Genotype
From WormBaseWiki
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)” 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
Genotype Postgres Tables
- gno_identifier
- gno_curator
- gno_name
- 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 - gen_identifier - Genotype primary ID #Note: This is automatically assigned
- Curator - gen_curator - NOT DUMPED - Curator (Dropdown)
- Name - gen_name - Name - Big text
- Gene - gen_gene - Gene - ?Gene (Multi-ontology)
- Variation (Unknown Zygosity) - gen_variation - Variation - ?Variation (Multi-ontology)
- Homozygous Variation - gen_homo_variation - Variation - ?Variation Homozygous (Multi-ontology)
- Heterozygous (w/WT) Variation - gen_hetwt_variation - Variation - ?Variation Heterozygous_with_wildtype (Multi-ontology)
- Heteroallelic Variation - gen_hetal_variation - Variation - ?Variation Heteroallelic_combination (Multi-ontology)
- Rearrangement (Unknown Zygosity) - gen_rearrangement - Rearrangement - ?Rearrangement (Multi-ontology)
- Homozygous Rearrangement - gen_homo_rearrangement - Rearrangement - ?Rearrangement Homozygous (Multi-ontology)
- Heterozygous (w/WT) Rearrangement - gen_hetwt_rearrangement - Rearrangement - ?Rearrangement Heterozygous_with_wildtype (Multi-ontology)
- Heteroallelic Rearrangement - gen_hetal_rearrangement - Rearrangement - ?Rearrangement Heteroallelic_combination (Multi-ontology)
- Transgene (Unknown Zygosity) - gen_transgene - Transgene - ?Transgene (Multi-ontology)
- Homozygous Transgene - gen_homo_transgene - Transgene - ?Transgene Homozygous (Multi-ontology)
- Heterozygous (w/WT) Transgene - gen_hetwt_transgene - Transgene - ?Transgene Heterozygous_with_wildtype (Multi-ontology)
- Heteroallelic Transgene - gen_hetal_transgene - Transgene - ?Transgene Heteroallelic_combination (Multi-ontology)
- Other Component - gen_othercomp - Other_component - Big text
- Species - gen_species - Species - ?Species (Dropdown)
- Remark - gen_remark - Remark - Big text
- Paper - gen_paper - Reference - ?Paper (Ontology)
- NO DUMP - gen_nodump - NOT DUMPED - toggle