Skip to main content

Table 1 Genotype-phenotype curation in different projects uses different ontologies and methodologies

From: Integrating phenotype ontologies across multiple species

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)
  1. 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.