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From: Scott C. <ca...@cs...> - 2005-12-13 22:02:03
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Thanks for looking! It is odd that it won't open in preview. I have both MacOS X 10.3 and 10.4 and it opens on both of them. On Tue, 2005-12-13 at 12:29 -0800, Leonore Reiser wrote: > Hey Scott > I did check out the page- yesterday-but the poster pdf wouldnt open > -at least with preview. I can try acrobat- but just to let you know. > Leonore > > On 12/13/05, Scott Cain <ca...@cs...> wrote: > Hello, > > Unfortunately, I couldn't make it to the Biocurators meeting > last > weekend, but even more unfortunate was that my poster > describing a > simple, beginning approach to developing a common gene page > (or really, > a common set of labels for gene page construction) didn't > arrive in > California until Monday morning (Thanks, FedEx!). > > As an alternative, I would like to encourage you to visit a > page on the > GMOD website set up for discussion of common gene page > development, > where you can download a pdf of my poster, as well as > contribute > comments and get a link to the subscription form for the > common gene > page discussion mailing list. Please come and take a look: > > http://www.gmod.org/node/114 > > Thanks, > Scott > > > PS: Anonymous comments are allowed, although they are > moderated to > eliminate spam. > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. > ca...@cs... > GMOD Coordinator (http://www.gmod.org/) > 216-392-3087 > Cold Spring Harbor Laboratory > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep > through log files > for problems? Stop! Download the new AJAX search engine that > makes > searching your log files as easy as surfing > the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gmod-gene-page mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gene-page > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Leonore R. <leo...@gm...> - 2005-12-13 20:29:47
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Hey Scott I did check out the page- yesterday-but the poster pdf wouldnt open -at least with preview. I can try acrobat- but just to let you know. Leonore On 12/13/05, Scott Cain <ca...@cs...> wrote: > > Hello, > > Unfortunately, I couldn't make it to the Biocurators meeting last > weekend, but even more unfortunate was that my poster describing a > simple, beginning approach to developing a common gene page (or really, > a common set of labels for gene page construction) didn't arrive in > California until Monday morning (Thanks, FedEx!). > > As an alternative, I would like to encourage you to visit a page on the > GMOD website set up for discussion of common gene page development, > where you can download a pdf of my poster, as well as contribute > comments and get a link to the subscription form for the common gene > page discussion mailing list. Please come and take a look: > > http://www.gmod.org/node/114 > > Thanks, > Scott > > > PS: Anonymous comments are allowed, although they are moderated to > eliminate spam. > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. ca...@cs... > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > _______________________________________________ > Gmod-gene-page mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gene-page > > |
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From: Scott C. <ca...@cs...> - 2005-12-13 16:31:08
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Hello, Unfortunately, I couldn't make it to the Biocurators meeting last weekend, but even more unfortunate was that my poster describing a simple, beginning approach to developing a common gene page (or really, a common set of labels for gene page construction) didn't arrive in California until Monday morning (Thanks, FedEx!). As an alternative, I would like to encourage you to visit a page on the GMOD website set up for discussion of common gene page development, where you can download a pdf of my poster, as well as contribute comments and get a link to the subscription form for the common gene page discussion mailing list. Please come and take a look: http://www.gmod.org/node/114 Thanks, Scott PS: Anonymous comments are allowed, although they are moderated to eliminate spam. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Vasanth R. S. <vs...@in...> - 2005-02-03 13:04:52
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Mike, You can find the html version too here http://eugenes.org:7072/all/gene-report-examples/doc/UnifiedGenePageCmp1.htm Thanks, Vasanth On Thu, 3 Feb 2005, Michael Thon wrote: > Vasanth - Great! except your url is for an ms word document. Could you > post an html version? > Cheers > Mike Thon > > On Feb 2, 2005, at 6:05 PM, Vasanth Ragunathan Singan wrote: > > > Hi GMOD Gene Page group, > > > > Based on the suggestions from various members of this group, we at the > > Genome Informatics lab have compiled a comparison with the GeneSummary > > suggestions from Flybase. > > > > Attached is a HTML document of the comparison. > > > > The full documentation of this can be found at > > http://eugenes.org:7072/all/gene-report-examples/doc/ > > UnifiedGenePageCmp1.doc > > > > Looking forward for suggestions from you. > > > > thanks, > > Vasanth > > > > > > ---------------------------------- > > Vasanth Singan > > Graduate Research Assistant, > > Genome Informatics Laboratory, > > Indiana University - Bloomington > > > > vs...@in... > > ---------------------------------- > > <html> > > > > <head> > > <meta http-equiv="Content-Type" content="text/html; > > charset=windows-1252"> > > <title>Following are the suggestions fr</title> > > <style> > > <!-- > > p.MsoNormal > > {mso-style-parent:""; > > margin-bottom:.0001pt; > > font-size:12.0pt; > > font-family:"Times New Roman"; > > margin-left:0in; margin-right:0in; margin-top:0in} > > h2 > > {margin-top:12.0pt; > > margin-right:0in; > > margin-bottom:3.0pt; > > margin-left:0in; > > page-break-after:avoid; > > font-size:14.0pt; > > font-family:Arial; > > font-style:italic} > > --> > > </style> > > </head> > > > > <body> > > > > <p class="MsoNormal">FlyBase suggested GeneSummary contents from > > GeneSummary.dtd; > > version 0.3; 12 Jun 2004,</p> > > <p > > class="MsoNormal"> http://eugenes.org/all/gene-report-examples/ > > conf/GeneSummary.dtd</p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">CATEGORIES</p> > > <p class="MsoNormal"> BASIC_INFORMATION,</p> > > <p class="MsoNormal"> LOCATION,</p> > > <p class="MsoNormal"> GENE_PRODUCT,</p> > > <p class="MsoNormal"> GENE_ONTOLOGY,</p> > > <p class="MsoNormal"> SIMILAR_GENES,</p> > > <p class="MsoNormal"> FUNCTION,</p> > > <p class="MsoNormal"> REAGENTS,</p> > > <p class="MsoNormal"> LITERATURE,</p> > > <p class="MsoNormal"> SUMMARY,</p> > > <p class="MsoNormal"> ADDITIONAL_INFORMATION</p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">BASIC_INFORMATION = primary gene info </p> > > <p class="MsoNormal"> Symbol </p> > > <p class="MsoNormal"> Full_name </p> > > <p class="MsoNormal"> Synonyms (text|Name)</p> > > <p class="MsoNormal"> GeneID </p> > > <p class="MsoNormal"> Species </p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">LOCATION : location in genome</p> > > <p class="MsoNormal"> Chromosome </p> > > <p class="MsoNormal"> Scaffold </p> > > <p class="MsoNormal"> Genome_map </p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">GENE_PRODUCT : products of genes at sequence and > > above > > levels</p> > > <p class="MsoNormal"> Polypeptides > > (Polypeptide|Description|note)</p> > > <p class="MsoNormal"> Transcripts > > (Transcript|Description|note)</p> > > <p class="MsoNormal"> Polypeptide (text|db_xref)</p> > > <p class="MsoNormal"> Transcript > > (text|Polypeptide|db_xref)</p> > > <p class="MsoNormal"> Gene_type </p> > > <p class="MsoNormal"> Sequence (text|db_xref)</p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">GENE_ONTOLOGY : standardized GeneOntology.org > > parts</p> > > <p class="MsoNormal"> Molecular_function (text|goterm)</p> > > <p class="MsoNormal"> Biological_process (text|goterm)</p> > > <p class="MsoNormal"> Cellular_component (text|goterm)</p> > > <p class="MsoNormal"> goevidence </p> > > <p class="MsoNormal"> goterm (text|goevidence|ref)</p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">FUNCTION : catch-all for higher level gene > > actions; better > > name?</p> > > <p class="MsoNormal"> Protein_domains (db_xref|note)</p> > > <p class="MsoNormal"> External_links (db_xref|url|note)</p> > > <p class="MsoNormal"> Expressions (Expression|note)</p> > > <p class="MsoNormal"> Expression (text|Phenotype)</p> > > <p class="MsoNormal"> Phenotypes (Phenotype|note)</p> > > <p class="MsoNormal"> Phenotype </p> > > <p class="MsoNormal"> Interactions (Interaction|note)</p> > > <p class="MsoNormal"> Interaction </p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">REAGENTS : PCR, cDNA, EST, ... elements (REAGENTS > > is used > > now be a few MODs)</p> > > <p class="MsoNormal"> Add an ALLELES/VARIANTS? > > REAGENTS_AND_VARIANTS ?</p> > > <p class="MsoNormal"> Reagent (text|db_xref|note)</p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">SIMILAR_GENES : list of related organism genes, > > probably > > blast-computed from proteins</p> > > <p class="MsoNormal"> (alternate names : similarities, > > related_genes, homologs, > > orthologs)</p> > > <p class="MsoNormal"> Similarity > > (Species|db_xref|Description|Symbol|Evalue|Percent)</p> > > <p class="MsoNormal"> Evalue </p> > > <p class="MsoNormal"> Percent </p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">LITERATURE : relevant experimental references</p> > > <p class="MsoNormal"> (alternate names : Bibliography, > > References)</p> > > <p class="MsoNormal"> Reference (text|ref|note)</p> > > <p class="MsoNormal"> </p> > > <p class="MsoNormal">SUMMARY : a human-readable text summary of gene > > information</p> > > <span style="font-size: 12.0pt; font-family: Times New > > Roman"> SUMMARY (text|html)</span><p > > class="MsoNormal"> </p> > > <p class="MsoNormal">Following are the suggestions from various > > members of the > > working group and the above GeneSummary equivalents marked with > > red.</p> > > <p class="MsoNormal"> </p> > > <h2>Arabidopsis</h2> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt">Locus > > Info*</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Systematic Locus Identifier* > > <span style="color: red">BASIC_INFORMATION (GeneID)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Gene Name* <span style="color: > > red">BASIC_INFORMATION (Full_name)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Gene Alias(es)* <span > > style="color: red">BASIC_INFORMATION (Synonyms)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Gene Model Type (e.g. protein > > coding, miRNA, unknown...etc.)*</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> <span > > style="color: red">GENE_PRODUCT (GeneModel)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Physical/Genetic Linkage Map > > Location (chromosome, coordinates)*</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > > style="color: red"> LOCATION > > (Chromosome|Genome_map|Map)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Summary/Brief Description*</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > > style="color: red"> > > SUMMARY</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Annotated Sequence (gene features > > annotated + EVIDENCE* that is</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> -is > > the structure experimentally verified or predicted and what is > > the</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > evidence)</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > History</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Function/Biological Role/Expression/Localization</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > GO Annotations <span > > style="color: red">GENE_ONTOLOGY</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt">Gene Expression Data (Microarray, EST, SAGE, MPSS, in-situ, > > etc..) <span style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > (supra- cellular) Localization > > (immunohistochemistry, GFP/YFP)</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt">Alleles and Phenotypes <span style="color: > > red">FUNCTION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Sequence Variation (nt sequence > > [C->A at 2344 bp] and coding</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > sequence change[ e.g.nonsense mutation at AA 467]) <span style="color: > > red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Variation Type:(e.g. insertion, > > deletion, etc..) <span style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Mutagen: e.g. EMS, RNAi et... > > <span style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Type: e.g. hypermorph, > > neomorph,etc.. <span style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Phenotype <span style="color: > > red">FUNCTION (Phenotype)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Pathways and Interactions <span style="color: > > red">FUNCTION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Genetic Pathways <span > > style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Metabolic Pathways <span > > style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Signaling Pathways <span > > style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Interacting Partners (binds to > > DNA/binds to Protein/modifies X)</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> <span > > style="color: red">FUNCTION (Interactions)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Protein * </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Sequence*</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Domains/Motifs* <span > > style="color: red">FUNCTION (Protein_domains)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Post-translational modifications > > <span style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Tryptic Digest Patterns <span > > style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > pI* <span style="color: red">(not > > specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Molecular Weight* <span > > style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Homologies* <span style="color: > > red">(SIMILAR_GENES)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Reagents <span style="color: red">REAGENTS > > </span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Clones <span > > style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Antibodies <span style="color: > > red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Strains (e.g. seed stocks) <span > > style="color: red">(not specified)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Literature <span style="color: > > red">LITERATURE</span></pre> > > <h2>Rat Genome Database</h2> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt">DATABASE ID <span style="color: red">BASIC_INFORMATION > > (GeneID)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > SYMBOL & NAME <span style="color: red">BASIC_INFORMATION > > (Symbol|Full_name)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > ALIAS_SYMBOL & NAME <span style="color: red">BASIC_INFORMATION > > (Synonyms)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > DESCRIPTION - brief (~250 char) text; basic info, including > > function,</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > process, disease, etc.; why someone would be interested in the gene > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> SEQUENCE ACC IDs with links <span style="color: > > red">SUMMARY</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > GenBank/EMBL/DDBJ</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > > > mRNA</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > > > protein</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > > > genomic</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > > > contig</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > > > unigene</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Refseq (mRNA and protein)</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Primers</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > REFERENCES <span style="color: red">LITERATURE > > (Reference)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Curated - database ID and other > > IDs, e.g., PubMed </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Others > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > EXTERNA.L DATABASE IDs and LINKS <span style="color: red">FUNCTION > > (External_links)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Uniprot</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Ensembl</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Entrez gene</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > OMIM</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Kegg</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Reactome</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > BIND</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > etc.</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > MAPPING DATA <span style="color: red">LOCATION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Chromosome <span style="color: > > red">LOCATION (Chromosome)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Band </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Position on > > specific maps (genetic, RH) <span style="color: red">LOCATION > > (map)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Genomic position - start and stop > > plus build</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > .5in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Links to images such as browser images (we actually show the </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > .5in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> browser image in addition to links.) <span > > style="color: red">LOCATION (Genome_map)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt">RELATED GENES <span style="color: > > red">SIMILAR_GENES</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt">Splice variants <span style="color: red">SIMILAR_GENES > > (Similarity) (Description)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt">Pseudogenes <span style="color: red">SIMILAR_GENES > > (Similarity) (Description)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt">Alleles <span style="color: red">SIMILAR_GENES (Similarity) > > (Description)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > etc.</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > OTHER DB OBJECTS ASSOC. WITH THE GENE </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Strains</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > QTL</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > ESTs</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > SSLP</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > etc.</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > HOMOLOGS <span style="color: red">SIMILAR_GENES</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> GENE > > TYPE <span style="color: red">GENE_PRODUCT (Gene_type)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Splice variant </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Pseudogene > > </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Alleles </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> GENE > > EVIDENCE </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Known </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Predicted by > > homology</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Predicted by EST evidence</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > etc.</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > BIOLOGICAL DATA (CONTROLLED VOCAB/ONTOLOGIES/TEXT) <span style="color: > > red">GENE_ONTOLOGY</span> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Biological Process <span style="color: > > red">GENE_ONTOLOGY (Biological_process)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Cellular Component <span style="color: red">GENE_ONTOLOGY > > (Cellular_component)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Disease </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Domains <span style="color: red">FUNCTION > > (Protein_domains)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Drugs effects</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> EC > > number</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Evolution</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Expression <span style="color: red">FUNCTION (Expression)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Family </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> Homology details <span style="color: > > red">SIMILAR_GENES</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Molecular Function <span style="color: red">FUNCTION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > > style="color: red"> </span>Mutation/over- and underexpression</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Pathway</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Phenotype <span style="color: red">FUNCTION (Phenotype)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Physical interaction <span style="color: red">FUNCTION > > (Phenotype)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Protein modifications</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Regulation</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Size</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > Transcript structure</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > etc</pre> > > <b><i><span style="font-size: 14.0pt; font-family: Arial"> > > <br clear="all" style="page-break-before: always"> > > </span></i></b><h2>SGD Saccharomyces Genome Database</h2> > > <p class="MsoNormal"> </p> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> basic information <span style="color: > > red">BASIC_INFORMATION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> standard gene name > > <span style="color: red">BASIC_INFORMATION (Full_name)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> systematic locus name > > <span style="color: red">BASIC_INFORMATION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> alias <span > > style="color: red">BASIC_INFORMATION (Synonyms)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> feature type </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> locus > > description</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> GO annotations <span > > style="color: red">GENE_ONTOLOGY</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > molecular function <span style="color: red">GENE_ONTOLOGY > > (Molecular_function)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > biological process <span style="color: red">GENE_ONTOLOGY > > (Biological_process)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > cellular component <span style="color: red">GENE_ONTOLOGY > > (Cellular_component)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > evidence codes and references <span style="color: > > red">GENE_ONTOLOGY (goevidence </span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > > style="color: > > red"> > > > > > > > > > > | goterm)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> pathways</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> gene name > > description</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> gene product <span > > style="color: red">GENE_PRODUCT</span> </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> mutant phenotypes > > <span style="color: red">FUNCTION (Phenotypes)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > phenotype type </pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > phenotype</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > details and references</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> sequence information > > <span style="color: red">LOCATION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > mapping info <span style="color: red">LOCATION > > (Genome_map)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > last update dates (coordinates and sequence)</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > subfeature details</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > subfeature > > type</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > relative > > coordinates</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > chromosomal > > coordinates <span style="color: red">LOCATION > > (Chromosome)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> external links <span > > style="color: red">FUNCTION (External_links)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > Entrez</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > E.C.