BioPax vs. OBO and ontologies

Question

[danaru]

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!

Answer 1

[AfinaM]

I think you will need to understand the fundamental of ontology first and how it works. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735951/ is one of the publication that helped me to understand how ontology works in biology.

Then, you can choose which set of vocabulary that you would like to use for your project. If I'm not mistaken both BioPAX and OBO has their own set of controlled vocabulary but there is also an on-going version of BioPAX in OBO. In OBO there are many other ontologies as well. You can check which is most suitable for your project.

Surely we are unable to predict what will we have in the future but that is what ontology is for. It allows us to expand or combine even with different set of vocabulary without disrupting its whole structure. Just make sure that you have covered the most basic fundamental of your project (but we can still add this when needed due to the nature of ontology itself, so I think it is good).

I can recommend a book titled Introduction to Bio-Ontologies by Peter N. Robinson & Sebastian Bauer, it does provide introduction to ontologies used in biology although might be a bit outdated.

It's been a while since I used ontology but hope this helps and good luck. :)

Answer 2

[cannin]

The main purpose of BioPAX is to provide a way to structure information about molecular interactions. If your work is highly focused on molecular interactions (e.g., protein A interacts with protein B) BioPAX may be a good fit for you. BioPAX is a controlled vocabulary for some things, but it makes use other vocabularies (see Best Practices in http://www.biopax.org/release/biopax-level3-documentation.pdf) to see how elements are defined using resources external to BioPAX. You mention describing experiments; maybe you mean something like this: https://www.protocols.io/view/mcscrb-seq-protocol-p9kdr4w (this level of detail is probably difficult with BioPAX or OBO). Some structuring is better than no structuring.

Some helpful BioPAX links:

• See the documentation http://www.biopax.org/release/biopax-level3-documentation.pdf to see what BioPAX can how contain.
• To generate BioPAX for many interactions you will likely need to write code to iterate over some input. Here is example code

Answer 3

[gary.bader]

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.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.