ReviewComputational and structural biotechnology journal2024
BioPAX in 2024: Where we are and where we are heading.
Review in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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0 citing papers in PubMed.
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Authors and funding
4 authors.
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Abstract
In systems biology, the study of biological pathways plays a central role in understanding the complexity of biological systems. The massification of pathway data made available by numerous online databases in recent years has given rise to an important need for standardization of this data. The BioPAX format (Biological Pathway Exchange) emerged in 2010 as a solution for standardizing and exchanging pathway data across databases. BioPAX is a Semantic Web format associated to an ontology. It is highly expressive, allowing to finely describe biological pathways at the molecular and cellular levels, but the associated intrinsic complexity may be an obstacle to its widespread adoption. Here, we report on the use of the BioPAX format in 2024. We compare how the different pathway databases use BioPAX to standardize their data and point out possible avenues for improvement to make full use of its potential. We also report on the various tools and software that have been developed to work with BioPAX data. Finally, we present a new concept of abstraction on BioPAX graphs that would allow to specifically target areas in a BioPAX graph needed for a specific analysis, thus differentiating the format suited for representation and the abstraction suited for contextual analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.