Difference between revisions of "WormBase Models"
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| AceDB class that details display etc. of objects in the other classes | | AceDB class that details display etc. of objects in the other classes | ||
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| Wen Chen | | Wen Chen | ||
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| Wen Chen | | Wen Chen | ||
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| ? | | ? | ||
| Wen Chen | | Wen Chen | ||
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| Used to capture molecules that influence gene activity and phenotypes. | | Used to capture molecules that influence gene activity and phenotypes. | ||
| [[User=kyook|Karen Yook]] | | [[User=kyook|Karen Yook]] | ||
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| 61 | | 61 | ||
| [[WormBase Model:Movie|Movie]] | | [[WormBase Model:Movie|Movie]] | ||
| Caltech | | Caltech | ||
| − | | | + | | This class needs fleshing out with descriptive data as the majority of the tags are enpty. |
| − | |||
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| + | | Done | ||
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| 62 | | 62 | ||
Revision as of 15:40, 4 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 | 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
5) Models discrepancy - Unused class ?Lab_Location lots of models refer to #Lab_Location which is not correct.
