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Re: [Gusdev-gusdev] representing gene symbols
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From: Joan M. <ma...@pc...> - 2003-05-14 18:17:45
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Steve, Alias is another gene name for a gene. Synonym is another gene_symbol for a gene. Perhaps to make it clearer it should be gene_symbol alternative (i.e. not approved) instead of synonym. and gene name alternative instead of alias. Joan Steve Fischer wrote: > Joan- > > can you explain what a gene alias is as opposed to a gene synonym? > > thanks, > steve > > Joan Mazzarelli wrote: > >> Hi all, >> >> I thought the point of this discussion was to figure out how to >> integrate into the tables which contain (or were created to contain) >> manual gene annotation assignments >> the gene information which we get from MGI/Gene cards sequence >> mappings. (although we may want to make recreate these tables for >> this and/or if PSU has certain needs) . >> >> BTW, although a gene symbol is approved it can also change (MGI >> versions for instance and also they have -pending), so this is >> another case where changes can occur. As it stands now, in the gene >> table we have the attribute gene_symbol where the approved human or >> mouse gene symbol is written for each gene when added by the annotator. >> Also, in the gene table there is name, where I envisioned using the >> new annotation tool, the approved gene name would be written. >> approved gene_symbol = Fzd4 >> approved gene name = frizzled homolog 4 (Drosophila) >> >> >> https://www.cbil.upenn.edu/cgi-bin/dotsgenes-curator/schemaBrowser.pl?db=GUSdev&table=DoTS::Gene&path=DoTS::Gene >> >> >> Now for the Current dots.GeneSynonym table, the annotator can add >> gene symbol synonyms for the gene and this is where they are written. >> >> https://www.cbil.upenn.edu/cgi-bin/dotsgenes-curator/schemaBrowser.pl?db=GUSdev&table=DoTS::GeneSynonym&path=DoTS::GeneSynonym >> >> >> I created GeneAlias for other (not approved) gene names for a gene to >> be used by the new annotation tool. >> >> https://www.cbil.upenn.edu/cgi-bin/dotsgenes-curator/schemaBrowser.pl?db=GUSdev&table=DoTS::GeneAlias&path=DoTS::GeneAlias >> >> >> >> For genes, they can have gene symbol synonyms and also gene name >> aliases. >> It not necessarily the case where every gene symbol synonym has a >> gene name alias which corresponds to it, as in the approved case above >> or vice versa. >> >> >> >> >> Joan >> >> >> >> Jonathan Crabtree wrote: >> >>> >>> Steve Fischer wrote: >>> >>>> right now in GUS, we have a bunch of tables and attribute that >>>> relate to gene symbols, names and aliases: >>>> >>>> Dots::Gene.name >>>> Dots::Gene.gene_symbol >>>> Dots::GeneAlias >>>> Sres::DbRef.gene_symbol (this is pretty clearly a hack. DbRef is >>>> intended to store references to external database entries. it is >>>> hackish to encode in the schema that we assume that such entries >>>> are gene records. they could easily be proteins or journals, >>>> whatever) >>> >>> >>> >>> >>> Yes, this is definitely a hack; I added some columns to the DbRef table >>> because I wanted to store 2-3 specific pieces of information for MGI >>> and >>> GeneCards entries, without creating another table. However, I disagree >>> that I "encoded" in the schema the assumption that these DbRef entries >>> are gene records; I think if you look more closely you will see that >>> all >>> of the newly-added columns (gene_symbol, chromosome, centimorgans) are >>> NULLable. Therefore the only assumption I am making is that one or >>> more >>> of these columns *may* be applicable to certain DbRefs. >>> >>>> 1. introduce a GeneName table: >>>> GeneName.gene_name_id >>>> GeneName.name --- the full name >>>> GeneName.symbol -- the symbol >>>> >>>> 2. introduce a GeneSynonym table: >>>> GeneSynonym.gene_name_id -- the GeneName it is a synonym for >>>> GeneSynonym.name -- the full name of the synonym >>>> GeneSynonym.symbol -- the symbol >>> >>> >>> >>> >>> Arnaud's point that a gene may have names, but no approved name is a >>> good >>> one. It suggests that GeneSynonym should reference Gene, not GeneName. >>> We might also consider renaming "GeneName" to "ApprovedGeneName" and >>> "GeneSynonym" to "GeneName". Arnaud's second point, that there are >>> potentially several different categories of names, suggests that we >>> follow the example of the TaxonName table, and add a 'name_class' >>> column >>> to GeneSynonym. (This could also be a controlled vocabulary.) Then I >>> think the only remaining question is whether we are sure that the only >>> kinds of approved names we will ever have are "gene name" and "gene >>> symbol". >>> >>> Jonathan >>> >>> >>> >>> ------------------------------------------------------- >>> Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara >>> The only event dedicated to issues related to Linux enterprise >>> solutions >>> www.enterpriselinuxforum.com >>> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> >> >> >> >> ------------------------------------------------------- >> Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara >> The only event dedicated to issues related to Linux enterprise solutions >> www.enterpriselinuxforum.com >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > |
