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.

Mungall et al. Genome Biology 2010 11:R2   doi:10.1186/gb-2010-11-1-r2

Open Data