</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > MIPS</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> > > > > SwissProt</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> dbxref_id</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> resources</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> literature <span > > style="color: red">LITERATURE</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> retrieve > > sequences</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> sequence analysis > > tools</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> protein info and > > structure</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> protein localization > > resources</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> external protein > > interaction db"s <span style="color: red">FUNCTION > > (External_links)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> external phenotype > > db"s <span style="color: red">FUNCTION > > (External_links)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> maps and displays <span > > style="color: red">LOCATION (Maps)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> sequence comparison > > resources</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> functional > > analysis</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> additional information <span style="color: > > red">ADDITIONAL_INFORMATION</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> locus history</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> expression > > datasets</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> associated > > researchers</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> community annotation</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> DNA and RNA > > details</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> protein details</pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> interactions <span > > style="color: red">FUNCTION (Interactions)</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> techniques and reagents > > <span style="color: red">REAGENTS</span></pre> > > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > > .0001pt"> alleles, strains, and > > phenotypes</pre> > > <p class="MsoNormal"> </p> > > > > </body> > > > > </html> > > > |
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From: Michael T. <mt...@ta...> - 2005-02-03 10:42:10
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Vasanth - Great! except your url is for an ms word document. Could you post an html version? Cheers Mike Thon On Feb 2, 2005, at 6:05 PM, Vasanth Ragunathan Singan wrote: > Hi GMOD Gene Page group, > > Based on the suggestions from various members of this group, we at the > Genome Informatics lab have compiled a comparison with the GeneSummary > suggestions from Flybase. > > Attached is a HTML document of the comparison. > > The full documentation of this can be found at > http://eugenes.org:7072/all/gene-report-examples/doc/ > UnifiedGenePageCmp1.doc > > Looking forward for suggestions from you. > > thanks, > Vasanth > > > ---------------------------------- > Vasanth Singan > Graduate Research Assistant, > Genome Informatics Laboratory, > Indiana University - Bloomington > > vs...@in... > ---------------------------------- > <html> > > <head> > <meta http-equiv="Content-Type" content="text/html; > charset=windows-1252"> > <title>Following are the suggestions fr</title> > <style> > <!-- > p.MsoNormal > {mso-style-parent:""; > margin-bottom:.0001pt; > font-size:12.0pt; > font-family:"Times New Roman"; > margin-left:0in; margin-right:0in; margin-top:0in} > h2 > {margin-top:12.0pt; > margin-right:0in; > margin-bottom:3.0pt; > margin-left:0in; > page-break-after:avoid; > font-size:14.0pt; > font-family:Arial; > font-style:italic} > --> > </style> > </head> > > <body> > > <p class="MsoNormal">FlyBase suggested GeneSummary contents from > GeneSummary.dtd; > version 0.3; 12 Jun 2004,</p> > <p > class="MsoNormal"> http://eugenes.org/all/gene-report-examples/ > conf/GeneSummary.dtd</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">CATEGORIES</p> > <p class="MsoNormal"> BASIC_INFORMATION,</p> > <p class="MsoNormal"> LOCATION,</p> > <p class="MsoNormal"> GENE_PRODUCT,</p> > <p class="MsoNormal"> GENE_ONTOLOGY,</p> > <p class="MsoNormal"> SIMILAR_GENES,</p> > <p class="MsoNormal"> FUNCTION,</p> > <p class="MsoNormal"> REAGENTS,</p> > <p class="MsoNormal"> LITERATURE,</p> > <p class="MsoNormal"> SUMMARY,</p> > <p class="MsoNormal"> ADDITIONAL_INFORMATION</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">BASIC_INFORMATION = primary gene info </p> > <p class="MsoNormal"> Symbol </p> > <p class="MsoNormal"> Full_name </p> > <p class="MsoNormal"> Synonyms (text|Name)</p> > <p class="MsoNormal"> GeneID </p> > <p class="MsoNormal"> Species </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">LOCATION : location in genome</p> > <p class="MsoNormal"> Chromosome </p> > <p class="MsoNormal"> Scaffold </p> > <p class="MsoNormal"> Genome_map </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">GENE_PRODUCT : products of genes at sequence and > above > levels</p> > <p class="MsoNormal"> Polypeptides > (Polypeptide|Description|note)</p> > <p class="MsoNormal"> Transcripts > (Transcript|Description|note)</p> > <p class="MsoNormal"> Polypeptide (text|db_xref)</p> > <p class="MsoNormal"> Transcript > (text|Polypeptide|db_xref)</p> > <p class="MsoNormal"> Gene_type </p> > <p class="MsoNormal"> Sequence (text|db_xref)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">GENE_ONTOLOGY : standardized GeneOntology.org > parts</p> > <p class="MsoNormal"> Molecular_function (text|goterm)</p> > <p class="MsoNormal"> Biological_process (text|goterm)</p> > <p class="MsoNormal"> Cellular_component (text|goterm)</p> > <p class="MsoNormal"> goevidence </p> > <p class="MsoNormal"> goterm (text|goevidence|ref)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">FUNCTION : catch-all for higher level gene > actions; better > name?</p> > <p class="MsoNormal"> Protein_domains (db_xref|note)</p> > <p class="MsoNormal"> External_links (db_xref|url|note)</p> > <p class="MsoNormal"> Expressions (Expression|note)</p> > <p class="MsoNormal"> Expression (text|Phenotype)</p> > <p class="MsoNormal"> Phenotypes (Phenotype|note)</p> > <p class="MsoNormal"> Phenotype </p> > <p class="MsoNormal"> Interactions (Interaction|note)</p> > <p class="MsoNormal"> Interaction </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">REAGENTS : PCR, cDNA, EST, ... elements (REAGENTS > is used > now be a few MODs)</p> > <p class="MsoNormal"> Add an ALLELES/VARIANTS? > REAGENTS_AND_VARIANTS ?</p> > <p class="MsoNormal"> Reagent (text|db_xref|note)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">SIMILAR_GENES : list of related organism genes, > probably > blast-computed from proteins</p> > <p class="MsoNormal"> (alternate names : similarities, > related_genes, homologs, > orthologs)</p> > <p class="MsoNormal"> Similarity > (Species|db_xref|Description|Symbol|Evalue|Percent)</p> > <p class="MsoNormal"> Evalue </p> > <p class="MsoNormal"> Percent </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">LITERATURE : relevant experimental references</p> > <p class="MsoNormal"> (alternate names : Bibliography, > References)</p> > <p class="MsoNormal"> Reference (text|ref|note)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">SUMMARY : a human-readable text summary of gene > information</p> > <span style="font-size: 12.0pt; font-family: Times New > Roman"> SUMMARY (text|html)</span><p > class="MsoNormal"> </p> > <p class="MsoNormal">Following are the suggestions from various > members of the > working group and the above GeneSummary equivalents marked with > red.</p> > <p class="MsoNormal"> </p> > <h2>Arabidopsis</h2> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt">Locus > Info*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Systematic Locus Identifier* > <span style="color: red">BASIC_INFORMATION (GeneID)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Gene Name* <span style="color: > red">BASIC_INFORMATION (Full_name)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Gene Alias(es)* <span > style="color: red">BASIC_INFORMATION (Synonyms)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Gene Model Type (e.g. protein > coding, miRNA, unknown...etc.)*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> <span > style="color: red">GENE_PRODUCT (GeneModel)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Physical/Genetic Linkage Map > Location (chromosome, coordinates)*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: red"> LOCATION > (Chromosome|Genome_map|Map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Summary/Brief Description*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: red"> > SUMMARY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Annotated Sequence (gene features > annotated + EVIDENCE* that is</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> -is > the structure experimentally verified or predicted and what is > the</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > evidence)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > History</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Function/Biological Role/Expression/Localization</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > GO Annotations <span > style="color: red">GENE_ONTOLOGY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Gene Expression Data (Microarray, EST, SAGE, MPSS, in-situ, > etc..) <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > (supra- cellular) Localization > (immunohistochemistry, GFP/YFP)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Alleles and Phenotypes <span style="color: > red">FUNCTION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Sequence Variation (nt sequence > [C->A at 2344 bp] and coding</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > sequence change[ e.g.nonsense mutation at AA 467]) <span style="color: > red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Variation Type:(e.g. insertion, > deletion, etc..) <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Mutagen: e.g. EMS, RNAi et... > <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Type: e.g. hypermorph, > neomorph,etc.. <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Phenotype <span style="color: > red">FUNCTION (Phenotype)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Pathways and Interactions <span style="color: > red">FUNCTION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Genetic Pathways <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Metabolic Pathways <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Signaling Pathways <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Interacting Partners (binds to > DNA/binds to Protein/modifies X)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> <span > style="color: red">FUNCTION (Interactions)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Protein * </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Sequence*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Domains/Motifs* <span > style="color: red">FUNCTION (Protein_domains)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Post-translational modifications > <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Tryptic Digest Patterns <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > pI* <span