Difference between revisions of "WormBase Models"
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| For WormBase Biological Topics pages added for WS225 | | For WormBase Biological Topics pages added for WS225 | ||
| Karen | | Karen | ||
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| + | |[[WormBase Model:Gene and Disease Ontology|Gene and Disease Ontology]] | ||
| + | | Caltech | ||
| + | | C. elegans as a model system to study disease and disease genes added WS236 | ||
| + | | Ranjana | ||
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== Action Targets == | == Action Targets == | ||
Revision as of 19:51, 4 October 2013
The A - Z of WormBase Models
Contents
Document created from WS218 models.
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 |
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.
