The DOI matches its Crossref record; 85 of the 85 references it cites were found in a registry or an index; none of the 43 sources its claims cite is checked for support yet.
The BioPAX community standard for pathway data sharing
Open accessAbstract
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
BioPAX is a community-developed OWL-based standard language for exchanging biological pathway data, covering metabolic and signaling pathways, molecular and genetic interactions, and gene regulation. It aims to reduce fragmentation across pathway databases and tools by making pathway data computable for visualization, analysis, and integration.
Key findings
- BioPAX provides an ontology, OWL-based syntax, and a validator; it supports metabolic pathways, signaling pathways, gene regulatory networks, molecular interactions, and genetic interactions, with Level 3 currently recommended.
- The paper reports that pathway and molecular interaction online resources grew from 190 in 2006 to 325 in 2010, a 70% increase, and that over 300 pathway or molecular interaction related data resources existed.
- Through BioPAX, “millions of interactions organized into thousands of pathways across many organisms” are available in computable form from a growing number of sources.
- BioPAX levels evolved incrementally: Level 1 supports metabolic pathways; Level 2 adds molecular interactions and post-translational modifications via PSI-MI; Level 3 adds signaling pathways, molecular state, gene regulation, and genetic interactions, but broke backwards compatibility.
Methods
- Not an empirical study; the paper describes a community consensus process, including more than 15 BioPAX workshops since November 2002, mailing lists, a community wiki, and incremental language levels.
- It describes ontology design, scope, validation, and coordination with related standards such as PSI-MI, SBGN, SBML, and CellML; no statistical analysis is reported.
- Evidence comes from referenced pathway databases, software tools, and use cases rather than a formal sample or experimental dataset.
Limitations
- The paper states that BioPAX does not support dynamic and quantitative aspects of biological processes, including temporal aspects of feedback loops and calcium waves; it coordinates with SBML and CellML for these.
- The paper states that experimental evidence is included only for molecular interactions because PSI-MI already defined it; visualization is not standardized by BioPAX but coordinated with SBGN; semantic integration remains difficult due to multiple abstractions, different controlled vocabularies, data incompleteness, or errors; and Level 3 broke backwards compatibility.
- Evident from the text: no empirical evaluation or benchmarking of adoption, interoperability, or user outcomes is reported; the paper is a descriptive community and standard report.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
0 of 43 cited sources checked · 0 supported · 0 flagged
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Using Paxtools and other tools, a range of BioPAX-aware software has been developed, including browsers, visualizers, querying engines, editors and converters (Table 2).”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As a result, researchers waste much time collecting information from different sources and converting its representation from one system to another.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Impediment: fragmentation of pathway databases
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share.”
§ BioPAX – A community standard for pathway data sharing > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“BioPAX can be used to help aggregate large pathway datasets by reducing the required collection and translation effort, for instance using software such as cPath43.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
- Not checked yetcites [43] Cerami, E.G., Bader, G.D., Gross, B.E. & Sander, C. cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 7, 497 (2006). source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, this growth poses a formidable challenge for pathway data collection and curation as well as for database, visualization and analysis software, as these data are often fragmented.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Challenge: strong growth of pathway databases
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Pathway representations frequently use abstractions for metabolic, signaling, gene regulation, protein interaction and genetic interaction and these serve as a starting point toward a shared language25.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Requirement: a shared language for pathways
What the sources say
- Not checked yetcites [25] Cary, M.P., Bader, G.D. & Sander, C. Pathway information for systems biology. FEBS Lett. 579, 1815–1820 (2005). source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“BioPAX follows the standard representation scheme of the Proteomics Standards Initiative Molecular Interaction (PSI-MI) format38.”
§ BioPAX – A community standard for pathway data sharing > What does BioPAX include?
What the sources say
- Not checked yetcites [38] Kerrien, S. et al. Broadening the horizon—level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 5, 44 (2007). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“Pathway data recorded in the literature (estimated from text-mining projects23 to be present in at least 10% of the over 20 million articles currently indexed by PubMed).”
§ BioPAX – A community standard for pathway data sharing > Introduction > Impediment: fragmentation of pathway databases
What the sources say
- Not checked yetcites [23] Hoffmann, R. et al. Text mining for metabolic pathways, signaling cascades, and protein networks. Sci. STKE 2005, pe21 (2005). source
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“The total volume of pathway data mapped by biologists and stored in databases has entered a rapid growth phase17, similar to the rapid expansion of biological sequence data after the introduction of automated sequencing technology.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Challenge: strong growth of pathway databases
What the sources say
- Not checked yetcites [17] Bader, G.D., Cary, M.P. & Sander, C. Pathguide: a pathway resource list. Nucleic Acids Res. 34, D504–D506 (2006). source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Once pathway data is translated into a standard computable language such as BioPAX, it is easier for software to access it and thereby support browsing, retrieval, visualization and analysis by biologists (Figure 5).”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Probably not a substantial claim. 47
- It may state two separate claims as one. 17
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available.”
§ BioPAX – A community standard for pathway data sharing > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks.”
- Also stated in: § Implementation: the BioPAX biological pathway exchange language · plain
“BioPAX supports representation of metabolic and signaling pathways, molecular and genetic interactions and gene regulation.”
