WormBase Models

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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 + Others Done
18 Contig Sanger ? Done
19 Database Sanger ? Done
20 Database_field Sanger ? Done
21 Expression_cluster Caltech ? Wen Chen Done
22 Expr_pattern Caltech ? Wen Chen Done
23 Expr_profile Caltech ? Done
24 Feature Sanger ? Paul Davis Mary Ann Done
25 Feature_data Sanger ?Class of data used to mark up features on Transcript data Done
26 Gene Sanger Envelope for collecting/connecting data pertaining to a single gene (Don't worry MA didn't write this) Mary Ann Done
27 Gene_class Sanger Used for describing and grouping a family of genes Mary Ann Done
28 Gene_cluster Sanger Used to denote a cluster of genes of a specific type - not maintained? Done
29 Gene_name Sanger ? Done
30 Gene_regulation Caltech Capture the data on change of gene B expression level when gene A is perturbed Xiaodong Wang Done
31 Genetic_code Sanger Allows for alternate genetic codes for Mitocondria and selenocysteine. Done
32 GO_code Caltech Used to capture the evidence (eg., 'IMP', Inferred from Mutant Phenotype) on which a GO annotation is based. Ranjana Kishore, Kimberly Van Auken Done
33 GO_term Caltech Used to capture the GO term name which belongs to either the biological process, cellular component or molecular function ontology developed by the GO consortium. Ranjana Kishore, Kimberly Van Auken Done
34 Grid Sanger Old data? do we still nedd it? Done
35 Grid_data Sanger Target for removal - Unused class, no data in WS218 Done
36 Grid_row Sanger Target for removal - Unused class, no data in WS218 Done
37 Homol_data Sanger Used for storing alignment data Done
38 Homology_group Caltech ? Done
39 Interaction Caltech ? Xiaodong Wang Done
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 phenotypes. Karen Yook
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 This model is used for the phenotype ontology and the objects that phenotypes are assigned to. Gary Schindleman
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 Sanger, Caltech (phenotypes) Caltech curates phenotypes of rearrangements. Sequence and object curation occurs at Sanger. Changes to the model needed to be approved by Sanger curators. Karen Yook (phenotype)
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 Used for capturing extrachromosomal and integrated genomic arrays used as tissue/cell markers, for rescuing genetic mutations, assaying gene function, and effects of gene overexpression. Wen Chen, Karen Yook
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, Caltech (phenotype) ? Mary Ann, Karen Yook (phenotype aspect) 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
105 #Phenotype_info Caltech Information attached to an object concerning a particular phenotype Wen Chen, Gary Schindelman, Karen Yook
106 #Feature_info

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