WormBase Models

From WormBaseWiki
Revision as of 18:03, 17 August 2010 by Schindelman (talk | contribs)
Jump to navigationJump to search

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 ? Xiaodong Wang Done
9 AO_code ? ? Raymond Done
10 Atlas OICR WORMBASE ATLAS (VIRTUAL WORM) - unused data class Done
11 Author Caltech ? Done
12 Balancer ? Unused class? Done
13 CDS Sanger ? Paul Davis + others Done
14 Cell Sanger/Caltech? ? Raymond Done
15 Cell_group Sanger/Caltech? ? Raymond Done
16 Clone Sanger ? Done
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 Capture the data on change of gene B expression level when gene A is perturbed Xiaodong Wang
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 ? Xiaodong Wang
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 remnant 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 This gives details of a mass-specttrometry experiment and XREFS the mass-spec peptides produced by that experiment Gary Williams Done
53 Mass_spec_peptide Sanger This gives the sequence of a mass-spectrometry peptide. Gary Williams Done
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 Annotate experimentally well-validated DNA-binding profiles and individual binding sites for transcription factors (TFs) Xiaodong Wang
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 Schindelman, 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 ? Xiaodong Wang Done
103 #Address Unused class? Done
104 #Mass_spec_data Sanger Describes details of a mass-spectrometry peptide Gary Williams Done

Action Targets

1) If you check your models I have started listing all unused 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 #Address hash

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

4) Author class should use #Address

5)