WormBase Models

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	?	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	?
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	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
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

5) Models discrepancy - Unused class ?Lab_Location lots of models refer to #Lab_Location which is not correct.