Difference between revisions of "WormBase Models"

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3) All address info should get stored in the #Addtess hash
 
3) All address info should get stored in the #Addtess hash
 
   Currently only used in the Person class, should unify all models to use the Address hash
 
   Currently only used in the Person class, should unify all models to use the Address hash
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 +
4) Author class should use #Address
 +
 +
5)

Revision as of 11:06, 10 August 2010

The A - Z of WormBase Models

Document created from WS218 models, so may differ from the current model used for your datatype.

Sanger CVS models.wrm

Models List

No. Class Institute Comment/Brief Description Curator(s)
1 2_point_data Sanger Done
2 3d_data ? This class is not used and the model should probably be merged into the ?Structure_data model? Done
3 Accession_number Sanger ? Done
4 Analysis ? This class is used along with ?Condition to store meta data about an experiment Done
5 Anatomy_function Caltech ? Raymond Done
6 Anatomy_name Caltech ? Raymond Done
7 Anatomy_term Caltech ? Raymond Done
8 Antibody Caltech ? Done
9 AO_code ? ? Raymond Done
10 Atlas OICR WORMBASE ATLAS (VIRTUAL WORM) - unused data class Done
11 Author Caltech ?
12 Balancer ? ?
13 CDS Sanger ? Paul Davis + others Done
14 Cell Sanger/Caltech? ? Raymond
15 Cell_group Sanger/Caltech? ? Raymond
16 Clone Sanger ?
17 Condition ? ? Wen Chen
18 Contig Sanger ?
19 Database Sanger ?
20 Database_field Sanger ?
21 Expression_cluster Caltech ? Wen Chen
22 Expr_pattern Caltech ? Wen Chen
23 Expr_profile Caltech ?
24 Feature Sanger ? Paul Davis Mary Anne
25 Feature_data Sanger ?Class of data used to mark up features on Transcript data
26 Gene Sanger Envelope for collecting/connecting data pertaining to a single gene Mary Ann
27 Gene_class Sanger Used for describing and grouping a family of genes Mary Ann
28 Gene_cluster Sanger Used to denote a cluster of genes of a specific type - not maintained?
29 Gene_name Sanger ?
30 Gene_regulation Caltech ?
31 Genetic_code Sanger Allows for alternate genetic codes for Mitocondria and selenocysteine.
32 GO_code Caltech ?
33 GO_term Caltech ?
34 Grid Sanger ?
35 Grid_data Sanger ?
36 Grid_row Sanger ?
37 Homol_data Sanger Used for storing alignment data
38 Homology_group Caltech ?
39 Interaction Caltech ?
40 Interval_col_conf ? ?
41 Jade Acedb? ?
42 Lab_Location Caltech ?
43 Laboratory Caltech ?
44 Library Sanger libraries used for sequencing of nematode ESTs // Information to come from Mark Blaxters
45 Life_stage Caltech ? Wen Chen
46 Locus Sanger This class is a reminent that should be cleaned up.
47 ManyMap Sanger ?
48 Map Sanger ?
49 Map_error Sanger ?
50 Map_offset Sanger ?
51 Map_position Sanger ?
52 Mass_spec_experiment Sanger ? Gary Williams
53 Mass_spec_peptide Sanger ? Gary Williams
54 Method ? AceDB class that details display etc. of objects in the other classes
55 Microarray Caltech ? Wen Chen
56 Microarray_experiment Caltech ? Wen Chen
57 Microarray_results Caltech ? Wen Chen
58 Mixed_grid_row Sanger ?
59 Molecule Caltech Used to capture molecules that influence gene activity and affect phenotypes. Karen
60 Motif Sanger ?
61 Movie Caltech ?
62 Multi_counts Sanger? ?
63 MultiMap ? Not used?
64 Multi_pt_data Sanger ?
65 Neurodata ? ?Not Used Raymond
66 Neuro_location ? ? Not Used Raymond
67 Oligo ? ?
68 Oligo_set ? ?
69 Operon Sanger Stores genes that are in Operons Paul Davis Done
70 Paper Caltech ?
71 PCR_product ? ?
72 Person Caltech ? Cecilia Nakamura
73 Person_name Caltech ?
74 Phenotype Caltech ?
75 Phenotype_Assay Caltech ?
76 Phenotype_name Caltech ?
77 Picture Caltech ?
78 Position_Matrix Caltech ?
79 Pos_neg_data Sanger ?
80 Protein Sanger ?
81 Pseudogene Sanger Stores the Pseudogene models Done
82 Rearrangement Caltech ?
83 ReconCellInfo OICR ?
84 Reconstruction OICR ?
85 Reference Caltech ?
86 RNAi Caltech Stores information pertaining to RNAi experiments, including RNAi probe targets, resulting phenotypes, and associated papers. Gary Schindleman, Chris Grove
87 SAGE_experiment Sanger ? Wen Chen
88 SAGE_tag Sanger ? Wen Chen
89 Sequence Sanger A broad class for storing genomic, Transcripts Sequence etc.
90 SK_map Caltech ?
91 SO_term Caltech ?
92 Species Sanger ?
93 Strain Sanger ?
94 Structure_data OICR ?
95 Timepoint OICR ?
96 Transcript Sanger Stores RNAgenes and the Full length Coding_transcripts Done
97 Transgene Caltech ?
98 Transposon Sanger Stores the Transposon span and S_child info Paul Davis
99 Transposon_family Sanger Used for grouping like ?Transposons Paul Davis
100 Variation Sanger ? Mary Ann Done
101 Variation_name Sanger ? Mary Ann Done
102 YH Caltech ? Done
103 #Address Unused class? Done

Action Targets

1) If you check your models I have started listing all unised tags in the bottom section of each page.

2) 3d_data and Structure_data should be merged

3) All address info should get stored in the #Addtess hash

  Currently only used in the Person class, should unify all models to use the Address hash

4) Author class should use #Address

5)