style="color: red">(not > specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Molecular Weight* <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Homologies* <span style="color: > red">(SIMILAR_GENES)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Reagents <span style="color: red">REAGENTS > </span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Clones <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Antibodies <span style="color: > red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Strains (e.g. seed stocks) <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Literature <span style="color: > red">LITERATURE</span></pre> > <h2>Rat Genome Database</h2> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">DATABASE ID <span style="color: red">BASIC_INFORMATION > (GeneID)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > SYMBOL & NAME <span style="color: red">BASIC_INFORMATION > (Symbol|Full_name)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > ALIAS_SYMBOL & NAME <span style="color: red">BASIC_INFORMATION > (Synonyms)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > DESCRIPTION - brief (~250 char) text; basic info, including > function,</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > process, disease, etc.; why someone would be interested in the gene > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> SEQUENCE ACC IDs with links <span style="color: > red">SUMMARY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > GenBank/EMBL/DDBJ</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > mRNA</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > protein</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > genomic</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > contig</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > unigene</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Refseq (mRNA and protein)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Primers</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > REFERENCES <span style="color: red">LITERATURE > (Reference)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Curated - database ID and other > IDs, e.g., PubMed </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Others > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > EXTERNA.L DATABASE IDs and LINKS <span style="color: red">FUNCTION > (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Uniprot</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Ensembl</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Entrez gene</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > OMIM</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Kegg</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Reactome</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > BIND</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > MAPPING DATA <span style="color: red">LOCATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Chromosome <span style="color: > red">LOCATION (Chromosome)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Band </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Position on > specific maps (genetic, RH) <span style="color: red">LOCATION > (map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Genomic position - start and stop > plus build</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > .5in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Links to images such as browser images (we actually show the </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > .5in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> browser image in addition to links.) <span > style="color: red">LOCATION (Genome_map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">RELATED GENES <span style="color: > red">SIMILAR_GENES</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Splice variants <span style="color: red">SIMILAR_GENES > (Similarity) (Description)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Pseudogenes <span style="color: red">SIMILAR_GENES > (Similarity) (Description)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Alleles <span style="color: red">SIMILAR_GENES (Similarity) > (Description)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > OTHER DB OBJECTS ASSOC. WITH THE GENE </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Strains</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > QTL</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > ESTs</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > SSLP</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > HOMOLOGS <span style="color: red">SIMILAR_GENES</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> GENE > TYPE <span style="color: red">GENE_PRODUCT (Gene_type)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Splice variant </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Pseudogene > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Alleles </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> GENE > EVIDENCE </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Known </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Predicted by > homology</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Predicted by EST evidence</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > BIOLOGICAL DATA (CONTROLLED VOCAB/ONTOLOGIES/TEXT) <span style="color: > red">GENE_ONTOLOGY</span> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Biological Process <span style="color: > red">GENE_ONTOLOGY (Biological_process)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Cellular Component <span style="color: red">GENE_ONTOLOGY > (Cellular_component)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Disease </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Domains <span style="color: red">FUNCTION > (Protein_domains)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Drugs effects</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> EC > number</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Evolution</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Expression <span style="color: red">FUNCTION (Expression)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Family </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Homology details <span style="color: > red">SIMILAR_GENES</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Molecular Function <span style="color: red">FUNCTION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: red"> </span>Mutation/over- and underexpression</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Pathway</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Phenotype <span style="color: red">FUNCTION (Phenotype)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Physical interaction <span style="color: red">FUNCTION > (Phenotype)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Protein modifications</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Regulation</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Size</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Transcript structure</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc</pre> > <b><i><span style="font-size: 14.0pt; font-family: Arial"> > <br clear="all" style="page-break-before: always"> > </span></i></b><h2>SGD Saccharomyces Genome Database</h2> > <p class="MsoNormal"> </p> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> basic information <span style="color: > red">BASIC_INFORMATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> standard gene name > <span style="color: red">BASIC_INFORMATION (Full_name)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> systematic locus name > <span style="color: red">BASIC_INFORMATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> alias <span > style="color: red">BASIC_INFORMATION (Synonyms)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> feature type </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> locus > description</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> GO annotations <span > style="color: red">GENE_ONTOLOGY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > molecular function <span style="color: red">GENE_ONTOLOGY > (Molecular_function)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > biological process <span style="color: red">GENE_ONTOLOGY > (Biological_process)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > cellular component <span style="color: red">GENE_ONTOLOGY > (Cellular_component)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > evidence codes and references <span style="color: > red">GENE_ONTOLOGY (goevidence </span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: > red"> > > > > > | goterm)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> pathways</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> gene name > description</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> gene product <span > style="color: red">GENE_PRODUCT</span> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> mutant phenotypes > <span style="color: red">FUNCTION (Phenotypes)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > phenotype type </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > phenotype</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > details and references</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> sequence information > <span style="color: red">LOCATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > mapping info <span style="color: red">LOCATION > (Genome_map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > last update dates (coordinates and sequence)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > subfeature details</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > subfeature > type</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > relative > coordinates</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > chromosomal > coordinates <span style="color: red">LOCATION > (Chromosome)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> external links <span > style="color: red">FUNCTION (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > Entrez</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > E.C.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > MIPS</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > SwissProt</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> dbxref_id</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> resources</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> literature <span > style="color: red">LITERATURE</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> retrieve > sequences</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> sequence analysis > tools</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> protein info and > structure</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> protein localization > resources</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> external protein > interaction db"s <span style="color: red">FUNCTION > (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> external phenotype > db"s <span style="color: red">FUNCTION > (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> maps and displays <span > style="color: red">LOCATION (Maps)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> sequence comparison > resources</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> functional > analysis</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> additional information <span style="color: > red">ADDITIONAL_INFORMATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> locus history</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> expression > datasets</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> associated > researchers</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> community annotation</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> DNA and RNA > details</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> protein details</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> interactions <span > style="color: red">FUNCTION (Interactions)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> techniques and reagents > <span style="color: red">REAGENTS</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> alleles, strains, and > phenotypes</pre> > <p class="MsoNormal"> </p> > > </body> > > </html> |
