Toward a Unified Gene Page
GMOD Meeting, April 2004,  Don Gilbert, gilbertd@indiana.edu

Gene Pages

 * Common parts of MOD gene pages
 * What could/should be unified?
 * Who will benefit?  Costs?
 * Web Reports AND XML ?
 * You: discuss, design common gene page

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
 * .. others?
 
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?

Common to gene pages?
 * 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)

Common tools?
 * Common gene page schema?
 * Labels CV/Ontology, XML DTD/template
 * Software, web templates ?
 * html, xml/xslt, perl, java
 * Adaptable to various databases?

Tasks
 * Now: Design your common gene page
 * Cut/paste sample XML pages into one 
 * Comment on what should be unified
 * Comment on best parts of MOD pages
 * After: Talk MODs into generating these

http://eugenes.org/all/gene-report-examples/
   HTML and XML



Fly Gene Page as XML
<gene id="FlyBase:FBgn0000253">
  <title>FlyBase: Cam</title> 
  <contents>Gene Synopsis</contents>

  <Symbol>Cam</Symbol>
  <Synonyms>CG8472;    CG8472;   .. </Synonyms>
  <Full_name>Calmodulin </Full_name>
  <FlyBase_ID>FBgn0000253</FlyBase_ID>
  <Date>28 Feb 04 </Date>

  <GENOMIC_ORGANIZATION>
    <Chromosome_arm>2R</Chromosome_arm>   ...
  </GENOMIC_ORGANIZATION>

  <Protein_domains>
    <db_xref id="InterPro:IPR002048">EF-hand family</db_xref>
  </Protein_domains>
  <External_links>
    <db_xref id="FlyGRID:FBgn0000253">Fly GRID</db_xref>
  </External_links>
  
  <EXPRESSION_PHENOTYPES>
    <Expression> ..   <Mutant_Phenotype> ...
  </EXPRESSION_PHENOTYPES>
  
  <GENE_PRODUCT>
  <Polypeptides>
      <Polypeptide id="FBpp0001929"> Cam<sup>+</sup>P148 <aasize>148</aasize> </Polypeptide>
   </Polypeptides>
   <Transcripts>..
  </GENE_PRODUCT>

  <GENE_ONTOLOGY>
    <Molecular_function>
      <goterm id="GO:0005509">calcium ion binding</goterm>
      <goterm id="GO:0005516">calmodulin binding</goterm> 
    </Molecular_function>
   <Biological_process>..
   <Cellular_component>..
  </GENE_ONTOLOGY>

  <Summary>
    D. melanogaster gene Calmodulin..
  </Summary>

</gene>

Yeast Gene Page as XML
<gene id="SGD:S0000313">
  <title>SGD: CMD1/YBR109C</title>
  <contents>Gene Report</contents>
  
  <BASIC_INFORMATION>
    <Standard_Name>CMD1</Standard_Name>
     <Systematic_Name>YBR109C</Systematic_Name>
     <Feature_Type>ORF, Verified</Feature_Type>
     <Description>master regulator of calcium mediated signalling</Description>
     <Gene_Product>calmodulin</Gene_Product>
    
    <Mutant_Phenotype id="YBR109C">
      <name>Systematic deletion</name><value>inviable</value>
    </Mutant_Phenotype>
  
    <Sequence_Coordinates id="S0000313">
      <location>II:458318-457875</location> ...
      <Genetic_position>53</Genetic_position>
    </Sequence_Coordinates>

   <External_links>
      <db_xref id="MIPS:YBR109C">MIPS</db_xref> ...
    </External_links>

  <GENE_ONTOLOGY id="CMD1">
    <Molecular_function>
        <goterm id="GO:0005509">calcium ion binding</goterm>
      </Molecular_function>
      <Biological_process>...
      <Cellular_component>...
  </GENE_ONTOLOGY>
 
   <SGDID>S0000313</SGDID>
</BASIC_INFORMATION>
  
 <RESOURCES> 
   <Genome_map id="S0000313" content="thumbnail">ORF map</Genome_map> 
   <Protein_Structure>
     <Prot_ref id="SCOP:S0000313">SCOP superfamily (MRC/Stanford)</Prot_ref>
    </Protein_Structure>
   <Interactions>
      <interact id="yeastrc:YBR109C#TH">YeastRC Two-Hybrid</interact>
   </Interactions>
 </RESOURCES> 
</gene>


Mouse Gene Page as XML
<gene id="MGI:88251">
  <title>MGI 2.98 - Marker Detail</title>
  <contents>Gene Detail</contents>
  
  <Symbol>Calm1<Symbol>
  <Name>calmodulin 1<Name>
  <ID>MGI:88251</ID>
  <Nomenclature id=737>Nomenclature History</Nomenclature>
  <Map_position>   Chromosome 12 ..  </Map_position>
  <Orthology> human;  rat </ Orthology>

  <Sequences>
    <Nucleotide>Entrez:NM_009790</Nucleotide>
  </Sequences>
   <Protein_domains>  
    <db_xref id="InterPro:IPR002048">Calcium-binding EF-hand</db_xref>
  </Protein_domains>  
  <Phenotypes>  
    <info id=737 type="locuscat">Mouse Locus Catalog<info>
  </Phenotypes> 

  <GENE_ONTOLOGY id=737>
    <Molecular_function>
      <goterm id="GO:0005509">calcium ion binding</goterm>
    </Molecular_function>
    <Biological_process>...
    <Cellular_component>...
  </GENE_ONTOLOGY>

  <Expression>
    <info id=737 type="gxdindex">GXD literature index (2)<info>
  </Expression>
  <External_links>
    <db_xref id="NIA:NAP094874-001">NIA Mouse Gene Index</db_xref>
  </External_links>
  <References>  
   <ref id=9345> J:9357
      Kluxen FW <i>et al.</i>, 
      "Opposite regulation of the mRNAs for parvalbumin and p19/6.8 in myotonic mouse muscle." Eur J Biochem 1988 Sep 1;176(1):153-8
    </ref>
  </References>  
</gene>


Worm Gene Page as XML
<gene id="WormBase:cmd-1">
  <title>WormBase: cmd-1</title>
  <contents>Gene Summary</contents>

  <Identification>
   <Brief_ID>cmd-1 encodes a putative homolog of calmodulin 1 that affects growth rate and fertility.</Brief_ID>
    <Species>Caenorhabditis elegans</Species>
    <Common_name>cmd-1
     <note>(CGC approved)</note>
    <Common_name>
   <Other_sequence>
      <db_xref id="Entrez:AJ132193">AJ132193</db_xref>
   <Other_sequence>
   <Gene_model id="T21H3.3">
      <Name>T21H3.3</Name>
      <Status>confirmed by cDNA(s)</Status>
   </Gene_model>
   <Ortholog>
      Putative <i>C. briggsae</i> ortholog
      <link id="CBG01097" type="ebsyn">CBG01097</link>
   </Ortholog>

  <GENE_ONTOLOGY>
    <Molecular_function>
      <goterm id="GO:0005509">calcium ion binding</goterm>
        <goevidence>IEA</goevidence>
    </Molecular_function>
    <Biological_process> ...
    <Cellular_component> ...
  </GENE_ONTOLOGY>

  <Location>
    <Genomic_Position>V:1156138..1157022</Genomic_Position>
  </Location>

  <Similarities id="WP:CE13902">
   <Similarity>
      <Species>C. briggsae</Species>
      <db_xref>BP:CBP00318</db_xref>
      <Description>gene CBG01097</Description>
      <E-value>5e-76</E-value>
      <Percent-length>99.3</Percent-length>
    </Similarity>
  </Similarities>
</gene>