Currently we are not aware of who is using PATO and for what. This is a preliminary list
Phenotype Annotation FTP Site
Temporary ftp site:
owl and obo downloads available soon
Model Organism Phenotype Annotation
ParameciumDB are using PATO for phenotype annotation
ZFIN and FlyBase are committed to in-depth phenotype annotations as part of an NCBO Project. As well as residing in each respective MOD's database, the data will also be collected in a central database called OBD-Phenotype. This database is being designed around technology such as OWL in order to make maximum use of the ontologies. We would also like to populate this database with other OBO-annotated data, phenotype and otherwise
MedakaDB are using a subset of PATO for phenotype annotation
NESCent, CToL, ZFIN collaboration
The National Evolutionary Synthesis Center (NESCent), ZFIN, and the CToL project have proposed using PATO for describing phenotypic variation (in particular, morphology) across related species (specifically, among Ostariophysi), and to relate those phenotypic variations to mutant phenotypes observed in Zebrafish, as recorded in the ZFIN database (using PATO, too).
The project is called "Linking Genomics to Evolution using Phenotype Ontologies" (or Phenomap in short).
MGI are using PATO to coordinate phenotype descriptions that are associated with diseases (currently OMIM IDs, but soon to be DO IDs)
If I have omitted or given short-shrift to anyone please write to the list and describe your project and/or add it to this page