All the following files can be downloaded freely for academic users.

Customized Ontologies in Open Biological and Biomedical Ontologies (OBO) format:
Description Download File size
Plant Phenotype and Trait Ontology PPTO.zip 20KB
Animal Phenotype and Trait Ontology APTO.zip 4KB
Mannually curated associations for each species:
Description Download File size
Cotton Association Cotton_Association.xlsx 2.08MB
Cotton_Association.txt 240.88KB
Japanese apricot Association Japanese_Apricot_Association.xlsx 177.06KB
Japanese_Apricot_Association.txt 20.52KB
Maize Association Maize_Association.xlsx 3.96MB
Maize_Association.txt 818.35KB
Rape seed Association Rape_Seeds_Association.xlsx 347.63KB
Rape_Seeds_Association.txt 65.84KB
Rice Association Rice_Association.xlsx 2.77MB
Rice_Association.txt 432KB
Sorghum Association Sorghum_Association.xlsx 114.00KB
Sorghum_Association.txt 21.12KB
Soybean Association Soybean_Association.xlsx 79.06KB
Soybean_Association.txt 14.23KB
Goat Association Goat_Association.xlsx 16.96KB
Goat_Association.txt 2.54KB
Pig Association Pig_Association.xlsx 57.90KB
Pig_Association.txt 10.48KB