Integrating phenotype ontologies across multiple species

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.

ISSN: 1474-760X