§ BioPAX – A community standard for pathway data sharing > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
- Also stated in: § Implementation: the BioPAX biological pathway exchange language · plain
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“BioPAX covers all major concepts familiar to biologists studying pathways, including metabolic and signaling pathways, gene regulatory networks and genetic and molecular interactions (Table 3).”
§ BioPAX – A community standard for pathway data sharing > What does BioPAX include?
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“For example, Reactome8 BioPAX formatted pathways are imported by the NCI/Nature Pathway Information Database (PID)9.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“BioPAX has been used in a number of these studies to collect and integrate large amounts of pathway information from multiple databases for analysis.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“many core classes have remained compatible with previous levels since Level 1”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Level 2 adds support for molecular interactions and post-translational protein modifications by integrating data structures from the PSI-MI format”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Molecular Weight must be a positive number.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Broader input came from mailing lists and a community wiki.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“For instance, PSI-MI to BioPAX and SBML to BioPAX converters are available (Table 2).”
§ BioPAX – A community standard for pathway data sharing > What is not covered?
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“software is provided for updating older BioPAX pathways to Level 3 (via Paxtools).”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“All BioPAX material (Table 1) is made freely available under open source licenses via a central website (http://www.biopax.org) in order to encourage broad adoption.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Level 3 involved a major redesign that necessitated breaking backwards compatibility.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“BioPAX is compatible with them through use of the W3C standard Web Ontology Language, OWL.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“For instance, the ChiBE and VisANT pathway visualization tools read BioPAX format22 and the WikiPathways website53, a community wiki for pathways, is working on using BioPAX to help import pathways from numerous sources, including manually edited pathways from biologists.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
- Not checked yetcites [22] Hu, Z. et al. VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res. 35, W625–W632 (2007). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Level 1 supports metabolic pathways”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“For instance, the ChiBE and VisANT pathway visualization tools read BioPAX format22 and the WikiPathways website53, a community wiki for pathways, is working on using BioPAX to help import pathways from numerous sources, including manually edited pathways from biologists.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
- Not checked yetcites [53] Pico, A.R. et al. WikiPathways: pathway editing for the people. PLoS Biol. 6, e184 (2008). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“a Small Molecule is related to the Chemical Structure class by the property structure.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“BioPAX defines the classes, properties and restrictions required to represent biological pathways and leaves creation of the individuals to users (data providers and consumers).”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“the descriptions of millions of interactions in thousands of pathways across many organisms from multiple databases are now available in BioPAX format.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Data collection
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Level 2 is backwards compatible with Level 1”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“For example, the Cytoscape network visualization software20 can read and display BioPAX formatted data as a network.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
- Not checked yetcites [20] Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003). source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Community members participated in developing functionality they were interested in, which was integrated into specific levels (See Supplementary Table S1).”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“The Pathway Tools software21 and CellDesigner pathway editor54 are developing support for BioPAX-based data exchange.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
- Not checked yetcites [21] Karp, P.D. et al. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform. 11, 40–79 (2010). source
- Not checked yetcites [54] Kitano, H., Funahashi, A., Matsuoka, Y. & Oda, K. Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23, 961–966 (2005). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“More than 15 BioPAX workshops have been held since November 2002, attended by a diverse set of participants.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Level 3 adds support for signaling pathways, molecular state, gene regulation and genetic interactions (Table 3).”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“in BioPAX, the Biochemical Reaction class is a ‘subclass of’ the Conversion class.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Incremental versions (or levels) of the BioPAX language were progressively developed at these workshops to focus the group’s efforts on attainable intermediate goals.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“A common, inclusive and computable pathway data language is necessary to share knowledge about pathway maps and to facilitate integration and use for hypothesis testing in biology24.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Requirement: a shared language for pathways
What the sources say
- Not checked yetcites [24] Racunas, S.A., Shah, N.H., Albert, I. & Fedoroff, N.V. HyBrow: a prototype system for computer-aided hypothesis evaluation. Bioinformatics 20 Suppl 1, i257–i264 (2004). source
Tests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence.
None of the sources cited for this claim have been checked yet.
In the paper
“Over 300 pathway or molecular interaction related data resources17 and many visualization and analysis software tools3,20-22 have been developed.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Impediment: fragmentation of pathway databases
What the sources say
- Not checked yetcites [17] Bader, G.D., Cary, M.P. & Sander, C. Pathguide: a pathway resource list. Nucleic Acids Res. 34, D504–D506 (2006). source
- Not checked yetcites [3] Demir, E. et al. PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 18, 996–1003 (2002). source
- Not checked yetcites [20] Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003). source
- Not checked yetcites [21] Karp, P.D. et al. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform. 11, 40–79 (2010). source
- Not checked yetcites [22] Hu, Z. et al. VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res. 35, W625–W632 (2007). source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For instance, visualization and analysis tools developed for one pathway database cannot be reused for others, making software development efforts more expensive.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Impediment: fragmentation of pathway databases
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Unfortunately, most of these databases and tools were originally developed to use their own pathway representation language, resulting in a heterogeneous set of resources that are extremely difficult to combine and use.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Impediment: fragmentation of pathway databases
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A shared language facilitates communication by reducing the number of translations required to exchange data between multiple sources (Figure 1).”