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From: Vasanth R. S. <vs...@in...> - 2005-02-03 00:06:00
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Hi GMOD Gene Page group, Based on the suggestions from various members of this group, we at the Genome Informatics lab have compiled a comparison with the GeneSummary suggestions from Flybase. Attached is a HTML document of the comparison. The full documentation of this can be found at http://eugenes.org:7072/all/gene-report-examples/doc/UnifiedGenePageCmp1.doc Looking forward for suggestions from you. thanks, Vasanth ---------------------------------- Vasanth Singan Graduate Research Assistant, Genome Informatics Laboratory, Indiana University - Bloomington vs...@in... ---------------------------------- |
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From: Bromberg, S. <SBr...@ma...> - 2004-10-21 15:27:07
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Here' a list from RGD. It includes a lot of what we use now (plus some we are planning) but I think it wouold be appropriate for most organisms. (I'm also attaching the file.) DATABASE ID SYMBOL & NAME ALIAS_SYMBOL & NAME DESCRIPTION - brief (~250 char) text; basic info, including function, process, disease, etc.; why someone would be interested in the gene SEQUENCE ACC IDs with links GenBank/EMBL/DDBJ mRNA protein genomic contig unigene Refseq (mRNA and protein) Primers REFERENCES Curated - database ID and other IDs, e.g., PubMed Others EXTERNA.L DATABASE IDs and LINKS Uniprot Ensembl Entrez gene OMIM Kegg Reactome BIND etc. MAPPING DATA Chromosome Band Position on specific maps (genetic, RH) Genomic position - start and stop plus build Links to images such as browser images (we actually show the browser image in addition to links.) RELATED GENES Splice variants Pseudogenes Alleles etc. OTHER DB OBJECTS ASSOC. WITH THE GENE Strains QTL ESTs SSLP etc. HOMOLOGS GENE TYPE Splice variant Pseudogene Alleles GENE EVIDENCE Known Predicted by homology Predicted by EST evidence etc. BIOLOGICAL DATA (CONTROLLED VOCAB/ONTOLOGIES/TEXT) Biological Process Cellular Component Disease Domains Drugs effects EC number Evolution Expression Family Homology details Molecular Function Mutation/over- and underexpression Pathway Phenotype Physical interaction Protein modifications Regulation Size Transcript structure etc <<gene page.doc>> Susan K. Bromberg, Ph.D. Curation Team Leader Rat Genome Database (http://www.rgd.mcw.edu) Bioinformatics Research Center (http://www.brc.mcw.edu) Medical College of Wisconsin 8701 Watertown Plank Rd. Milwaukee, WI 53226 414-456-7515 sbr...@ma... |
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From: Leonore R. <lr...@ac...> - 2004-10-15 22:11:42
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Ok here is something of a wish list- I've asterisked ones that at a minimum should be there since of course, what we know/ can show depends upon the available data. I concur with Stacia that all assertions should be supported with tracable evidence/methodologies. I also dont mean to imply that every MOD should physically store all of the information presented here. For example, TAIR does not store information/alignments for homology but does link to this information in other databases. But if the information is available...be nice to find. I wonder if it helps to distinguish between minimal information for a SEQUENCED locus vs. GENETICALLY defined. For now- Ill assume were are talking about sequenced genes and not single recessive mutants or QTLs. -Leonore Reiser Locus Info* Systematic Locus Identifier* Gene Name* Gene Alias(es)* Gene Model Type (e.g. protein coding, miRNA, unknown...etc.)* Physical/Genetic Linkage Map Location (chromosome, coordinates)* Summary/Brief Description* Annotated Sequence (gene features annotated + EVIDENCE* that is -is the structure experimentally verified or predicted and what is the evidence) History Function/Biological Role/Expression/Localization GO Annotations Gene Expression Data (Microarray, EST, SAGE, MPSS, in-situ, etc..) (supra- cellular) Localization (immunohistochemistry, GFP/YFP) Alleles and Phenotypes Sequence Variation (nt sequence [C->A at 2344 bp] and coding sequence change[ e.g.nonsense mutation at AA 467]) Variation Type:(e.g. insertion, deletion, etc..) Mutagen: e.g. EMS, RNAi et... Type: e.g. hypermorph, neomorph,etc.. Phenotype Pathways and Interactions Genetic Pathways Metabolic Pathways Signaling Pathways Interacting Partners (binds to DNA/binds to Protein/modifies X) Protein * Sequence* Domains/Motifs* Post-translational modifications Tryptic Digest Patterns pI* Molecular Weight* Homologies* Reagents Clones Antibodies Strains (e.g. seed stocks) Literature ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lr...@ac... The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- |
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From: Don G. <gil...@bi...> - 2004-10-15 18:05:38
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Stacia, That looks great; thanks very much. Could we get one more organism/database point of view on this minimal biology summary of gene information? From there we would have a good starting point for discussing our commonalities. Worms, Rats, Mice, Mustard Weeds, others: speak up or miss a chance at winning this contest. I forgot to say what the prize is. Mostly that many biologists and bioinformaticians will thank you for your effort ! Maybe we could ask one of the genome sequencing projects to let you name a newly computed gene ? Drosophila has such funky gene names - how about a gene named Stacia? - Don -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gil...@in...--http://marmot.bio.indiana.edu/ |
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From: Stacia E. <st...@ge...> - 2004-10-15 16:55:33
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oops, i accidentally sent this to the wrong GMOD address... Begin forwarded message: > From: Stacia Engel <st...@ge...> > Date: October 15, 2004 9:53:18 AM PDT > To: bio...@az..., > gmo...@li... > Cc: SGD Curators <sgd...@ge...> > Subject: gene page contest entry > > Hi GMOD gene page folks, > > Here is an entry for Don's gene page contest. I'm not sure if this is > exactly what you're looking for, but I haven't seen any other entries > (besides Don's) come through yet, so I'm kind of winging this - I hope > it's helpful! > > Focusing on biology, below is a list of what could be considered a > minimal set of information that biologists and other bioscientists > would want to know (or be able to retrieve) about a particular locus. > Not all categories will apply to all loci, of course. > > Thanks, > Stacia > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Stacia R. Engel, Ph.D. > Scientific Curator > Saccharomyces Genome Database > Department of Genetics > Stanford University School of Medicine > 300 Pasteur Drive > Stanford, CA 94305 USA > st...@ge... > www.yeastgenome.org > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > basic information > standard gene name > systematic locus name > alias > feature type > locus description > GO annotations > molecular function > biological process > cellular component > evidence codes and references > pathways > gene name description > gene product > mutant phenotypes > phenotype type > phenotype > details and references > sequence information > mapping info > last update dates (coordinates and sequence) > subfeature details > subfeature type > relative coordinates > chromosomal coordinates > external links > Entrez > E.C. > MIPS > SwissProt > dbxref_id > resources > literature > retrieve sequences > sequence analysis tools > protein info and structure > protein localization resources > external protein interaction db's > external phenotype db's > maps and displays > sequence comparison resources > functional analysis > additional information > locus history > expression datasets > associated researchers > community annotation > DNA and RNA details > protein details > interactions > techniques and reagents > alleles, strains, and phenotypes |
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From: Don G. <gil...@bi...> - 2004-10-07 21:37:17
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This is my gene page contest entry, listing common elements and categories for organism gene pages -- Don ## from GeneSummary.dtd; version 0.3; 12 Jun 2004 ## http://eugenes.org/all/gene-report-examples/conf/GeneSummary.dtd --categories BASIC_INFORMATION, LOCATION, GENE_PRODUCT, GENE_ONTOLOGY, SIMILAR_GENES, FUNCTION, REAGENTS, LITERATURE, SUMMARY, ADDITIONAL_INFORMATION BASIC_INFORMATION = primary gene info what else could be added? subtracted? --element BASIC_INFORMATION (GeneID|Symbol|Full_name|Species|Synonyms|Date) --element Symbol --element Full_name --element Synonyms (text|Name) --element GeneID --element Species LOCATION : location in genome --element LOCATION (Chromosome|Genome_map|Map|Scaffold) --element Chromosome --element Scaffold --element Genome_map GENE_PRODUCT : products of genes at sequence and above levels --element GENE_PRODUCT (Gene_type|GeneModel|Polypeptides|Transcripts|Sequence) --element Polypeptides (Polypeptide|Description|note) --element Transcripts (Transcript|Description|note) --element Polypeptide (text|db_xref) --element Transcript (text|Polypeptide|db_xref) --element Gene_type --element Sequence (text|db_xref) GENE_ONTOLOGY : standardized GeneOntology.org parts --element GENE_ONTOLOGY (Molecular_function|Biological_process|Cellular_component) --element Molecular_function (text|goterm) --element Biological_process (text|goterm) --element Cellular_component (text|goterm) --element goevidence --element goterm (text|goevidence|ref) FUNCTION : catch-all for higher level gene actions might want better name --element FUNCTION (Expressions|Phenotypes|Interactions|Protein_domains|External_links) --element Protein_domains (db_xref|note) --element External_links (db_xref|url|note) --element Expressions (Expression|note) --element Expression (text|Phenotype) --element Phenotypes (Phenotype|note) --element Phenotype --element Interactions (Interaction|note) --element Interaction REAGENTS : PCR, cDNA, EST, ... elements (REAGENTS is used now be a few MODs) Add an ALLELES/VARIANTS block, or merged here? REAGENTS_AND_VARIANTS ? --element REAGENTS (Reagent) --element Reagent (text|db_xref|note) SIMILAR_GENES : list of related organism genes, probably blast-computed from proteins alternate names : similarities, related_genes, homologs, orthologs --element SIMILAR_GENES (Similarity) --element Similarity (Species|db_xref|Description|Symbol|Evalue|Percent) --element Evalue --element Percent LITERATURE : relevant experimental references alternate names : Bibliography, References, ... --element LITERATURE (Reference) --element Reference (text|ref|note) SUMMARY : a human-readable text summary of gene information --element SUMMARY (text|html) Primitive types may be in many fields --element Title --element Type --element Description --element Source --element Identifier --element Creator --element Publisher --element Subject --element Date --element Rights --element Name --element note --element url --element db_xref --element ref (Title|Type|Description|Source|Identifier|Creator|Publisher|Subject|Date|Rights) Here is an example from Calmodulin gene from RGD: ===================================================================== Title: RGD Gene Report: Calm1 Source: RGD href=http://rgd.mcw.edu/query/query.cgi?id=2257 Type: Gene Report ====== BASIC_INFORMATION ====== GeneID: 2257 Symbol: Calm1 Full_name: Calm1 Synonyms: Date: 01-JUL-04 ====== LOCATION ====== Genome_map: RGD Genome Annotation Map: Map Locations for Calm1: Cytogenetic 6 q31-q32 genome assembly 6 ====== GENE_PRODUCT ====== Transcripts: has two alternative splicing forms created by utilization of different polyadenylation addition sites ====== GENE_ONTOLOGY ====== Molecular_function: calcium ion binding IEA 727223 , ID=GO:102799 protein binding IEA 727223 , ID=GO:103029 Biological_process: G-protein coupled receptor protein signaling pathway IEA 727223 , ID=GO:110472 Cellular_component: cytoplasm IEA 727223 , ID=GO:119094 ... more Cell components ... ====== SIMILAR_GENES ====== ====== FUNCTION ====== Expressions: expressed strongly in neuronal cells in the adult rat brain 634682 External_links: NM_031969, ID=Nucleotide:NM_031969 ... more database links here ... ====== REAGENTS ====== ====== LITERATURE ====== Reference: NCBI rat LocusLink and RefSeq merged data July 26, 2002 Reference: Yus-Najera E, etal., J Biol Chem 2002 Aug 9;277(32):28545-53. Reference: Ni B, etal., Brain Res Mol Brain Res 1992 Mar;13(1-2):7-17. note: Search Pubmed for articles about Rat Calm1 ====== SUMMARY ====== ====== ADDITIONAL_INFORMATION ====== -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gil...@in...--http://marmot.bio.indiana.edu/ |
