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From: Arnaud K. <ax...@sa...> - 2003-11-27 17:48:32
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Hi We would like to populate some of the GUS Controlled Vocabulary tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of SRes tables. Are these resources available in XML format or in SQL statements from gusdb website or from CVS ? cheers and happy thanksgiving !! Arnaud |
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From: Steve F. <sfi...@pc...> - 2003-12-01 16:11:19
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Arnaud- first, about DoTS::GeneInstanceCategory. we don't seem to be using this table. its empty in our instance. second, about the other vocabs. there is no central resource available. each is dealt with individually. for example, sres.taxon has a plugin which loads data from ncbi. sres.anatomy exists uniquely in our db and was created manually. so, to best answer your question we would need to know which CVs you want to populate. steve Arnaud Kerhornou wrote: > Hi > > We would like to populate some of the GUS Controlled Vocabulary > tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of > SRes tables. > Are these resources available in XML format or in SQL statements from > gusdb website or from CVS ? > > cheers and happy thanksgiving !! > Arnaud > > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Arnaud K. <ax...@sa...> - 2003-12-01 18:01:43
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Hi Steve Steve Fischer wrote: > Arnaud- > > first, about DoTS::GeneInstanceCategory. we don't seem to be using > this table. its empty in our instance. We want to generate gene, RNA and protein entries and link them to corresponding gene, RNA and protein feature entries. This is done using the Gene, RNA and Protein Instance entries. There is a FK to a GeneInstanceCategory entry in GeneInstance and this can not be null. The same for RNAInstance and for ProteinInstance, I'm not sure what they are for. > > > second, about the other vocabs. there is no central resource > available. each is dealt with individually. for example, sres.taxon > has a plugin which loads data from ncbi. sres.anatomy exists uniquely > in our db and was created manually. I'm thinking of CVs such as Taxon with has its own plugin and that the data can be retrieve from NCBI. There are a few ones, GUS specific, that we could share, e.g. SRes::OntologyRelationshipType <http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=SRes::OntologyRelationshipType&path=SRes::OntologyRelationshipType> (AFAIR two entries "part_of" and "is_a"). They could be stored in XML format or as SQL statements. I'm thinking of others CVs, I'll prepare a list. > > so, to best answer your question we would need to know which CVs you > want to populate. > > steve > > Arnaud Kerhornou wrote: > >> Hi >> >> We would like to populate some of the GUS Controlled Vocabulary >> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of >> SRes tables. >> Are these resources available in XML format or in SQL statements from >> gusdb website or from CVS ? >> >> cheers and happy thanksgiving !! >> Arnaud >> >> |
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From: Steve F. <sfi...@pc...> - 2003-12-01 18:40:52
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arnaud- i should have been more precise about DoTS::GeneInstanceCategory. We have one row for it: "unknown". In general, it seems that our our CVs are either: - loaded from an external source (by a plugin) - our own invention (manually created). For the latter case, I agree that CBIL might want to make those available to the GUS project in the form of XML. If my recollection is correct, PSU has a copy of our GUS data from about a year or so ago. Is that right? The basic question is whether our current GUS XML is powerful enough to express, eg, the anatomy CV. If so, then we could write it to XML and make it available. steve Arnaud Kerhornou wrote: > Hi Steve > > Steve Fischer wrote: > >> Arnaud- >> >> first, about DoTS::GeneInstanceCategory. we don't seem to be using >> this table. its empty in our instance. > > > We want to generate gene, RNA and protein entries and link them to > corresponding gene, RNA and protein feature entries. This is done > using the Gene, RNA and Protein Instance entries. > There is a FK to a GeneInstanceCategory entry in GeneInstance and this > can not be null. The same for RNAInstance and for ProteinInstance, I'm > not sure what they are for. > >> >> >> second, about the other vocabs. there is no central resource >> available. each is dealt with individually. for example, sres.taxon >> has a plugin which loads data from ncbi. sres.anatomy exists >> uniquely in our db and was created manually. > > > I'm thinking of CVs such as Taxon with has its own plugin and that the > data can be retrieve from NCBI. > There are a few ones, GUS specific, that we could share, e.g. > SRes::OntologyRelationshipType > <http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=SRes::OntologyRelationshipType&path=SRes::OntologyRelationshipType> > (AFAIR two entries "part_of" and "is_a"). They could be stored in XML > format or as SQL statements. I'm thinking of others CVs, I'll prepare > a list. > >> >> so, to best answer your question we would need to know which CVs you >> want to populate. >> >> steve >> >> Arnaud Kerhornou wrote: >> >>> Hi >>> >>> We would like to populate some of the GUS Controlled Vocabulary >>> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch >>> of SRes tables. >>> Are these resources available in XML format or in SQL statements >>> from gusdb website or from CVS ? >>> >>> cheers and happy thanksgiving !! >>> Arnaud >>> >>> > |
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From: Arnaud K. <ax...@sa...> - 2003-12-02 18:14:48