§ BioPAX – A community standard for pathway data sharing > Introduction > Requirement: a shared language for pathways
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✗ Based: failsProbably not a substantial claim. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“BioPAX reuses a number of standard controlled vocabularies defined by other groups. For example, Gene Ontology40 is used to describe cellular location, PSI-MI vocabularies38 are used to define evidence codes, experimental forms, interaction types, relationship types and sequence modifications, and Sequence Ontology41 is used to define types of sequence regions, such as a promoter region on DNA in”
§ BioPAX – A community standard for pathway data sharing > What does BioPAX include?
What the sources say
- Not checked yetcites [40] Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000). source
- Not checked yetcites [38] Kerrien, S. et al. Broadening the horizon—level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 5, 44 (2007). source
- Not checked yetcites [41] Eilbeck, K. et al. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44 (2005). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level.”
§ BioPAX – A community standard for pathway data sharing > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While independent research efforts are needed to find the best ways to represent pathways, community coordination and agreement on one or a few standard sets of semantics is necessary to be able to efficiently integrate pathway data from multiple sources on a large scale.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Impediment: fragmentation of pathway databases
Tests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence.
None of the sources cited for this claim have been checked yet.
In the paper
“In addition, molecular profiling methods, such as RNA profiling using microarrays or protein quantification using mass spectrometry, provide large amounts of information about the dynamics of cellular pathway components and increase the power of pathway analysis techniques18,19.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Challenge: strong growth of pathway databases
What the sources say
- Not checked yetcites [18] Huang, W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1–13 (2009). source
- Not checked yetcites [19] Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D. & Ideker, T. Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 3, 140 (2007). source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“It is implemented as an ontology, a formal system of describing knowledge (Box 1) that helps structure pathway data so that it is more easily processed by computer software (Figure 2).”
§ BioPAX – A community standard for pathway data sharing > Introduction > Implementation: the BioPAX biological pathway exchange language
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Typical biological queries, such as “What reactions involve my protein of interest?” generate more complete answers when querying these larger pathway datasets.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Finally, it provides a validator that uses a set of rules to verify whether a BioPAX document is complete, consistent and free of common errors.”
§ BioPAX – A community standard for pathway data sharing > Introduction > Implementation: the BioPAX biological pathway exchange language
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“A number of recent papers have used this pathway analysis workflow to highlight genes and pathways that are active in specific model organisms or diseased tissues, such as breast cancer, using gene and protein expression, copy number variants (CNVs) and SNPs19,44-49.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
- Not checked yetcites [19] Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D. & Ideker, T. Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 3, 140 (2007). source
- Not checked yetcites [44] Cline, M.S. et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366–2382 (2007). source
- Not checked yetcites [45] Efroni, S., Carmel, L., Schaefer, C.G. & Buetow, K.H. Superposition of transcriptional behaviors determines gene state. PLoS ONE 3, e2901 (2008). source
- Not checked yetcites [46] Ideker, T., Ozier, O., Schwikowski, B. & Siegel, A.F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 Suppl 1, S233–S240 (2002). source
- Not checked yetcites [47] Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008). source
- Not checked yetcites [48] Wu, G., Feng, X. & Stein, L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11, R53 (2010). source
- Not checked yetcites [49] Pinto, D. et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368–372 (2010). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, community workshops support a positive feedback cycle of knowledge sharing that has led to an accepted BioPAX language and development of better software and databases.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Solutions are discovered in independent research groups and incorporated in new data models and community best practices, which then enable identification of new issues.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✗ Based: failsProbably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“BioPAX is developed via community consensus among data providers, tool developers and pathway data users.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
- Rests on an assumption: Community consensus is an effective way to develop a standard.
In the paper
“Such linked, structured data form the basis of the semantic web, an extension of the WWW that promises improved information management and search capability61.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
What the sources say
- Not checked yetcites [61] Berners-Lee, T. & Hendler, J. Publishing on the semantic web. Nature 410, 1023–1024 (2001). source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the process of achieving community consensus spurs innovation in the field of pathway informatics.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✗ Checkable: fails✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Advantages of implementing BioPAX using OWL are that both the ontology and the individuals and values can be stored in the same XML-based format, which makes data transmission easier.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
- Rests on an assumption: Representing and sharing knowledge using ontologies is simplified by the availability of OWL.
- Rests on an assumption: OWL is a standard ontology language supported by useful software tools for editing, transmitting, querying, reasoning, and visualizing.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Community discussion helps resolve technical knowledge representation issues faced by many data providers and users and facilitates the convergence to common terminology and representation.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“BioPAX does not support this, but coordinates with the SBML and CellML mathematical modeling languages55,56 and a growing software toolset supporting biological process simulation57 which cover these aspects.”
§ BioPAX – A community standard for pathway data sharing > What is not covered?
What the sources say
- Not checked yetcites [55] Lloyd, C.M., Halstead, M.D. & Nielsen, P.F. CellML: its future, present and past. Prog. Biophys. Mol. Biol. 85, 433–450 (2004). source
- Not checked yetcites [56] Hucka, M. et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The database and tool support (Table 2) of a common language aids the creation, analysis, visualization and interpretation of integrated pathway maps.”
§ BioPAX – A community standard for pathway data sharing > How does the BioPAX community work?
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Because Reactome data were available in BioPAX format, and Cytoscape could already read BioPAX format, this new feature was easy to implement.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Tools to edit OWL, such as Protégé65, have been developed by the Semantic Web community and adopted in the life sciences.”
