[Gmod-gene-page] Gene page contest entry (d.gilbert)

[Don G. <gil...@bi...>]

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/