BioPAX versus OBO

[Dana Rubin]

Hello, 

I started to explore ontologies for creating a database for describing lab experiments in a machine-readable format.

I find it hard to rely only on BioPAX as I am not completely sure yet what experiments will come up in the future and if BioPAX can currently support all of the features I need.

I saw that OBO has many ontologies too, and I am a little confused regarding what's the difference and if I can use both BioPAX and OBO. 

I am new to the world of biological ontologies(and ontologies in general), so any relevant article/ advice/ book is welcome!

Thanks!

[Augustin Luna]

I think you also posted on Biostars, see the response there:
https://www.biostars.org/p/9468646/#9469473

Augustin Luna

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[Gary Bader]

Hi Dana - great question. What are you trying to accomplish with your use of ontologies? BioPAX was designed for data exchange of biological pathways represented using a few paradigms: biochemical (e.g. including chemical reactions), gene regulatory networks, molecular interaction networks, genetic interaction networks, and to cover the information that is currently included in pathway databases like Reactome, BioCyc, PANTHER and many others. As was mentioned, it makes use of other ontologies like Gene Ontology, which is available in OBO format. BioPAX is available in OWL format, which is an international standard for ontologies.

Gary

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