Difference between revisions of "WormBase Model:Protein"
From WormBaseWiki
Jump to navigationJump to search (Created page with '__TOC__ WormBase Models == Curator Comments/Description == == Model == <pre> </pre> == Proposed Changes ==') |
|||
(One intermediate revision by the same user not shown) | |||
Line 5: | Line 5: | ||
== 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