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From: Don G. <gil...@bi...> - 2004-10-07 21:32:17
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Dear gene page readers, This last May I wrote: > As a target goal, a proposal for unified gene pages could be ready for > GMOD meeting in Fall 2004. We missed this goal, but people at this week's GMOD meeting reiterated a desire to work together for a common gene summary. Contest of the week: List the biological contents, and their overall categories, common to model organism gene pages. Please reply to this group with your list by 15 October. Rules: 1. Focus on biology now, leave computing to later. The major need is to distill biological knowledge about genes to say what MODs should be representing in a common way. 2. Look over example MOD gene pages. The approach suggested of removing HTML to look at content, labels and organization struck a chord in meeting discussion. 3. Your contents and organization need not be common to all MOD pages, but should reflect a "minimal" set of important gene attributes that most organisms share, and most bioscientists want as reference. I've broken rule 1 by spending some time over the summer computing on this. You can find example gene pages, along with a Gene Page Scraper that will turn existing MOD gene pages into some semblence of common structure, here http://eugenes.org/all/gene-report-examples/ Here a starter list of common gene attributes * Names, symbols/IDs, synonyms * Map locations * Sequences * Reagents * Gene ontology * Similar Genes * Database cross-refs, External links * Alleles, Transcripts * Proteins, Structure and Domains * Expression and Mutant Phenotypes * Gene Interactions * Literature references * Summary Text GMOD Gene Page Working Group ------------------------------------------------ This group will discuss and propose a common gene page that model organism/genome database members can agree to produce in some form. All interested parties can contribute. -- Don -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gil...@in...--http://marmot.bio.indiana.edu/ |
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From: Mathis, J. <jm...@mc...> - 2004-10-05 17:14:37
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Hi Don, Just wanted to drop a quick line as you had suggested at the GMOD meeting to show that i am interested in helping with this. I also believe that some curators at RGD will also be interested. when i get back I will pass along the info and have them sign up for this list as well. Regards, Jed Mathis |
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From: Pankaj J. <pj...@co...> - 2004-05-04 15:23:50
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Don Gilbert said: > > Pankaj, > > Here is an experiment for you. Take your template_gene_page_entry and go > look at other MODs standard gene pages. See what you have that others > do (maybe labelled differently), and mark those fields in your > template somehow as common (asterisk, color-coded, ..). >> http://ascus.plbr.cornell.edu/~gramene/gene/template_gene_page_entry.html. > I will do that. > Do the other MOD common fields have labels that > might be more general use for an average biologist? > (e.g. I'm not sure what 'Systematic ORF name' is for a gene, even > though SGD also uses it. Would plain 'Name' be as informative?). > I guess at some point it will be a problem if not included, because a gene is named with some authentic label like cam1, atpA etc. only when the real functional info is available, whereas with so many genomes getting sequenced, every gene has a (locus) identifier (systematic name) in the genome assembly. Its kind of an accession. So quite often this gene is addressed by its identifier in the literature and that is what the users may be searching for. SGD calls it systematic identifier, TAIR calls it Locus id and at some point rice may use it too as we have recommended its use. > You include GO parts beyond term: evidence, etc. Some MODs do, > others don't. Is this an issue for us (e.g. basic info versus detailed)? > We can get rid of the extended info, but I think when the alleles are included in curation, then the main curation will be of alleles with details. On the gene page it may just be summary of info ported from allele associations. Reason being an allele may not have an activity which another allele of the same gene may have, because of mutation/knockout etc. So in a nutshell Gene can have all the possible associations and features but not an allele. > 'Location/Map' parts could be separated out of the general gene > info block, but does it make more sense to keep with it? You are right for db purposes this info comes from a separate table. > -- Don > -- Pankaj Jaiswal Gramene Database www.gramene.org |
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From: Pankaj J. <pj...@co...> - 2004-05-04 15:18:17
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Hi Don, This is a great beginning and came in at a very appropriate time. We at Gramene are working on resolving some of the issues in our gene centric presentation strategy. I have tried to capture some of the very early thoughts from our side in this document at http://ascus.plbr.cornell.edu/~gramene/gene/template_gene_page_entry.html. Will be working on the updates soon. Even before we begin, I think we need to define some of the very basic concepts that we are going to put together. Thanks Pankaj Don Gilbert wrote: > > Dear organism database folks, > > One outcome of the April 04 GMOD meeting is a working group to decide if > and how we can create a 'Unified Gene Page' for organism databases. You > either volunteered for this group, or were volunteered by someone else > :) There is no required work except that at some point each > represented MOD will want you to vote on how to proceed with group > recommendations. > > I'm hopeful we can accomplish something this summer, and have > suggestions/recommendations by fall 2004 GMOD meeting. Please use the > gmo...@li... for discussion, unless there is a > need for non-public talk. See attached doc for the background and focus > of this group to let you better decide. > > I'd suggest this to start: > > - Focus on biology now, leave computing to later. The major need > is to distill biological knowledge about genes to say what > MODs should be representing in a common way. > > - Look over example MOD gene pages. The approach suggested of > removing HTML to look at content, labels and organization struck a chord > in meeting discussion. XML-izing gene pages is not necessary, > but is one useful way to distill common information and structure. > > - Create a few sample unified pages, and show them > around for comment. We should ask for input from gene page > consumers: scientists who study a few or many genes across > organisms; data miners who use gene pages in bulk (academic, govt., > industry, other databases). > > - Speak up if you want to actively help. I've been working on this > subject since 1999 -- some one else may have better luck in a new > approach at consensus. If you are, or know of, someone with a strong > biology background who uses different MOD gene pages, interested in > organizing this group, please say so. Even if we decide this topic > should be shelved, at least we should gather evidence on why the cost > to unify gene pages is not worth the effort. > > > Would you confirm if you indeed are willing to join this group, if I > have your correct e-mail, affiliation, name, and if it is ok to add > your name/e-mail to public documents? If you are not the best > person for this group, please suggest someone else at your MOD. > > > -- Don Gilbert > > > GMOD: Unified Gene Page Working Group > > TAIR: Leonore Reiser (lr...@ac...; www.arabidopsis.org) > GO: Suzanna Lewis (su...@fr...; geneontology.org) > MGI: Joel Richardson (je...@in...; www.informatics.jax.org) > SGD: Kara Dolinksi (dol...@pr... ; www.yeastgenome.org) > dictyBase: Eric Just (dictybase.org) > RGD: Dean Pasko (dp...@mc...; rgd.mcw.edu) > Wormbase: Raymond Lee (ra...@ca..., wormbase.org) > Gramene: Pankaj Jaiswal (pj...@co...; gramene.org) > EcoCyc/BioCyc: Ingrid Keseler (ke...@ai...) > Zenbase: Jeff Bowes (bo...@uc...; www.xenbase.org) > SGN: Lukas Mueller (la...@co...; www.sgn.cornell.edu) > MaizeGDB: Trent Sigfried (dev...@ia...; maizegdb.org) > FlyBase: Don Gilbert (gil...@in...; flybase.net, eugenes.org) > > NOTE: need email for Eric Just (dictybase.org) > Maybe add locuslink devs; ensembl devs; genecards devs? > ------------------------------------------------ > > > > Toward a Unified Gene Page > GMOD Gene Page Working Group > 2 May 2004 > ------------------------------------------------ > > This group will discuss and propose a common gene page that model > organism/genome database members can agree to produce in some form. All > interested parties can contribute. > > Mail list: > gmo...@li... > > Web home: > http://eugenes.org/all/gene-report-examples/ > (add gmod gene-page project) > > Participants: > (participants from 12+ MODs to be added after confirmation ..) > > > INTRODUCTION > ------------------------------------------------ > There may be a long-standing desire among genome data consumers and > producers to unify the documents describing organism genes (gene pages) > that are provided by many model organism/genome databases (MODs). > There remain questions of whether this desire exceeds costs of effort > to make unified gene pages. > > Discussion of common gene report web pages and software should build on > existing expertise of MODs. These projects have years of experience > working with life scientists to produce gene pages that capture the > essense of knowledge from the databases, and make it understandable and > useful to scientists. For most MODs, the gene page is probably the most > highly used reference document that people come to MOD web sites for. At > FlyBase.net, these account for over a third of all calls, far surpassing > any other single use category. > > > PLAN > ------------------------------------------------ > One outcome of the April 04 GMOD meeting is organization of a working > group to decide how to proceed to reach some consensus on this topic. > Members are drawn from several existing and new MODs, and others > interested in unified gene pages. > > These points need discussion: > * What are common parts of MOD gene pages? > * What could/should be unified? > * Who will benefit? Costs? > * Web Reports AND/OR XML ? > > Suggested starting points: > > - Focus on biology now, leave computing to later. The major need > is to distill biological knowledge about genes to say what > MODs should be representing in a common way. > > - Look over example MOD gene pages. The approach suggested of > removing HTML to look at content, labels and organization struck a chord > in meeting discussion. XML-izing gene pages is not necessary, > but is one useful way to distill common information and structure. > > - Create a few sample unified