ArticlePLoS computational biology2013
Using biological pathway data with paxtools.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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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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Who cites it
38 citing papers in PubMed, 67 citations in OpenAlex.
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- Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.Journal of integrative bioinformatics · 2024Article
- Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using semantic web technologies.Bioinformatics (Oxford, England) · 2023Article
- Cytoscape.js 2023 update: a graph theory library for visualization and analysis.Bioinformatics (Oxford, England) · 2023Article
- BET inhibition induces vulnerability to MCL1 targeting through upregulation of fatty acid synthesis pathway in breast cancer.Cell reports · 2022Article
- Heuristic shortest hyperpaths in cell signaling hypergraphs.Algorithms for molecular biology : AMB · 2022Article
- PyBioPAX: biological pathway exchange in Python.Journal of open source software · 2022Article
- Article
- Reactome and the Gene Ontology: digital convergence of data resources.Bioinformatics (Oxford, England) · 2021Article
- Platelet Proteomes, Pathways, and Phenotypes as Informants of Vascular Wellness and Disease.Arteriosclerosis, thrombosis, and vascular biology · 2021Review
- Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.Nucleic acids research · 2020Article
- Hypergraph-based connectivity measures for signaling pathway topologies.PLoS computational biology · 2019Article
- CODA-ML: context-specific biological knowledge representation for systemic physiology analysis.BMC bioinformatics · 2019Article
- PathMe: merging and exploring mechanistic pathway knowledge.BMC bioinformatics · 2019Article
- The Role of Systems Biologic Approach in Cell Signaling and Drug Development Responses-A Mini Review.Medical sciences (Basel, Switzerland) · 2018Review
- Platelet procoagulant phenotype is modulated by a p38-MK2 axis that regulates RTN4/Nogo proximal to the endoplasmic reticulum: utility of pathway analysis.American journal of physiology. Cell physiology · 2018Article
- New perspectives: systems medicine in cardiovascular disease.BMC systems biology · 2018Article
- From word models to executable models of signaling networks using automated assembly.Molecular systems biology · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
Abstract
A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools.
Indexed as
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What OpenQuestion holds
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.