§ BioPAX – A community standard for pathway data sharing > Future community goals > Language evolution
What the sources say
- Not checked yetcites [65] Wheeler, D.L. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35, D5–D12 (2007). source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“For instance, protein expression data was combined with pathway information to highlight the importance of apoptosis in a mouse model of heart disease50.”
§ BioPAX – A community standard for pathway data sharing > Uses of pathway information in BioPAX language
What the sources say
- Not checked yetcites [50] Isserlin, R. et al. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics 10, 1316–1327 (2010). source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper relies on this without support.
BioPAX is the only community standard for biological pathway exchange to and from databases.
“BioPAX is the only community standard for biological pathway exchange to and from databases, but coordinates with other standards in related areas (Figure 6).”
The paper relies on this without support.
Formal representation is required for computer software to make use of information.
“Formal representation is required for computer software to make use of information.”
The paper relies on this without support.
A formal representation allows consistent communication of knowledge between individuals or computer systems and helps manage complexity in information processing by breaking knowledge into clear concepts.
“A formal representation allows for consistent communication of knowledge between individuals or computer systems and helps manage complexity in information processing as knowledge is broken down into clear concepts that can be considered independently.”
The paper relies on this without support.
Ontologies enable integration of knowledge between independent resources linked on the WWW.
“Ontologies also enable integration of knowledge between independent resources linked on the World Wide Web (WWW).”
The paper relies on this without support.
Representing and sharing knowledge using ontologies is simplified by the availability of OWL.
“Representing and sharing knowledge using ontologies is simplified by availability of the standard web ontology language (OWL) (http://www.w3.org/TR/owl-features/).”
The paper relies on this without support.
OWL is a standard ontology language supported by useful software tools for editing, transmitting, querying, reasoning, and visualizing.
“OWL is a standard ontology language that is supported by useful software tools for editing, transmitting, querying, reasoning and visualizing.”
The paper relies on this without support.
Community consensus is an effective way to develop a standard.
“BioPAX is developed via community consensus among data providers, tool developers and pathway data users.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source doesn’t support the claim as written.
In the citing paper
“Whereas SBML and CellML focus on quantitative modelling and dynamic simulation, BioPAX concentrates primarily on quantitative processes and visualization [15, 30].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [15]
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“For this reason, systems biology model representation has become standardized using XML-based languages SBML [10, 13], CellML [14], and BioPAX [15].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [15]
The cited source says what the claim attributes to it.
In the citing paper
“BioPAX (Biological Pathway Exchange) is an ontology, a formal systems of describing knowledge that structures biological pathway data making it more easily processed by computer software [15]. It describes the biological semantics of metabolic, signaling, molecular, gene-regulatory, and genetic interaction networks [15].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [15]
Citations
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · cited 2×
“For example, the Cytoscape network visualization software 20 can read and display BioPAX-formatted data as a network.”
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108 · cited 1×
“In addition, molecular profiling methods, such as RNA profiling using microarrays, or protein quantification using mass spectrometry, provide large amounts of information about the dynamics of cellular pathway components and increase the power of pathway analysis techniques 18,19 .”
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,695
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
The Cancer Genome Atlas Research Network (2008) · Nature · doi:10.1038/nature07385 · Cited by 7,735
The phosphatidylinositol 3-Kinase–AKT pathway in human cancer
Vivanco, I., & Sawyers, C. L. (2002) · Nature reviews. Cancer · doi:10.1038/nrc839 · Cited by 6,155 · cited 1×
“Here we use the AKT signaling pathway 26,27 as an example to show how a typical pathway diagram that can only be interpreted by people ( Fig.”
ExPASy: the proteomics server for in-depth protein knowledge and analysis
Gasteiger, E. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg563 · Cited by 5,602
The KEGG resource for deciphering the genome
Kanehisa, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,120 · cited 1×
“Since then, several groups have developed methods and databases for organizing pathway information 3–16 , but only recently have groups collaborated as part of the BioPAX project to develop a generally accepted standard way of representing these pathway maps.”
BioGRID: a general repository for interaction datasets
Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960 · cited 1×
“• Molecular interactions, notably protein-protein 32–36 and protein-DNA interactions 37 , involve two or more ‘physical entities’.”
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw377 · Cited by 10,799
“…set libraries from HumanCyc (15), a Nucleic Acids Research, 2016, Vol. 44, Web Server issue W91 metabolic pathway resource stored in BioPAX format (16); gene and small-molecule perturbations from the LINCS L1000 data set; NCI-Nature pathways (17); protein complexes from the NURSA project (18);…”
BackgroundThe Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
Self-citationLarge-scale gene function analysis with the PANTHER classification system
Mi, H., Muruganujan, A., Casagrande, J. T., & Thomas, P. D. (2013) · Nature Protocols · doi:10.1038/nprot.2013.092 · Cited by 2,496
“Second, the PANTHER pathway supports community standards, and all pathways are available in SBML (systems biology markup language 26 , BioPAX (biological pathway exchange format) 27 and SBGN 25 formats.”
MethodSelf-citationPANTHER : Making genome‐scale phylogenetics accessible to all
Thomas, P. D., Ebert, D., Muruganujan, A., Mushayahama, T., Albou, L., & Mi, H. (2022) · Protein Science · doi:10.1002/pro.4218 · Cited by 2,010
“14 We joined in the effort to create the BioPAX standard for sharing annotated pathway information, 15 and have made PANTHER Pathways available in this format since that time.”