pages, and show them > around for comment. We should ask for input from gene page > consumers: scientists who study a few or many genes across > organisms; data miners who use gene pages in bulk (academic, govt., > industry, other databases). > > - Speak up if you want to actively help. I've been working on this > subject since 1999 -- some one else may have better luck in a new > approach at consensus. If you are, or know of, someone with a strong > biology background who uses different MOD gene pages, interested in > organizing this group, please say so. Even if we decide this topic > should be shelved, at least we should gather evidence on why the cost > to unify gene pages is not worth the effort. > > As a target goal, a proposal for unified gene pages could be ready for > GMOD meeting in Fall 2004. There is a GMOD mailing list for discussion, > and any documents, sample pages, and software can be deposited at > gmod.sourceforge.net. The euGenes.org gene page service is also > available for such, and test cases. > > > WORKING DOCUMENTS > ------------------------------------------------ > We likely should create a 'gene-page' CVS project at > gmod.sourceforge.net for documents and samples. There are example gene > pages (see below, above), some sample extracted content (HTML -> XML). > DGG has a preliminary 'Gene Page Scraper' that automates in Perl the > by-hand methods I used for removing HTML styles, extracting common > content of MOD gene pages. Useful to gene-data-miners even if not > otherwise, though it likely has a short lifespan as web page design > changes will break it. > > > BACKGROUND (MEOW/euGenes effort) > ------------------------------------------------ > In 1999, attendees of the Model Eukaryote Organism Workshop proposed to > develop a common set of summary gene information. A test website grew > out of this, produced primarily by Bill Gelbart and Don Gilbert. This > was produced by extracting common gene information from existing MODs > public data. Don has continued the MEOW effort at common summary gene > information as euGenes.org, though it never achieved the desired goal of > having each MOD contribute common summary data. The euGenes effort, > without MOD contributions or external funding, has only middling > success at trying to maintain current gene summary pages in the face of > effort needed to match changing genome data. > > The Generic Model Organism Database project (GMOD) arose from related > thoughts (and grant agency spurs for cost-effectiveness) that there > should be common effort at building databases, software tools, and > common practice methods for developing new organism databases, and > updating existing ones. This has been an NIH funded project with many > MOD participants, and as of 2004 is beginning to bear fruit in terms of > commonly usable MOD components. > > With many more organism genome databases coming into being in decade > 2000, the usefulness of having common gene information and documents is > growing, both among database providers and the many customers of these > (from individuals to academic, government and industrial R&D labs, and > other bioinformatics database developers). A hopeful new goal of GMOD is > to tackle the 'Unified Gene Page' question again, with fresh perspective > and see if a new consensus on utility > > Along with MODs, there are numerous bioinformatics web/database services > that have gene-related reports, and can offer useful insights to this > topic. Many of these are found as External_Links on MOD gene pages. > Often these draw the gene summary data from MODs, in ways similar to the > data mining MEOW/euGenes was constructed with, which is another cost of > having > non-unified gene information. > > > FIRST SUMMARY GENE PAGE PROPOSAL > (extract of Model Eukaryote Organism Workshop, W. Gelbart, Feb. 1999 > http://eugenes.org/docs/meow-startup.txt ) > ------------------------------------------------ > ... to establish a common interface for the major model eukaryotic > organism databases. This interface would be offered as the default > homepage for nonspecialists wishing to access any of the participating > databases. ... This home page would provide gene/gene product query > access to based on gene symbol, gene product characteristics, chromosome > position and perhaps homology (if we can agree on criteria to be used). > Our view is that this will satisfy the needs of many nonspecialist users > without forcing them to learn the intricasies and idiosyncracies of each > of our sites. ... We had discussed a design principle that each gene > "page" would contain no more than one screenful of information. > Further, the gene pages should as much as possible focus on > coin-of-the-realm molecular biological terminology rather than > species-specific jargon. I suggest we try to flesh out what a typical > page would contain. Here are some suggestions for relevant fields on > the "gene report page", in order to get a discussion started: > > *Valid terms: > -Gene symbol > -Gene full name > -Gene identifier number > > *Synonyms: > -Symbol synonyms > -Full name synonyms > -Secondary gene identifier numbers > > *Map location information: > -Chromosome and genetic map position > -Molecular map information (simple graphic of DNA length, > encoded transcript(s) and CDS(s) if available) > > *Gene product information: > -Functional information (from function ontology if available) > -Structural information (from InterProt) > -Homology information with other "MEOW" organisms (we would > need to agree on some computable criteria for this field, > which is of course not trivial) > > *Links to extended gene information in the specialty model organism DBs. > *Brief free text gene summary (a few lines at most). > > > APRIL 2004 OUTLINE > ------------------------------------------------ > Example work is at > http://eugenes.org/all/gene-report-examples/ > > Common gene attributes (drawn from existing MOD pages) > * Names, symbols/IDs, synonyms > * Map locations > * Sequences > * Reagents > * Gene ontology > * Similar Genes > * Database cross-refs, External links > * Alleles, Transcripts > * Proteins, Structure and Domains > * Expression and Mutant Phenotypes > * Gene Interactions > * Literature references > * Summary Text > > Common to gene pages? > * Labels - are these same things? > -- Gene / locus / orf > -- Homolog / ortholog / relationship / similarity > -- Citation / publication / reference > * Organization of document > -- Section headers > -- Important at top, common ordering? > * Structure and size of default document > -- Tabular, text, document-like, ... > -- One screen or long report > * Graphics (maps, icons, ...) > * Further Detail options > * Layout and Design (colors, formatting, fonts ..) > > What is customizable? > * MOD customizations > -- Look and Feel > -- Details & Extensions > * Customer choices > -- Best for organism community (org. standard) > -- Best for general reader (general standard) > -- Best for beginners or experts (simple,complex) > > Example Gene Pages > > Common Gene XML? > * Computable text of gene page ? > -- "what you see (web page) is also what your computer can read" > -- simple and human-readable, or complex and detailed > * XML variants, tabular, other? > -- Ace2XML, NCBI XML, others > -- Samples (Web -> XML) > > > COMPARE EXISTING MOD GENE PAGES > ----------------------------------------------------------- > For a start at gathering this common experience into a set of common > values and practice in gene page presentation, I picked a highly > homologous eukaryote gene Calmodulin, and pulled out gene reports on > these from these organism databases: > yeast - SGD > arabidopsis - TAIR > zebrafish - ZFIN > worm - WormBase > rice - Gramene > human - LocusLink > mouse - MGI > rat - RGD > mosquito - Ensembl > fly - FlyBase, euGenes, LocusLink, Ensembl > (see same gene from different viewpoints) > > There are several Calmodulin(-like) genes/org, I just used one from each > source. Find these at http://eugenes.org/all/gene-report-examples/ > or ftp://eugenes.org/eugenes/gene-report-examples/ > > - Don Gilbert > > 24 Apr 2004 - These have been updated to current versions. > As well, four gene pages are translated from HTML to XML, for > cut/paste/edit to design common gene pages. The XML should > (theoretically, with right software/templates) > allow regeneration of the original web pages. > > 5 Sep 2003 - Example gene web page reports from several model > organism databases. > > URLs for the Cam gene pages (Sept 2003; updated Apr 2004 - > alternate reports removed to focus on common summary pages) > --------------------------------------------------------- > > http://flybase.net/cgi-bin/fbidq.html?FBgn0000253 > > http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=S0000313 > > http://www.informatics.jax.org/searches/ accession_report.cgi?id=MGI:88251 > > http://www.arabidopsis.org/servlets/TairObject?type=locus&id=29764 > > http://www.wormbase.org/db/gene/gene?name=cmd-1;class=Locus > > http://rgd.mcw.edu/query/query.cgi?id=2257 > > http://www.gramene.org/perl/protein_search?acc=P29612 > > ## newly inferred zebrafish calm1a gene > http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-030131-8308 > > -------- summary services ----- > > http://www.ensembl.org/Anopheles_gambiae/ geneview?gene=ENSANGG00000010211 > http://www.ensembl.org/Drosophila_melanogaster/geneview?gene=CG8472 > > http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=801 > http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=24242 > http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=36329 > http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=12313 > > http://bioinfo.weizmann.ac.il/cards-bin/carddisp?CALM1 > > http://eugenes.org/cgi-bin/moidq.html?FBgn0000253 > http://eugenes.org/cgi-bin/moidq.html?AGgn0010211 > http://eugenes.org/cgi-bin/moidq.html?HUgn0000801 > http://eugenes.org/cgi-bin/moidq.html?MGgn0000995 > http://eugenes.org/cgi-bin/moidq.html?CEgn0016585 > http://eugenes.org/cgi-bin/moidq.html?ATgn0005396 > http://eugenes.org/cgi-bin/fbidq.html?SGgn0000313 > http://eugenes.org/cgi-bin/moidq.html?ZFgn0000878 > > > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gil...@in... -- http://marmot.bio.indiana.edu/ > -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ |
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From: Don G. <gil...@bi...> - 2004-05-04 02:36:30
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T> SGD calls it systematic identifier, TAIR calls it Locus id ... THis is the sort of area we as a group may be able to help with. Everyone with a genome has the same kind of information: 'real' gene name and annotation ID/systematic ORF name/Locus id/... This later is named in various ways, and leads folks looking at multiple genomes to wonder what the name is refering to. I don't know if there is a common practice / accepted name for these, but let us hunt around and recommend one. - Don |
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From: Don G. <gil...@bi...> - 2004-05-04 00:43:58
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Pankaj, Here is an experiment for you. Take your template_gene_page_entry and go look at other MODs standard gene pages. See what you have that others do (maybe labelled differently), and mark those fields in your template somehow as common (asterisk, color-coded, ..). > http://ascus.plbr.cornell.edu/~gramene/gene/template_gene_page_entry.html. Do the other MOD common fields have labels that might be more general use for an average biologist? (e.g. I'm not sure what 'Systematic ORF name' is for a gene, even though SGD also uses it. Would plain 'Name' be as informative?). You include GO parts beyond term: evidence, etc. Some MODs do, others don't. Is this an issue for us (e.g. basic info versus detailed)? 'Location/Map' parts could be separated out of the general gene info block, but does it make more sense to keep with it? -- Don |
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From: Don G. <gil...@in...> - 2004-05-03 00:05:08
