are no new tables or columns related to GO terms. I'm not sure that it's the best possible approach. Perhaps this needs to be revisited? Jonathan On Sep 8, 2005, at 9:56 AM, Mark Heiges wrote: > Thanks for the info, and for your wiki posting on the subject > ( http://www.gusdb.org/wiki/index.php/GusSchemaGoOntologies ). > > While we are on the subject... I want to store the 'with/from' > annotation file field for some of our annotations. Digging around > in the Bioperl2Gus module (thanks to the authors who included nice > documentation in the comments) it looks such links are made via > GOAssociationInstance-> Evidence-> ExternalDatabaseEntry. Is that > (still) the Right Way for GUS3.5? > > -Mark > > Mark Heiges > C210 Life Sciences Building > Center for Tropical and Emerging Global Diseases > University of Georgia, Athens, GA 30602 > TEL: (706) 542-1447 FAX: (706) 542-3582 > > On Sep 8, 2005, at 8:10 AM, Jonathan Schug wrote: > > >> Sanjeev: >> >> The table dots.GoAssociationInstanceLoe is a 'controlled' >> vocabulary of that indicate the different lines of evidence one >> might use when assigning a GO term to an entity. We developed it >> because we load GO term associations from multiple sources. For >> example, the PlasmoDB project got GO annotations from the >> sequencing centers and we also made our own GO function term >> predictions. The link in dots.GoAssociationInstance to this table >> allows us to distinguish the two. >> >> I would use GUS::Common::Plugin::UpdateGusFromXML to load >> dots.GoAssociationInstanceLoe. Here's an example of the XML you >> might use as input to that plugin: >> >> <DoTS.GOAssociationInstanceLOE> >> <name>Human Annotators</name> >> <description>Members of a team of experts look at the gene name >> and think up a GO term.</description> >> </DoTS.GOAssociationInstanceLOE> >> >> <DoTS.GOAssociationInstanceLOE> >> <name>Automatic Annotation</name> >> <description>A very smart programs looks at the DNA sequence and >> thinks up a GO term.</description> >> </DoTS.GOAssociationInstanceLOE> >> >> This bit of XML defines two source of annotation; you can define >> more by running the plugin again or by putting more in the file. >> Note that dots.GoAssociationInstance also has an >> external_database_release_id column which can pin-point the source >> of the data very precisely. The goal of >> dots.GoAssociationInstanceLoe is a broad classification of >> sources. Remember there is also the evidence code which also >> indicates how the association was formed. If you don't think >> you'll care about categorizing sources in this way, just enter a >> single 'some method' in dots.GoAssociationInstanceLoe and use that >> for all association sources. >> >> Hope that helped. >> >> Jonathan >> >> Jonathan Schug, Ph.D. >> >> Center for Bioinformatics >> Computational Biology and Informatics Lab >> University of Pennsylvania >> >> js...@pc... >> (215) 573-3113 voice >> (215) 573-3111 fax >> >> 1413 Blockley Hall, Philadelphia, PA 19014-6021 >> >> >> >> On Sep 7, 2005, at 10:51 PM, Chris Stoeckert wrote: >> >> >>> Hi Sanjeev, >>> These tables were created for our GO prediction pipeline (see >>> http://www.cbil.upenn.edu/GO/). You might want to check if this >>> is really appropriate to what you want to do. >>> The person responsible for this (Dave Barkan) has left the group. >>> Jonathan, Debbie any insights to provide? >>> Thanks, >>> Chris >>> >>> On Sep 6, 2005, at 10:22 AM, Kumar, Sanjeev (Contr) wrote: >>> >>> >>> >>>> Hi, >>>> I am trying to load GOAssociation data by usingga >>>> GUS::GOPredict::Plugin::LoadGoAssoc >>>> plug in in GUS3.0 . >>>> I am getting an error at the initial stage of data load. It is >>>> looking >>>> for data in >>>> table called "Dots.GOASSOCIATIONINSTANCELOE" , because >>>> "Dots.GOASSOCIATIONINSTANCE" has >>>> foreign key relationship with the first table. >>>> I don't know how I am going to get data in the >>>> "Dots.GOASSOCIATIONINSTANCELOE" table. >>>> >>>> Can some one help me? >>>> >>>> Thanks >>>> Sanjeev >>>> >>>> >>>> ------------------------------------------------------- >>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>> September 19-22, 2005 * San Francisco, CA * Development >>>> Lifecycle Practices >>>> Agile & Plan-Driven Development * Managing Projects & Teams * >>>> Testing & QA >>>> Security * Process Improvement & Measurement * http:// >>>> www.sqe.com/bsce5sf >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>> >>> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * >> Testing & QA >> Security * Process Improvement & Measurement * http://www.sqe.com/ >> bsce5sf >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
