Difference between revisions of "Genotype"
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== Model issues == | == Model issues == | ||
− | * Model proposal on [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing this Google Doc] | + | * Model proposal, including proposed changes to other classes, on [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing this Google Doc] |
+ | * Database build will need to populate the "Gene" tag with genes inferred from the variation-to-gene mapping pipeline, if they are not already manually populated by the curator/Postgres | ||
+ | ** Genes inferred automatically by the build process should get an #Evidence hash entry of "Inferred_automatically" | ||
+ | * The "Gene" tag will get automatically populated by the OA dumper for ?Rearrangement and ?Transgene objects | ||
+ | ** Genes referenced in ?Rearrangement objects' "Gene_inside" tag will populate the "Gene" tag in the ?Genotype object | ||
+ | ** Genes referenced in a ?Transgene object's corresponding ?Construct object's (from "Construct" and "Coinjection" tags) "Driven_by_gene", "Gene" and "3_UTR" tags will populate the "Gene" tag in the ?Genotype object | ||
+ | * Disease assertions (and relevant paper connections) will be dumped by the Disease Model Annotation OA | ||
+ | |||
== Genotype Postgres Tables == | == Genotype Postgres Tables == |
Revision as of 15:03, 25 February 2020
Contents
Rationale
To enable curators (disease curators and then maybe phenotype curators) to annotate directly to entire genotypes, the ?Genotype class has been proposed. The decision was made that any ?Genotype object should reflect the entire genotype of a particular worm or strain of worms, to the extent that it is known, rather than partial genotypes. The initial data model allows for direct associations to disease model annotations (curated in the disease OA), whereby genotype associations to diseases (DO terms) would then be made during the Postgres curation database dump.
Issues
Action items
?Genotype model
Initial proposal:
?Genotype Genotype_name UNIQUE ?Text // e.g. “unc-1(e103);unc-2(e234)”; eventually to be automatically generated Genotype_synonym ?Text // To capture literal representations in the literature Genotype_component Gene ?Gene XREF Component_of_genotype #Evidence Variation ?Variation XREF Component_of_genotype Rearrangement ?Rearrangement XREF Component_of_genotype Transgene ?Transgene XREF Component_of_genotype Other_component UNIQUE ?Text // Free text components including RNAi Disease_info Models_disease ?DO_term XREF Disease_model_genotype Modifies_disease ?DO_term XREF Disease_modifier_genotype Models_disease_in_annotation ?Disease_model_annotation XREF Genotype Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_genotype Species UNIQUE ?Species Remark ?Text Reference ?Paper XREF Genotype
Model issues
- Model proposal, including proposed changes to other classes, on this Google Doc
- Database build will need to populate the "Gene" tag with genes inferred from the variation-to-gene mapping pipeline, if they are not already manually populated by the curator/Postgres
- Genes inferred automatically by the build process should get an #Evidence hash entry of "Inferred_automatically"
- The "Gene" tag will get automatically populated by the OA dumper for ?Rearrangement and ?Transgene objects
- Genes referenced in ?Rearrangement objects' "Gene_inside" tag will populate the "Gene" tag in the ?Genotype object
- Genes referenced in a ?Transgene object's corresponding ?Construct object's (from "Construct" and "Coinjection" tags) "Driven_by_gene", "Gene" and "3_UTR" tags will populate the "Gene" tag in the ?Genotype object
- Disease assertions (and relevant paper connections) will be dumped by the Disease Model Annotation OA
Genotype Postgres Tables
- gno_identifier
- gno_curator
- gno_name
- gno_synonym
- gno_gene
- gno_variation
- gno_rearrangement
- gno_transgene
- gno_othercomp
- gno_species
- gno_remark
- gno_paper
- gno_nodump
Genotype OA
- pgid - the postgres ID - NOT DUMPED
- ID - gno_identifier - Genotype primary ID #Note: This is automatically assigned
- Curator - gno_curator - NOT DUMPED - Curator (Dropdown)
- Name - gno_name - Name - Big text
- Synonym - gno_synonym - Genotype_synonym - Big Text (multiple entries bar "|" separated)
- Gene - gno_gene - Gene - ?Gene (Multi-ontology)
- Variation - gno_variation - Variation - ?Variation (Multi-ontology)
- Rearrangement - gno_rearrangement - Rearrangement - ?Rearrangement (Multi-ontology)
- Transgene - gno_transgene - Transgene - ?Transgene (Multi-ontology)
- Other Component - gno_othercomp - Other_component - Big text
- Species - gno_species - Species - ?Species (Dropdown)
- Remark - gno_remark - Remark - Big text
- Paper - gno_paper - Reference - ?Paper (Multi-ontology)
- NO DUMP - gno_nodump - NOT DUMPED - toggle