Difference between revisions of "WormBase Model:Protein"
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== Curator Comments/Description == | == 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 == | == Model == | ||
<pre> | <pre> | ||
| + | ///////////////////////////////// | ||
| + | // | ||
| + | // ?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 | ||
</pre> | </pre> | ||
== Proposed Changes == | == Proposed Changes == | ||
| + | ==unused tags== | ||
| + | |||
| + | Display | ||
| + | |||
| + | View Default_view | ||
| + | |||
| + | Brigpep | ||
| + | |||
| + | 3d_data | ||
| + | |||
| + | DNA_homol | ||
Latest revision as of 08:49, 5 October 2010
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
