WormBase Models

From WormBaseWiki
Jump to: navigation, search

The A - Z of WormBase Models

Document created from WS218 models.

Sanger CVS models.wrm

The intention of this page is to allow all curators to see the models that they curated data for, it is not intended for this to be a development area, more for visualisation and clarity of the acedb models.

"#" indicates a Hash that can be used in multiple places in the models file.

This is not a complete list of models as new ones have been created since the document was 1st produced and also some are classes that are necessary for acedb to function correctly.

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

No. Class Institute Comment/Brief Description Curator(s) Status
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.

WS223_Models.wrm

WS224_Models.wrm

WS225_Models.wrm

WS226_Models.wrm

WS227_Models.wrm

WS228_Models.wrm

WS229_Models.wrm

WS230_Models.wrm

WS231_Models.wrm

WS232_Models.wrm

WS233_Models.wrm

WS234_Models.wrm

WS235_Models.wrm

WS236_Models.wrm

WS237_Models.wrm

WS238_Models.wrm

WS239_Models.wrm

WS240_Models.wrm

WS241_Models.wrm

WS242_Models.wrm

WS243_Models.wrm

WS244_Models.wrm

WS245_Models.wrm