MethodSelf-citationEnrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Merico, D., Isserlin, R., Stueker, O., Emili, A., & Bader, G. D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013984 · Cited by 2,235
“Future work will include incorporating molecular interaction network and pathway information [47,48] into gene-set analysis methods, as has successfully been done for gene expression analysis [49,50,51,52,53].”
MethodSelf-citationThe Reactome pathway knowledgebase
Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1102 · Cited by 1,889
“Reactome is open-source and open-data, and we have continuously supported the major open-data standards in the domain, including BioPAX levels 2 and 3 (24), PSI MITAB (18), Protégé (http://protege.”
MethodSelf-citationReactome: a database of reactions, pathways and biological processes
Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1018 · Cited by 1,751
“Reactome is part of the BioPAX Consortium to develop a data-exchange language to describe pathways, reactions and interactions (29).”
BackgroundSelf-citationMi, H., Muruganujan, A., & Thomas, P. D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1118 · Cited by 1,739
“This service is used by the tool that generates BioPAX data.”
MethodInfluentialSelf-citationHornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B. W., Latham, V. M., & Sullivan, M. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1122 · Cited by 1,636
“The Downloadable Data set section provides downloads of six different modi-fication type data sets, an archive of all protein sequences in PSP and the PSP Kinase-Substrate data set in three formats: a tab-delimited text file, a Cytoscape Plugin (36) and a file in BioPAX (37) format.”
MethodSelf-citationA travel guide to Cytoscape plugins
Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., Lotia, S., Pico, A. R., Bader, G. D., & Ideker, T. (2012) · Nature Methods · doi:10.1038/nmeth.2212 · Cited by 1,496
“Cytoscape imports interaction data in various generic tabular formats including CSV (comma-separated values), TSV (tab-separated values) and Excel, along with network-specific formats such as SIF (simple interaction file, originally developed for Cytoscape), XGMML (Extensible Graph Markup and Modeling Language), GML (…”
BackgroundSelf-citationThe IntAct molecular interaction database in 2012
Kerrien, S., Aranda, B., Breuza, L., Bridge, A. J., Broackes-Carter, F., Chen, C. C. L., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U. G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1088 · Cited by 1,151
“In addition to the original PSI-MI XML and PSI-MITAB standard formats, we have added the possibility of exporting to BioPAX (13) levels 2 and 3 formats which is an RDF-based format widely used for the exchange of biological pathway data.”
MethodThe BioCyc collection of microbial genomes and metabolic pathways
Karp, P. D., Billington, R., Caspi, R., Fulcher, C. A., Latendresse, M., Kothari, A., Keseler, I. M., Krummenacker, M., Midford, P. E., Ong, Q., et al. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx085 · Cited by 1,005
Self-citationThe ConsensusPathDB interaction database: 2013 update
Kamburov, A., Stelzl, U., Lehrach, H. R., & Herwig, R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1055 · Cited by 808
“BioPAX Level 3 export Networks viewed with the interaction visualization tool can now be exported in BioPAX Level 3 (4) format.”
MethodInfluentialPathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
Self-citationLiu, Z., Wu, C., Miao, H., & Wu, H. (2015) · Database · doi:10.1093/database/bav095 · Cited by 555
“The users can employ some tools such as Sig2BioPax (43) to convert the regulations into the BioPAX Level 3 format (44).”
MethodWikiPathways: building research communities on biological pathways
Kelder, T., van Iersel, M., Hanspers, K., Kutmon, M., Conklin, B. R., Evelo, C. T., & Pico, A. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1074 · Cited by 521
“WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia.”
BackgroundSelf-citationVEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis
Abhinand, C. S., Raju, R., Soumya, S. J., Arya, P. S., & Sudhakaran, P. R. (2016) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-016-0352-8 · Cited by 526
“These categories are in consensus with the NetPath pathway resource (Kandasamy et al. 2010; Raju et al. 2011) for the conversion of pathway data into community data formats such as PSI-MI, BioPAX and SBML by computational biologists (Hucka et al. 2003; Hermjakob et al. 2004; Demir et al. 2010).”
MethodEcoCyc: a comprehensive database of Escherichia coli biology
Keseler, I. M., Collado‐Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama‐Castro, S., Muñiz-Rascado, L., Bonavides-Martínez, C., Paley, S., Krummenacker, M., Altman, T., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1143 · Cited by 498
Self-citationPathVisio 3: An Extendable Pathway Analysis Toolbox
Kutmon, M., van Iersel, M., Bohler, A., Kelder, T., Nunes, N. M., Pico, A. R., & Evelo, C. T. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004085 · Cited by 465
Self-citationToward interoperable bioscience data
Sansone, S.-A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., et al. (2012) · Nature Genetics · doi:10.1038/ng.1054 · Cited by 475
WikiPathways: capturing the full diversity of pathway knowledge
Kutmon, M., Riutta, A., Nunes, N. M., Hanspers, K., Willighagen, E., Bohler, A., Mélius, J., Waagmeester, A., Sinha, S. R., Miller, R. A., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1024 · Cited by 418
“One of the best ways to access our BioPAX content is via Pathway Commons (14), which validates and compiles pathway models from many resources.”