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Toward a Unified Gene Page GMOD Gene Page Working Group 2 May 2004 ------------------------------------------------ This group will discuss and propose a common gene page that model organism/genome database members can agree to produce in some form. All interested parties can contribute. Mail list: gmo...@li... Web home: http://eugenes.org/all/gene-report-examples/ (add gmod gene-page project) Participants: (participants from 12+ MODs to be added after confirmation ..) INTRODUCTION ------------------------------------------------ There may be a long-standing desire among genome data consumers and producers to unify the documents describing organism genes (gene pages) that are provided by many model organism/genome databases (MODs). There remain questions of whether this desire exceeds costs of effort to make unified gene pages. Discussion of common gene report web pages and software should build on existing expertise of MODs. These projects have years of experience working with life scientists to produce gene pages that capture the essense of knowledge from the databases, and make it understandable and useful to scientists. For most MODs, the gene page is probably the most highly used reference document that people come to MOD web sites for. At FlyBase.net, these account for over a third of all calls, far surpassing any other single use category. PLAN ------------------------------------------------ One outcome of the April 04 GMOD meeting is organization of a working group to decide how to proceed to reach some consensus on this topic. Members are drawn from several existing and new MODs, and others interested in unified gene pages. These points need discussion: * What are common parts of MOD gene pages? * What could/should be unified? * Who will benefit? Costs? * Web Reports AND/OR XML ? Suggested starting points: - Focus on biology now, leave computing to later. The major need is to distill biological knowledge about genes to say what MODs should be representing in a common way. - Look over example MOD gene pages. The approach suggested of removing HTML to look at content, labels and organization struck a chord in meeting discussion. XML-izing gene pages is not necessary, but is one useful way to distill common information and structure. - Create a few sample unified pages, and show them around for comment. We should ask for input from gene page consumers: scientists who study a few or many genes across organisms; data miners who use gene pages in bulk (academic, govt., industry, other databases). - Speak up if you want to actively help. I've been working on this subject since 1999 -- some one else may have better luck in a new approach at consensus. If you are, or know of, someone with a strong biology background who uses different MOD gene pages, interested in organizing this group, please say so. Even if we decide this topic should be shelved, at least we should gather evidence on why the cost to unify gene pages is not worth the effort. As a target goal, a proposal for unified gene pages could be ready for GMOD meeting in Fall 2004. There is a GMOD mailing list for discussion, and any documents, sample pages, and software can be deposited at gmod.sourceforge.net. The euGenes.org gene page service is also available for such, and test cases. WORKING DOCUMENTS ------------------------------------------------ We likely should create a 'gene-page' CVS project at gmod.sourceforge.net for documents and samples. There are example gene pages (see below, above), some sample extracted content (HTML -> XML). DGG has a preliminary 'Gene Page Scraper' that automates in Perl the by-hand methods I used for removing HTML styles, extracting common content of MOD gene pages. Useful to gene-data-miners even if not otherwise, though it likely has a short lifespan as web page design changes will break it. BACKGROUND (MEOW/euGenes effort) ------------------------------------------------ In 1999, attendees of the Model Eukaryote Organism Workshop proposed to develop a common set of summary gene information. A test website grew out of this, produced primarily by Bill Gelbart and Don Gilbert. This was produced by extracting common gene information from existing MODs public data. Don has continued the MEOW effort at common summary gene information as euGenes.org, though it never achieved the desired goal of having each MOD contribute common summary data. The euGenes effort, without MOD contributions or external funding, has only middling success at trying to maintain current gene summary pages in the face of effort needed to match changing genome data. The Generic Model Organism Database project (GMOD) arose from related thoughts (and grant agency spurs for cost-effectiveness) that there should be common effort at building databases, software tools, and common practice methods for developing new organism databases, and updating existing ones. This has been an NIH funded project with many MOD participants, and as of 2004 is beginning to bear fruit in terms of commonly usable MOD components. With many more organism genome databases coming into being in decade 2000, the usefulness of having common gene information and documents is growing, both among database providers and the many customers of these (from individuals to academic, government and industrial R&D labs, and other bioinformatics database developers). A hopeful new goal of GMOD is to tackle the 'Unified Gene Page' question again, with fresh perspective and see if a new consensus on utility Along with MODs, there are numerous bioinformatics web/database services that have gene-related reports, and can offer useful insights to this topic. Many of these are found as External_Links on MOD gene pages. Often these draw the gene summary data from MODs, in ways similar to the data mining MEOW/euGenes was constructed with, which is another cost of having non-unified gene information. FIRST SUMMARY GENE PAGE PROPOSAL (extract of Model Eukaryote Organism Workshop, W. Gelbart, Feb. 1999 http://eugenes.org/docs/meow-startup.txt ) ------------------------------------------------ ... to establish a common interface for the major model eukaryotic organism databases. This interface would be offered as the default homepage for nonspecialists wishing to access any of the participating databases. ... This home page would provide gene/gene product query access to based on gene symbol, gene product characteristics, chromosome position and perhaps homology (if we can agree on criteria to be used). Our view is that this will satisfy the needs of many nonspecialist users without forcing them to learn the intricasies and idiosyncracies of each of our sites. ... We had discussed a design principle that each gene "page" would contain no more than one screenful of information. Further, the gene pages should as much as possible focus on coin-of-the-realm molecular biological terminology rather than species-specific jargon. I suggest we try to flesh out what a typical page would contain. Here are some suggestions for relevant fields on the "gene report page", in order to get a discussion started: *Valid terms: -Gene symbol -Gene full name -Gene identifier number *Synonyms: -Symbol synonyms -Full name synonyms -Secondary gene identifier numbers *Map location information: -Chromosome and genetic map position -Molecular map information (simple graphic of DNA length, encoded transcript(s) and CDS(s) if available) *Gene product information: -Functional information (from function ontology if available) -Structural information (from InterProt) -Homology information with other "MEOW" organisms (we would need to agree on some computable criteria for this field, which is of course not trivial) *Links to extended gene information in the specialty model organism DBs. *Brief free text gene summary (a few lines at most). APRIL 2004 OUTLINE ------------------------------------------------ Example work is at http://eugenes.org/all/gene-report-examples/ Common gene attributes (drawn from existing MOD pages) * Names, symbols/IDs, synonyms * Map locations * Sequences * Reagents * Gene ontology * Similar Genes * Database cross-refs, External links * Alleles, Transcripts * Proteins, Structure and Domains * Expression and Mutant Phenotypes * Gene Interactions * Literature references * Summary Text Common to gene pages? * Labels - are these same things? -- Gene / locus / orf -- Homolog / ortholog / relationship / similarity -- Citation / publication / reference * Organization of document -- Section headers -- Important at top, common ordering? * Structure and size of default document -- Tabular, text, document-like, ... -- One screen or long report * Graphics (maps, icons, ...) * Further Detail options * Layout and Design (colors, formatting, fonts ..) What is customizable? * MOD customizations -- Look and Feel -- Details & Extensions * Customer choices -- Best for organism community (org. standard) -- Best for general reader (general standard) -- Best for beginners or experts (simple,complex) Example Gene Pages Common Gene XML? * Computable text of gene page ? -- "what you see (web page) is also what your computer can read" -- simple and human-readable, or complex and detailed * XML variants, tabular, other? -- Ace2XML, NCBI XML, others -- Samples (Web -> XML) COMPARE EXISTING MOD GENE PAGES ----------------------------------------------------------- For a start at gathering this common experience into a set of common values and practice in gene page presentation, I picked a highly homologous eukaryote gene Calmodulin, and pulled out gene reports on these from these organism databases: yeast - SGD arabidopsis - TAIR zebrafish - ZFIN worm - WormBase rice - Gramene human - LocusLink mouse - MGI rat - RGD mosquito - Ensembl fly - FlyBase, euGenes, LocusLink, Ensembl (see same gene from different viewpoints) There are several Calmodulin(-like) genes/org, I just used one from each source. Find these at http://eugenes.org/all/gene-report-examples/ or ftp://eugenes.org/eugenes/gene-report-examples/ - Don Gilbert 24 Apr 2004 - These have been updated to current versions. As well, four gene pages are translated from HTML to XML, for cut/paste/edit to design common gene pages. The XML should (theoretically, with right software/templates) allow regeneration of the original web pages. 5 Sep 2003 - Example gene web page reports from several model organism databases. URLs for the Cam gene pages (Sept 2003; updated Apr 2004 - alternate reports removed to focus on common summary pages) --------------------------------------------------------- http://flybase.net/cgi-bin/fbidq.html?FBgn0000253 http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=S0000313 http://www.informatics.jax.org/searches/ accession_report.cgi?id=MGI:88251 http://www.arabidopsis.org/servlets/TairObject?type=locus&id=29764 http://www.wormbase.org/db/gene/gene?name=cmd-1;class=Locus http://rgd.mcw.edu/query/query.cgi?id=2257 http://www.gramene.org/perl/protein_search?acc=P29612 ## newly inferred zebrafish calm1a gene http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-030131-8308 -------- summary services ----- http://www.ensembl.org/Anopheles_gambiae/ geneview?gene=ENSANGG00000010211 http://www.ensembl.org/Drosophila_melanogaster/geneview?gene=CG8472 http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=801 http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=24242 http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=36329 http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=12313 http://bioinfo.weizmann.ac.il/cards-bin/carddisp?CALM1 http://eugenes.org/cgi-bin/moidq.html?FBgn0000253 http://eugenes.org/cgi-bin/moidq.html?AGgn0010211 http://eugenes.org/cgi-bin/moidq.html?HUgn0000801 http://eugenes.org/cgi-bin/moidq.html?MGgn0000995 http://eugenes.org/cgi-bin/moidq.html?CEgn0016585 http://eugenes.org/cgi-bin/moidq.html?ATgn0005396 http://eugenes.org/cgi-bin/fbidq.html?SGgn0000313 http://eugenes.org/cgi-bin/moidq.html?ZFgn0000878 -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gil...@in... -- http://marmot.bio.indiana.edu/ |