Displaying posts tagged with

“Gene Ontology”

The allure of the superficial

A new paper from my lab and Patsy Babbitt’s lab in UCSF has recently been published  in  PLoS Computational Biology. It is something of a cautionary tale for quantitative biologists, especially  bioinformaticians and system biologists. Genomics has ushered biology into the  data rich sciences. Bioinformatics, developing alongside genomics, provided the tools necessary to decipher genomic […]

CACAO: Community Assessment of Community Annotation with Ontologies

I’m at College Station airport, Texas, waiting for my delayed flight and hope that the weather in Dallas lets up within the hour. A good time to take a break and blog. College Station is the home of Texas A&M University, which is a place I am always happy to visit. The scientists here are […]

Going to GOA, pt. 2: children of a lesser GO

The source file associated with this post can be downloaded here. The last time I talked about how to read a GOA gene_associations file into a Python dictionary data structure.  Our goal was to find all genes that are annotated as hydrolases in the GOA gene_associations file. The tricky part is, most enzymes are not […]

Going to GOA: pt. 1

GOA, the Gene Ontology Annotation, provide Gene Ontology annotation to proteins in UniProt. It also provides GO annotations to several genome projects: Chicken, Arabidopsis, Fly, Human, Mouse, Rat and Cow. Anyone working on any of those genomes, or on UniProt and is interested in annotation, would most likely need to query GOA once in a […]