MethodSelf-citationThe Comparative Toxicogenomics Database's 10th year anniversary: update 2015
Davis, A. P., Grondin, C., Lennon-Hopkins, K., Saraceni-Richards, C. A., Sciaky, D., King, B. L., Wiegers, T. C., & Mattingly, C. J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku935 · Cited by 388
“The appeal and utility of structured notations are evident nowadays with the emergence of other bio-languages, such as BioPax (15) and BEL (http: //www.”
BackgroundSystems Toxicology: From Basic Research to Risk Assessment
Sturla, S. J., Boobis, A. R., FitzGerald, R., Hoeng, J., Kavlock, R. J., Schirmer, K., Whelan, M., Wilks, M. F., & Peitsch, M. C. (2014) · Chemical Research in Toxicology · doi:10.1021/tx400410s · Cited by 371
PharmGKB: The Pharmacogenomics Knowledge Base
Thorn, C. F., Klein, T. E., & Altman, R. B. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-435-7_20 · Cited by 362
“This information is captured in the database in a Biopax [20] compatible format that can be downloaded and used in pathway analysis packages.”
MethodGama‐Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muñiz-Rascado, L., Solano-Lira, H., Jacinto, V. J., Weiss, V., García-Sotelo, J. S., López-Fuentes, A., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1110 · Cited by 353
“RegulonDB is also accessible in BioPAX format, as we have contributed also in the expansion of this pathway exchange format (13).”
Self-citationGetting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics
Cunningham, H., Tablan, V., Roberts, A., & Bontcheva, K. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002854 · Cited by 373
“Several resources are modelled using schemata from the BioPAX data exchange language [62].”
MethodPathway Commons 2019 Update: integration, analysis and exploration of pathway data
Rodchenkov, I. V., Babur, Ö., Luna, A., Aksoy, B. A., Wong, J. V., Fong, D., Franz, M., Siper, M. C., Cheung, M., Wrana, M., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz946 · Cited by 318
“Data is collected from providers in the Biological Pathway Exchange (BioPAX) Level 3 (8) and the Proteomics Standards Initiative Molecular Interaction (PSI-MI) formats (9), and stored uniformly in BioPAX format.”
Self-citationControlled vocabularies and semantics in systems biology
Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.77 · Cited by 316
Self-citationSBML Level 3: an extensible format for the exchange and reuse of biological models
Keating, S., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F., Finney, A., Gillespie, C. S., Helikar, T., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199110 · Cited by 301
“Some of the primary standardization efforts in COMBINE, such as BioPAX (Demir et al , 2010) and NeuroML (Gleeson et al , 2010), are more domain-specific than SBML; others, such as CellML (Lloyd et al , 2004), overlap SBML’s primary domains but offer alternative abstractions; and finally, still…”
Self-citationEDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
Ison, J., Kalaš, M., Jonassen, I., Bolser, D. M., Uludağ, M., McWilliam, H., MALONE, J. M., López, R., Pettifer, S. R., & Rice, P. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt113 · Cited by 284
Galdzicki, M., Clancy, K., Oberortner, E., Pocock, M., Quinn, J. Y., Rodríguez, C., Roehner, N., Wilson, M., Adam, L., Anderson, J. C., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2891 · Cited by 288
“In this way, the modeling extension leverages the significant work done in the development of standards for modeling biological organisms, such as SBML 17 , the ‘Biological Pathways Exchange’ (BioPAX) 30 , and the ‘Systems Biology Graphical Notation’ (SBGN) 31 .”
MethodThe role of ontologies in biological and biomedical research: a functional perspective
Hoehndorf, R., Schofield, P. N., & Gkoutos, G. V. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv011 · Cited by 278
“Some data exchange standards are now being designed with data verification in mind, and a prime example is the BioPAX standard for pathway data sharing, which is based on formalized knowledge in OWL [86].”
BackgroundA Guide to Conquer the Biological Network Era Using Graph Theory
Koutrouli, M., Karatzas, E., Páez-Espino, D., & Pavlopoulos, G. A. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00034 · Cited by 279
“Apart from the simple file formats such as the tab-delimited, CSV, SIF, Excel and adjacency matrix, several others like the BioPAX (Demir et al., 2010), SBML ( Hucka et al., 2003), PSI-MI (Hermjakob et al., 2004b), CML (Murray-Rust et al., 2001), and CellML (Lloyd et al., 2004) have been introduced for biological data…”
MethodPathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
Karp, P. D., Latendresse, M., Paley, S., Krummenacker, M., Ong, Q., Billington, R., Kothari, A., Weaver, D. S., Lee, T., Subhraveti, P., et al. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv079 · Cited by 267
Self-citationPathway Analysis: State of the Art
García-Campos, M. A., Enríquez, J. E., & Lemus, E. H. (2015) · Frontiers in Physiology · doi:10.3389/fphys.2015.00383 · Cited by 292
“Pathway standard languages such as BioPAX, SBGN, and SBML already support compartments in their pathway ontologies (Hucka et al., 2003; Le Novere et al., 2009; Demir et al., 2010).”
