Using BioPAX as a standard for disease modules
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Quirin Manz
May 11, 2023, 10:37:28 PM5/11/23
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Dear BioPAX community,
Does anyone have experience using BioPAX as a data standard for exchanging network-based disease or active modules?
As far as I have read into and played with BioPAX, many classes already present the main components of a disease module, such as protein-protein interactions, the corresponding gene, and drugs.
Conversely, BioPAX level 3 does not support essential entities like genomic variants, phenotypes, side effects, or disorders and their associations properly.
Although there were efforts to extend BioPAX, namely BioPAX+ (https://doi.org/10.1007/978-3-030-04284-4_28), there seems to be no progress in this direction in recent years.
I am happy for any input on this topic and maybe a recommendation on whether you think it makes sense to build a standard for disease modules as an extension of BioPAX or from scratch.
Best regards,
Quirin Manz
Does anyone have experience using BioPAX as a data standard for exchanging network-based disease or active modules?
As far as I have read into and played with BioPAX, many classes already present the main components of a disease module, such as protein-protein interactions, the corresponding gene, and drugs.
Conversely, BioPAX level 3 does not support essential entities like genomic variants, phenotypes, side effects, or disorders and their associations properly.
Although there were efforts to extend BioPAX, namely BioPAX+ (https://doi.org/10.1007/978-3-030-04284-4_28), there seems to be no progress in this direction in recent years.
I am happy for any input on this topic and maybe a recommendation on whether you think it makes sense to build a standard for disease modules as an extension of BioPAX or from scratch.
Best regards,
Quirin Manz
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