I am looking to generate some pathway data and had planned on using the BioPAX format. I have now come across the BEL format and am wondering what the differences are between the BioPAX and BEL formats. When would you use one format over another? Is one becoming "obsolete" over the other? Are there even competing uses for these formats?
If your goal is to interoperate with other data providers and consumers (including software), BioPAX is likely a better choice. It is the only biological pathway standard supported widely by pathway databases (not considering SBML, which is about mathematical modelling) and tools like Cytoscape. BEL may be useful to capture data more quickly for certain modelling or analysis purposes (e.g. examining causal relationships). BEL may also be easier to compute on more naturally as a network, whereas BioPAX has a more complex ontology structure. BioPAX is more strict because it tries to encourage the use of standard knowledge representation paradigms (e.g. biochemical reactions, gene regulatory networks, molecular interactions). This is important if you will integrate your data with others who will have used the same paradigms. BEL allows more freedom to define relationships and entities, which is more flexible, but may come at the expense of being more difficult to reconcile between independent creators of BEL documents. There is a lot of data in BioPAX format (e.g. Pathway Commons v8 has 1.3 million interactions) from many pathway data providers that support BioPAX. I'm not aware that BEL is supported specifically by any publicly available curated pathway database (I could be wrong), but it is in use in companies and specific communities, like https://sbvimprover.com/, BioCreative and NDEX - http://www.ndexbio.org/. I don't think either language is obsolete - they are both actively used, though BioPAX is more established, at least as measured by the number of open source/open access software tools and databases that support it. BioPAX came out of academia and was developed in an inclusive, community oriented manner involving dozens of pathway data providers and users (see the authors of the BioPAX paper from 2010 - http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html - and http://co.mbine.org/ for more information about the process) and BEL was developed in a company (Selventa) who subsequently open sourced it. The BEL group wrote a comparison of BioPAX and BEL in 2011 at http://wiki.openbel.org/download/attachments/819563/A%20Comparison%20of%20BEL%20V1.0%20and%20BioPAX%20Level3.pdf?api=v2 This document makes some useful points, but is not totally accurate - i.e. some of the limitations mentioned for BioPAX are not actually limitations - for instance their "tissue damage" example is encodable in BioPAX with a black box pathway design pattern even though they claim it isn't. I'm a BioPAX developer, so am more familiar with BioPAX. BEL users or developers can chime in for their perspective.
As one of the OpenBEL community members, I agree with what Gary has said. BioPax is much more structured and descriptive in regards to capturing pathways. BEL is designed for more of an overall view of biology representing multi-scale qualitative biology from molecular interactions to associating organism phenotypes to molecular events. There are currently more academic resources in BioPAX than BEL, but we are working to address that. Ingenuity and Thomson Metacore are available in BEL, and several bioPharmas are using BEL.
To me, BEL is the Biological version of the Chemical Reaction Language. Something easy enough to write on the whiteboard, but computationally tractable for reasoning both with and without data. Given data to process with it (e.g. RNA or Protein expression data or Metabolomics data), you can create quantitative results by combining data with the qualitative BEL knowledge representation.
BEL was created in private and used that way for years, but we felt it was useful beyond Selventa and is a living standard. We are in the last few weeks of deploying BEL 2.0 and have proposals to work on for BEL 2+ around genomic feature association to molecular events and population level effects. We are trying to balance complexity, computational tractability, and expressivity. At some point, we need to create a way to interoperate between BioPAX, SMBL and BEL as they all have specific strengths and weaknesses as they are tools for different purposes.
Thanks for the informative response!
The strict format of BioPAX will seem to benefit the application I am working on. Although, I am still curious in BEL. Would like to hear thoughts from BEL developers as well...?
