WormBase Model:Protein

From WormBaseWiki

Contents 1 Curator Comments/Description 2 Model 3 Proposed Changes 4 unused tags

WormBase Models

Curator Comments/Description

We can think about retiring the Wormpep/Brigpep tags as this a doesn't scale and is only used by the subclasses.wrm file for

pulling out the set of Live proteins for a given species, the added benefit of these tags is removed as the subclasses also

gueries the species tag which slows it back up.

Model

/////////////////////////////////
//
// ?Protein class
//
/////////////////////////////////

?Protein  Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Length + checksum
          Display View ?View
                  Default_view UNIQUE ?View
          DB_info Database ?Database ?Database_field UNIQUE ?Accession_number XREF Protein
                  Gene_name  ?Text
                  Description   UNIQUE ?Text
                  Molecular_weight Float #Evidence
          Origin  Species UNIQUE ?Species   //XREF Protein in geneace
                  Wormpep // for C. elegans or C. briggsae  proteins, used by subclass definitions
                  Brigpep // 
                  History Int Text ?Text //history logging [020801 krb]
                  Live       // replace use of 'Inactive' krb 06/12/01
          Visible Corresponding_CDS ?CDS XREF Corresponding_protein
                  Expr_pattern ?Expr_pattern XREF Protein
                  Homology_group ?Homology_group XREF Protein // added [031120 krb]
                  Ortholog_gene ?Gene XREF Ortholog_other #Evidence //[change Ortholog others to link to proteins rather than accessions]
                  3d_data ?3d_data XREF Protein
                 // Structure_data ?Structure_data XREF Corresponding_protein #Evidence
          Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
                Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
                Structure_homol ?Structure_data XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
                Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
                Homol_homol ?Homol_data XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
          Feature ?Method Int Int UNIQUE Float  // display according to method
          Contains_peptide ?Mass_spec_peptide
          Remark ?Text #Evidence

Proposed Changes

unused tags

Display

View Default_view

Brigpep

3d_data

DNA_homol