BackgroundSoftware for systems biology: from tools to integrated platforms
Ghosh, S., Matsuoka, Y., Asai, Y., Hsin, K., & Kitano, H. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3096 · Cited by 260
“…standards, which have been developed for different purposes; two widely used standards are the Systems Biology Markup Language (SBML) 57 and the Biological Pathways exchange (BioPAX) 58 format, both of which were designed to represent biomolecu‑ lar networks from different perspectives.”
MethodNDEx, the Network Data Exchange
Pratt, D. R., Chen, J., Welker, D., Rivas, R., Pillich, R., Rynkov, V., Ono, K., Miello, C., Hicks, L. D., Szalma, S., et al. (2015) · Cell Systems · doi:10.1016/j.cels.2015.10.001 · Cited by 250
“…relationships (Franceschini et al., 2013; Orchard et al., 2014; Stark et al., 2011; Warde-Farley et al., 2010) in both simple and complex formats (Demir et al., 2010; Le Novè re et al., 2006; Mi et al., 2010; OpenBEL, 2011) condensed collections of data into structured findings useful for…”
BackgroundProceedings of the 2017 Winter Simulation Conference
Chan, W.-M., D’Ambrogio, A., Zacharewicz, G., Mustafee, N., Wainer, G., & Page, E. (2017) · HAL · Cited by 251
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics
Wittig, U., Rey, M., Weidemann, A., Kania, R., & Müller, W. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1065 · Cited by 204
Bioinformatics and Systems Biology of the Lipidome
Subramaniam, S., Fahy, E., Gupta, S., Sud, M., Byrnes, R. W., Cotter, D., Dinasarapu, A. R., & Maurya, M. R. (2011) · Chemical Reviews · doi:10.1021/cr200295k · Cited by 218
Towards reproducible computational drug discovery
Schaduangrat, N., Lampa, S., Simeon, S., Gleeson, M. P., Spjuth, O., & Nantasenamat, C. (2020) · Journal of Cheminformatics · doi:10.1186/s13321-020-0408-x · Cited by 208
graphite - a Bioconductor package to convert pathway topology to gene network
Sales, G., Calura, E., Cavalieri, D., & Romualdi, C. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-20 · Cited by 204
VANTED v2: a framework for systems biology applications
Rohn, H., Junker, A., Hartmann, A., Grafahrend‐Belau, E., Treutler, H., Klapperstück, M., Czauderna, T., Klukas, C., & Schreiber, F. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-139 · Cited by 192
From word models to executable models of signaling networks using automated assembly
Gyori, B. M., Bachman, J. A., Subramanian, K., Muhlich, J. L., Galescu, L., & Sorger, P. K. (2017) · Molecular Systems Biology · doi:10.15252/msb.20177651 · Cited by 188
“…models can automatically be constructed from a single high-level biochemical assertion Box 2 : BioPAX and BEL BioPAX is a widely used format for describing biological interactions that facilitates exchange and integration of pathway information from multiple sources (Demir et al , 2010 ).”
BackgroundGramene database in 2010: updates and extensions
Youens‐Clark, K., Buckler, E. S., Casstevens, T. M., Chen, C., DeClerck, G., Derwent, P., Dharmawardhana, P. D., Jaiswal, P., Kersey, P. J., Karthikeyan, A. S., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1148 · Cited by 176
“The pathways from rice and sorghum, both developed by Gramene, are provided in a web-based browsable form as well as for bulk download in several options including the BioPax (24) and Systems Biology Markup Language (SBML) (25) formats for advanced users.”
MethodSelf-citationMcDonagh, E. M., Whirl‐Carrillo, M., Garten, Y., Altman, R. B., & Klein, T. E. (2011) · Biomarkers in Medicine · doi:10.2217/bmm.11.94 · Cited by 174
Self-citationPath2Models: large-scale generation of computational models from biochemical pathway maps
Büchel, F., Rodríguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., Mittag, F., Schubert, M., Glont, M., Golebiewski, M., et al. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-116 · Cited by 173
“PID provides human pathways in the BioPAX format Level 3, which specifies a ControlType attribute for each interaction.”
MethodInfluentialSelf-citationFunctional connectivity of emotional processing in depression
Carballedo, A., Scheuerecker, J., Meisenzahl, E., Schoepf, V., Bokde, A., Möller, H.-J., Doyle, M., Wiesmann, M., & Frodl, T. (2011) · Journal of Affective Disorders · doi:10.1016/j.jad.2011.06.021 · Cited by 156
Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review
Kenner, B., Chari, S. T., Kelsen, D., Klimstra, D. S., Pandol, S. J., Rosenthal, M., Rustgi, A. K., Taylor, J. A., Yala, A., Abul-Husn, N., et al. (2021) · Pancreas · doi:10.1097/mpa.0000000000001762 · Cited by 158
Self-citationPathBank: a comprehensive pathway database for model organisms
Wishart, D. S., Li, C., Marcu, A., Badran, H., Pon, A., Budinski, Z., Patron, J., Lipton, D., Cao, X. D., Oler, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz861 · Cited by 148
“Every PathBank pathway is downloadable in several machine-readable and image formats including BioPAX, SBML, PWML, SBGN, RXN, PNG and SVG. PathBank also supports community annotations and submissions through the web-based Path- Whiz pathway illustrator.”
MethodInfluentialOstaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E., Evelo, C. T., Hasenauer, J., et al. (2020) · Scientific Data · doi:10.1038/s41597-020-0477-8 · Cited by 135
“We invite curators to join the project and contribute to building a solid foundation of COVID-19 molecular and cellular mechanisms using systems biology standards [15] [16] [17] .”