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Steve Fischer wrote: > arnaud- > > i should have been more precise about DoTS::GeneInstanceCategory. We > have one row for it: "unknown". > > In general, it seems that our our CVs are either: > - loaded from an external source (by a plugin) > - our own invention (manually created). > > For the latter case, I agree that CBIL might want to make those > available to the GUS project in the form of XML. If my recollection > is correct, PSU has a copy of our GUS data from about a year or so > ago. Is that right? We've got XML data files used to populate gusdev CV tables (ExternalDatabase, AlgorithmParamKey, AlgorithmParamKeyType, RNASequenceType and SequenceType). I don't know if they are the ones you're talking about. We've updated ExternalDatabase XML to be used with GUS3. I don't think we need to update the other ones. AFAIK we don't have Anatomy, DevelopmentStage or Disease but I don't think we need them at the moment. I can see another table, SRes.EnzymeClass that we will want to populate. How shall we do it ? cheers Arnaud > The basic question is whether our current GUS XML is powerful enough > to express, eg, the anatomy CV. If so, then we could write it to XML > and make it available. > > steve > > Arnaud Kerhornou wrote: > >> Hi Steve >> >> Steve Fischer wrote: >> >>> Arnaud- >>> >>> first, about DoTS::GeneInstanceCategory. we don't seem to be using >>> this table. its empty in our instance. >> >> >> >> We want to generate gene, RNA and protein entries and link them to >> corresponding gene, RNA and protein feature entries. This is done >> using the Gene, RNA and Protein Instance entries. >> There is a FK to a GeneInstanceCategory entry in GeneInstance and >> this can not be null. The same for RNAInstance and for >> ProteinInstance, I'm not sure what they are for. >> >>> >>> >>> second, about the other vocabs. there is no central resource >>> available. each is dealt with individually. for example, sres.taxon >>> has a plugin which loads data from ncbi. sres.anatomy exists >>> uniquely in our db and was created manually. >> >> >> >> I'm thinking of CVs such as Taxon with has its own plugin and that >> the data can be retrieve from NCBI. >> There are a few ones, GUS specific, that we could share, e.g. >> SRes::OntologyRelationshipType >> <http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=SRes::OntologyRelationshipType&path=SRes::OntologyRelationshipType> >> (AFAIR two entries "part_of" and "is_a"). They could be stored in XML >> format or as SQL statements. I'm thinking of others CVs, I'll prepare >> a list. >> >>> >>> so, to best answer your question we would need to know which CVs you >>> want to populate. >>> >>> steve >>> >>> Arnaud Kerhornou wrote: >>> >>>> Hi >>>> >>>> We would like to populate some of the GUS Controlled Vocabulary >>>> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch >>>> of SRes tables. >>>> Are these resources available in XML format or in SQL statements >>>> from gusdb website or from CVS ? >>>> >>>> cheers and happy thanksgiving !! >>>> Arnaud >>>> >>>> |
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From: Arnaud K. <ax...@sa...> - 2003-12-01 18:43:48
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I have one rectification to make, see below. On Mon, 1 Dec 2003, Arnaud Kerhornou wrote: > Hi Steve > > Steve Fischer wrote: > > > Arnaud- > > > > first, about DoTS::GeneInstanceCategory. we don't seem to be using > > this table. its empty in our instance. > > We want to generate gene, RNA and protein entries and link them to > corresponding gene, RNA and protein feature entries. This is done using > the Gene, RNA and Protein Instance entries. > There is a FK to a GeneInstanceCategory entry in GeneInstance and this > can not be null. The same for RNAInstance and for ProteinInstance, I'm > not sure what they are for. > > > > > > > second, about the other vocabs. there is no central resource > > available. each is dealt with individually. for example, sres.taxon > > has a plugin which loads data from ncbi. sres.anatomy exists uniquely > > in our db and was created manually. > > I'm thinking of CVs such as Taxon with has its own plugin and that the > data can be retrieve from NCBI. I meant I'm not thinking of CVs such as Taxon. > There are a few ones, GUS specific, that we could share, e.g. > SRes::OntologyRelationshipType > <http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=SRes::OntologyRelationshipType&path=SRes::OntologyRelationshipType> > (AFAIR two entries "part_of" and "is_a"). They could be stored in XML > format or as SQL statements. I'm thinking of others CVs, I'll prepare a > list. > > > > > so, to best answer your question we would need to know which CVs you > > want to populate. > > > > steve > > > > Arnaud Kerhornou wrote: > > > >> Hi > >> > >> We would like to populate some of the GUS Controlled Vocabulary > >> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of > >> SRes tables. > >> Are these resources available in XML format or in SQL statements from > >> gusdb website or from CVS ? > >> > >> cheers and happy thanksgiving !! > >> Arnaud > >> > >> > |
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From: Joan M. <ma...@pc...> - 2003-12-02 03:20:11
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Hi Arnaud, > > We want to generate gene, RNA and protein entries and link them to > corresponding gene, RNA and protein feature entries. This is done > using the Gene, RNA and Protein Instance entries. > There is a FK to a GeneInstanceCategory entry in GeneInstance and this > can not be null. The same for RNAInstance and for ProteinInstance, I'm > not sure what they are for. We originally created GeneInstanceCategory, RNAInstanceCategory and ProteinInstanceCategory to describe using a controlled vocabulary the "origin" of a particular instance at the central dogma level. For example, the origin of a particular RNAInstance (or RNASequence) might be "assembly" and another RNAInstance of that RNA might be "mRNA" (perhaps a NCBI RefSeq). We have no plans to populate these three controlled vocabularies right now so you may want to create their vocabularies tailored to your own use. Joan |
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