Table 1.
Genotype-phenotype curation in different projects uses different ontologies and methodologies
| Project | Organism | Methodology | Ontologies used | Entities annotated |
|---|---|---|---|---|
| MGI | Mouse | Pre-composed | MP | Genotypes |
| NIF | Mouse (neuro) | Post-composed | PATO, NIFSTD, | Organisms |
| WormBase | Caenorhabditis elegans | Both pre-composed and post-composed | WP | Genes |
| SGD | Saccharomyces cerevisiae | Pre-composed | APO | Genotypes |
| Gramene | Viridiplantae | Pre-composed | TO | Genotypes |
| FlyBase | Drosophila melanogaster | Post-composed | PATO, FBbt, GO | Genotypes, alleles |
| ZFIN | Danio rerio (Zebrafish) | Post-composed | PATO, ZFA | Genotypes |
| DictyBase | Dictyostelium discoideum | Post-composed | PATO, DDANAT | Genotypes |
| PATO OMIM-annotation project | Homo sapiens | Post-composed | PATO, FMA, CHEBI, CL, GO | Genotypes (corresponding to OMIM sub-records, for example OMIM:601653.0001) |
We exclude annotation efforts that use free text in place of a publicly available ontology or terminology (such as the various genome-wide association study projects), or those not specifically focused on genotypic curation. NIF: Neuroscience Information Framework; DDANAT: Dictyostelium Discoideum Anatomy Ontology; FBbt: FlyBase anatomy ontology; MGI, Mouse Genome Informatics group at Jackson Laboratory; NIFSTD: Neuroscience Information Framework Standardized Ontology; SGD, Saccharomyces Genome Database; ZFA, Zebrafish Anatomy ontology; ZFIN, Zebrafish Information Network.