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Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?
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From: Jian Lu <jl...@vb...> - 2005-09-19 13:57:59
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Jennifer, I did check other columns on GOSynonym. Most of the 'source_id' columns are empty, but 'text' are not, but they are the same as GOTerm's column 'name' or 'definition' content. So if there is not a secondary identifier, why should its text be loaded into GOSynonym? jld...@se... wrote: >Jian, > >None of the rows created by the plugin should be empty. Have you checked the >'text' column? Not every row will have a source_id because not everything >entered into GOSynonym has a secondary identifier, but they should all have >'text,' which is the column that holds the actual synonym. > >Jennifer > >Quoting Jian Lu <jl...@vb...>: > > > >>Hi Jennifer, >> >>That makes sense now. It really helps understand this plugin. >> >>However, I have a new question, why the plugin loads so many empty >>records on SRes.GOSynonym while loading those secondary identifiers? >> >> >>Thank you very much. >> >>Jian >> >>jld...@se... wrote: >> >> >> >>>Jian, >>> >>>I beleive that the behavior we are observing is actually a designed >>> >>> >>behavior. >> >> >>>The pattern that I observed in my last email indicated that everything that >>> >>> >>was >> >> >>>missing from the SRes.GOTerm table was a secondary identifier. After >>> >>> >>further >> >> >>>investigation we noticed that secondary identifiers are stored in the >>>SRes.GOSynonym table as source_ids. >>> >>>Please let us know if this resolves your problem, or if you encounter any >>>further issues when dealing with the plugin. >>> >>> >>>Jennifer >>> >>>Quoting Jian Lu <jl...@vb...>: >>> >>> >>> >>> >>> >>>>Steve, >>>> >>>>After further investigation of GO files and comparison of the database, >>>>here is the report: >>>> >>>>GO file information: >>>>!autogenerated-by: DAG-Edit version 1.419 rev 3 >>>>!saved-by: gocvs >>>>!date: Fri Aug 12 21:00:17 PDT 2005 >>>>!version: $Revision: 3.306 $ >>>> >>>>unique GO terms in component.ontology: 1745 >>>>unique GO terms in function.ontology: 7902 >>>>unique GO terms in process.ontology: 10370 >>>>unique GO terms in all three files: 20015 >>>> >>>>total loaded GO terms: 19395 >>>>total missing GO terms: 620 >>>> >>>> >>>>steve wrote: >>>> >>>> >>>> >>>> >>>> >>>>>jian- >>>>> >>>>>yes, we have used the plugin, but it has been changed a little >>>>>recently. can you do a grep on the file to count how many terms there >>>>>are in it? have you looked carefully at those entries in the file to >>>>>see if there is something that distinguishes them? can you count >>>>>how many rows actually are in the database that were put there by that >>>>>run of the plugin? >>>>> >>>>>thanks for your help, >>>>>steve >>>>> >>>>>Jian Lu wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Hi group, >>>>>> >>>>>>I downloaded Gene Ontology version 3.306 >>>>>>(component.ontology,function.ontology, process.ontology) and ran >>>>>>GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS >>>>>>database. >>>>>>Here is my command: >>>>>> >>>>>>ga GUS::Supported::Plugin::InsertGeneOntology --filePath >>>>>>/home/data/ontology --functionExtDbName 'GO Function' >>>>>>--processExtDbName 'GO Process' --componentExtDbName 'GO Component' >>>>>>--commit >>>>>> >>>>>> >>>>>>Everything looks fine, no errors. It returned a result as "Created >>>>>>19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 >>>>>>entries in GOSynonym. Skipped 0 total entries". >>>>>> >>>>>>But when I was doing other data checking, I found there are three GO >>>>>>terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. >>>>>>They do exist on the GO downloaded files. >>>>>>Has anyone used this plugin to load GO and checked its completeness? >>>>>>Please advise. Thanks. >>>>>> >>>>>>Jian >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>------------------------------------------------------- >>>>>>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: >>>Tame your development challenges with Apache's Geronimo App Server. >>>Download it for free - -and be entered to win a 42" plasma tv or your very >>>own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> >> >> |
