Difference between revisions of "WormBase Models"
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| A broad class for storing genomic, Transcripts Sequence etc. | | A broad class for storing genomic, Transcripts Sequence etc. | ||
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| Stores RNAgenes and the Full length Coding_transcripts | | Stores RNAgenes and the Full length Coding_transcripts | ||
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| 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. | | 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, [[User:Kyook|Karen Yook]] | | Wen Chen, [[User:Kyook|Karen Yook]] | ||
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| Stores the Transposon span and S_child info | | Stores the Transposon span and S_child info | ||
| [[User:Pdavis|Paul Davis]] | | [[User:Pdavis|Paul Davis]] | ||
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| Used for grouping like ?Transposons | | Used for grouping like ?Transposons | ||
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Revision as of 09:54, 5 October 2010
The A - Z of WormBase Models
Document created from WS218 models, so may differ from the current model used for your datatype.
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 | ? | Poss target for removal as it's not used. | Done | |
41 | Jade | Acedb? | ? | Done | |
42 | Lab_Location | ? | Target for removal - Unused class, no data in WS218 | Done | |
43 | Laboratory | Caltech | ? | Done | |
44 | Library | Sanger | libraries used for sequencing of nematode ESTs // Information to come from Mark Blaxters (This might be good for C. elegans seq project data?) | Done | |
45 | Life_stage | Caltech | ? | Wen Chen | Done |
46 | Locus | Sanger | This class is a remnant that should be cleaned up. - Lots of unused tags, a priority for cleanup. | Done | |
47 | ManyMap | AceDB | Internal class as the xace .c code is aware of it. | N/A | Done |
48 | Map | AceDB | Internal class? | N/A | Done |
49 | Map_error | AceDB | Internal class? | N/A | Done |
50 | Map_offset | Sanger | Internal class? | N/A | Done |
51 | Map_position | AceDB | Internal class? | N/A | Done |
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 | Done | |
55 | Microarray | Caltech | ? | Wen Chen | Done |
56 | Microarray_experiment | Caltech | ? | Wen Chen | Done |
57 | Microarray_results | Caltech | ? | Wen Chen | Done |
58 | Mixed_grid_row | Sanger | ? | Done | |
59 | Molecule | Caltech | Used to capture molecules that influence gene activity and phenotypes. | Karen Yook | Done |
60 | Motif | Sanger | ? | Done | |
61 | Movie | Caltech | This class needs fleshing out with descriptive data as the majority of the tags are enpty. | Done | |
62 | Multi_counts | Tied in with multi_ptd_data | Un-used so could possibly be retired? | Done | |
63 | MultiMap | ? | Not used - Acedb source code looks for this class, Keep. | Done | |
64 | Multi_pt_data | Sanger | ? | Done | |
65 | Neurodata | ? | ?Not Used | Raymond | Done |
66 | Neuro_location | ? | ? Not Used | Raymond | Done |
67 | Oligo | ? | ? | Done | |
68 | Oligo_set | ? | ? | Done | |
69 | Operon | Sanger | Stores genes that are in Operons | Paul Davis | Done |
70 | Paper | Caltech | ? | Done | |
71 | PCR_product | ? | ? | Done | |
72 | Person | Caltech | ? | Cecilia Nakamura | Done |
73 | Person_name | Caltech | ? | Done | |
74 | Phenotype | Caltech | This model is used for the phenotype ontology and the objects that phenotypes are assigned to. | Gary Schindleman | Done |
75 | Phenotype_Assay | Caltech | Unused class in WS218 (Could be removed if we run low on classes) | Done | |
76 | Phenotype_name | Caltech | ? | Done | |
77 | Picture | Caltech | ? | Done | |
78 | Position_Matrix | Caltech | Annotate experimentally well-validated DNA-binding profiles and individual binding sites for transcription factors (TFs) | Xiaodong Wang | Done |
79 | Pos_neg_data | Sanger | ? | Done | |
80 | Protein | Sanger | ? | Done | |
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) | Done |
83 | #ReconCellInfo | OICR | Done | ||
84 | Reconstruction | OICR | ? | Done | |
85 | Reference | Caltech | Target for removal - Unused data class, appears to have been replaced by paper (need to check acedb dependencies) | Done | |
86 | RNAi | Caltech | Stores information pertaining to RNAi experiments, including RNAi probe targets, resulting phenotypes, and associated papers. | Gary Schindelman, Chris Grove | Done |
87 | SAGE_experiment | Sanger | Could we not combine this with the ?Analysis class? | Wen Chen | Done |
88 | SAGE_tag | Sanger | ? | Wen Chen | Done |
89 | Sequence | Sanger | A broad class for storing genomic, Transcripts Sequence etc. | Done | |
90 | SK_map | Caltech | ? | Done | |
91 | SO_term | Caltech | ? | Done | |
92 | Species | Sanger | ? | Done | |
93 | Strain | Sanger | ? | Done | |
94 | Structure_data | OICR | ? | Done | |
95 | #Timepoint | OICR | ? | Done | |
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 | Done |
98 | Transposon | Sanger | Stores the Transposon span and S_child info | Paul Davis | Done |
99 | Transposon_family | Sanger | Used for grouping like ?Transposons | Paul Davis | Done |
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 | Caltech | This hash should be used in place of all address fields in other models. | 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 | Done |
106 | #Feature_info | Done | |||
107 | #SAGE_mapping_info | Done | |||
108 | #SAGE_data | Done | |||
109 | #SMap_info | 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) Models discrepancy - Unused class ?Lab_Location lots of models refer to #Lab_Location which is not correct.