The A - Z of WormBase Models

Models List

Status:

Done = Document added to wiki
Review complete = Models has been updated to remove unused tags etc.

No.	Class	Institute	Comment/Brief Description	Curator(s)	Status
1	2_point_data	Hinxton			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	Hinxton	?		Done
4	Analysis	Hinxton	This class is used along with ?Condition to store meta data about an experiment	Michael Paulini	Done
5	Anatomy_function	Caltech	?	Raymond	Done
6	Anatomy_name	Caltech	?	Raymond	Done
7	Anatomy_term	Caltech	?	Raymond	Done
8	Antibody	Caltech	Worm antibodies created by research laboratories.	Xiaodong Wang	Done
9	AO_code	Caltech	?	Raymond	Done
10	Atlas	OICR	WORMBASE ATLAS (VIRTUAL WORM) - unused data class		Done
11	Author	Caltech	?		Done
12	Balancer	?	Unused class?		Done
13	CDS	Hinxton	?	Paul Davis + others	Done
14	Cell	Hinxton/Caltech?	?	Raymond	Done
15	Cell_group	Hinxton/Caltech?	?	Raymond	Done
16	Clone	Hinxton	?		Done
17	Condition	Caltech	This model describes experimental sample conditions, such as life stage, genotype and preparation, mostly used for Microarray.	Wen Chen + Others	Done
18	Contig	Hinxton	?		Done
19	Database	Hinxton	?		Done
20	Database_field	Hinxton	?		Done
21	Expression_cluster	Caltech	Clustering results of genes with similar expression profile in large scale analysis such as microarray and chronogram.	Wen Chen	Done
22	Expr_pattern	Caltech	Conventional expression pattern analysis including reporter gene analysis, antibody staining, in situ, RT-PCR, Northern, Western ...	Wen Chen	Done
23	Expr_profile	Caltech	?		Done
24	Feature	Hinxton	?	Paul Davis Mary Ann	Done
25	Feature_data	Hinxton	?Class of data used to mark up features on Transcript data		Done
26	Gene	Hinxton	Envelope for collecting/connecting data pertaining to a single gene (Don't worry MA didn't write this)	Mary Ann	Done
27	Gene_class	Hinxton	Used for describing and grouping a family of genes	Mary Ann	Done
28	Gene_cluster	Hinxton	Used to denote a cluster of genes of a specific type - not maintained?		Done
29	Gene_name	Hinxton	?		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	Hinxton	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	Hinxton	Old data? do we still nedd it?		Done
35	Grid_data	Hinxton	Target for removal - Unused class, no data in WS218		Done
36	Grid_row	Hinxton	Target for removal - Unused class, no data in WS218		Done
37	Homol_data	Hinxton	Used for storing alignment data		Done
38	Homology_group	Caltech	That is used to store information about KOGS/eggNOGS/etc.		Done
39	Interaction	Caltech	?	Chris & Kimberly	Done
40	Interval_col_conf	?	Poss target for removal as it's not used.		Done
41	Jade	Acedb?	?		Done
42	#Lab_Location		No one uses this hash, poss remove?		Done
43	Laboratory	Caltech	?		Done
44	Library	Hinxton	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	Developmental life stages for C. elegans.	Wen Chen	Done
46	Locus	Hinxton	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	Hinxton	Internal class?	N/A	Done
51	Map_position	AceDB	Internal class?	N/A	Done
52	Mass_spec_experiment	Hinxton	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	Hinxton	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	This model describes microarray platforms, each object is a type of microarray chip.	Wen Chen	Done
56	Microarray_experiment	Caltech	This model describes microarray experiments, each object is an independent experiment.	Wen Chen	Done
57	Microarray_results	Caltech	This model describes spots of each microarray chip, each object is a spot on a type of microarray platform.	Wen Chen	Done
58	Mixed_grid_row	Hinxton	?		Done
59	Molecule	Caltech	Used to capture molecules that influence gene activity and phenotypes.	Karen Yook	Done
60	Motif	Hinxton	?		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	Hinxton	?		Done
65	Neurodata	?	?Not Used	Raymond	Done
66	Neuro_location	?	? Not Used	Raymond	Done
67	Oligo	?	?		Done
68	Oligo_set	?	?		Done
69	Operon	Hinxton	Stores genes that are in Operons	Paul Davis	Done
70	Paper	Caltech	Stores information about published papers, gazette articles, and meeting abstracts	Kimberly Van Auken	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	This model has been reworked removing unused tags	Daniela Raciti	Review complete
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	Hinxton	?		Done
80	Protein	Hinxton	?		Done
81	Pseudogene	Hinxton	Stores the Pseudogene models		Done
82	Rearrangement	Hinxton, Caltech (phenotypes)	Caltech curates phenotypes of rearrangements. Sequence and object curation occurs at Hinxton. Changes to the model needed to be approved by Hinxton 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	Hinxton	Could we not combine this with the ?Analysis class?	Wen Chen	Done
88	SAGE_tag	Hinxton	?	Wen Chen	Done
89	Sequence	Hinxton	A broad class for storing genomic, Transcripts Sequence etc.		Done
90	SK_map	Caltech	?		Done
91	SO_term	Caltech	?		Done
92	Species	Hinxton	?		Done
93	Strain	Hinxton	?		Done
94	Structure_data	OICR	?		Done
95	#Timepoint	OICR	?		Done
96	Transcript	Hinxton	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	Hinxton	Stores the Transposon span and S_child info	Paul Davis	Done
99	Transposon_family	Hinxton	Used for grouping like ?Transposons	Paul Davis	Done
100	Variation	Hinxton, Caltech (phenotype)	?	Mary Ann, Karen Yook (phenotype aspect)	Done
101	Variation_name	Hinxton	?	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	Hinxton	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
110	#Homol_info	Hinxton	Stores Homology Data (BLAST/BLAT)	Michael Paulini	Done

Models added post WS218

Class	Institute	Comment/Brief Description	Curator(s)
WBProcess	Caltech	For WormBase Biological Topics pages added for WS225	Karen
Gene and Disease Ontology	Caltech	C. elegans as a model system to study disease and disease genes added WS236	Ranjana
Construct	Caltech	Standardizing the curation of DNA plasmids used for generating variations and transgenes, and used for gene expression or gene regulation analysis	Karen, Daniela, Chris, Mary Ann, Xiaodong

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) Could we add species to all datasets.

Model Change Summaries

This section is used by the model curator to document the changes in a given release and should not be edited by anyone other than the Model Curator (Paul Davis)

It was decided to move this out of the normal CVS comments section coming from sanger, the CVS will now contain a link to the appropriate wiki page.