Difference between revisions of "Genotype"
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Reference ?Paper XREF Genotype | Reference ?Paper XREF Genotype | ||
</pre> | </pre> | ||
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+ | == Model issues == | ||
+ | |||
+ | <pre> | ||
+ | Disease_model_annotation Model_genotype ?Disease_model_annotation XREF Genotype | ||
+ | Modifier_genotype ?Disease_model_annotation XREF Modifier_genotype | ||
+ | </pre> | ||
+ | |||
+ | I don't believe the above fits with the acedb->datomic conversion can we lose the top level Disease_model_annotation tag? | ||
== Genotype Postgres Tables == | == Genotype Postgres Tables == |
Revision as of 17:46, 21 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 Disease_model_annotation Model_genotype ?Disease_model_annotation XREF Genotype Modifier_genotype ?Disease_model_annotation XREF Modifier_genotype Species UNIQUE ?Species Remark ?Text Reference ?Paper XREF Genotype
Model issues
Disease_model_annotation Model_genotype ?Disease_model_annotation XREF Genotype Modifier_genotype ?Disease_model_annotation XREF Modifier_genotype
I don't believe the above fits with the acedb->datomic conversion can we lose the top level Disease_model_annotation tag?
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