MethodSelf-citationBioModels Database: A Repository of Mathematical Models of Biological Processes
Chelliah, V., Laibe, C., & Novère, N. G. L. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-450-0_10 · Cited by 133
A network map of Interleukin-10 signaling pathway
Verma, R., Balakrishnan, L., Sharma, K., Khan, A. A., Advani, J., Gowda, H., Tripathy, S. P., Suar, M., Pandey, A., Gandotra, S., et al. (2015) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-015-0302-x · Cited by 133
Self-citationSystems medicine disease maps: community-driven comprehensive representation of disease mechanisms
Mazein, A., Ostaszewski, M., Kuperstein, I., Watterson, S., Novère, N. G. L., Lefaudeux, D., Meulder, B. D., Pellet, J., Balaur, I., Saqi, M. A. S., et al. (2018) · npj Systems Biology and Applications · doi:10.1038/s41540-018-0059-y · Cited by 127
“7,30 The maps should be made accessible in a variety of formats including SBML, 21 BioPAX 22 and Neo4j.”
Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization
Landeghem, S. V., Björne, J., Wei, C.-H., Hakala, K., Pyysalo, S., Ananiadou, S., Kao, H., Lu, Z., Salakoski, T., de Peer, Y. V., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055814 · Cited by 120
“Extracted event structures are typed associations of arbitrary numbers of participants – analogous to reactions in pathway representations such as SBML and BioPAX [12,13] – and cover fundamental molecular processes such as binding and phosphorylation, their regulatory control, and the identification of specifically ne…”
BackgroundReactome pathway analysis to enrich biological discovery in proteomics data sets
Haw, R., Hermjakob, H., D'Eustachio, P., & Stein, L. (2011) · PROTEOMICS · doi:10.1002/pmic.201100066 · Cited by 117
“These batch data dumps allow researchers to download lists of all proteins that participate in a pathway or sub-pathway and support data exchange, analysis and modeling [8, 36–38].”
BackgroundSelf-citationHucka, M., Nickerson, D. P., Bader, G. D., Bergmann, F., Cooper, J., Demir, E., Garny, A., Golebiewski, M., Myers, C. J., Schreiber, F., et al. (2015) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2015.00019 · Cited by 118
Self-citationRhea—a manually curated resource of biochemical reactions
Alcántara, R., Axelsen, K. B., Morgat, A., Belda, E., Coudert, E., Bridge, A. J., Cao, H., de Matos, P., Ennis, M., Turner, S., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1126 · Cited by 113
“BioPAX (23) is a collaborative effort to create a data exchange format for biological pathway data.”
BackgroundComprehensive network map of interferon gamma signaling
Bhat, M. Y., Solanki, H. S., Advani, J., Khan, A. A., Prasad, T. S. K., Gowda, H., Thiyagarajan, S., & Chatterjee, A. (2018) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-018-0486-y · Cited by 113
Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges
Chowdhury, S., & Sarkar, R. R. (2015) · Database · doi:10.1093/database/bau126 · Cited by 109
Data integration in biological research: an overview
Lapatas, V., Stefanidakis, M., Jiménez, R. C., Via, A., & Schneider, M. V. (2015) · Journal of Biological Research - Thessaloniki · doi:10.1186/s40709-015-0032-5 · Cited by 104
“Some of this initiatives are community initiatives or consortia like COMBINE [98], PSI [99], GAGH [100], INSDC [101], proteomeXchange [102], IMEx [88], BioPax [103] involved in the development of standards in one specific biological domain.”
BackgroundCOVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
Ostaszewski, M., Niarakis, A., Mazein, A., Kuperstein, I., Phair, R. D., Resendiz, A. O., Singh, V., Aghamiri, S. S., Acencio, M. L., Glaab, E., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110387 · Cited by 104
“…diagrams followed the guidelines developed by the Community, WikiPathways (Slenter et al , 2018) and Reactome (Jassal et al , 2020) based on systems biology standards (Le Nov (cid:4) ere et al , 2009; Demir et al , 2010; Keating et al , 2020) and persistent identifiers (Wimalaratne et al , 2018).”
MethodSelf-citationTSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling
Zhong, J., Sharma, J. N., Raju, R., Palapetta, S. M., Prasad, T. S. K., Huang, T., Yoda, A., Tyner, J. W., van Bodegom, D., Weinstock, D. M., et al. (2014) · Database · doi:10.1093/database/bau007 · Cited by 104
“5) (47), Biological PAthway eXchange (BioPAX level 3) (48) and Systems Biology Markup Language (SBML version 2.”
BackgroundSelf-citationBoué, S., Talikka, M., Westra, J. W., Hayes, W., Fabio, A. D., Park, J., Schlage, W. K., Sewer, A., Fields, B., Ansari, S., et al. (2015) · Database · doi:10.1093/database/bav030 · Cited by 103
“BioPAX (15) was designed to facilitate exchange of pathway information and is amenable to representing relationships from the scientific literature.”
BackgroundKorkut, A., Wang, W., Demir, E., Aksoy, B. A., Jing, X., Molinelli, E. J., Babur, Ö., Bemis, D. L., Sümer, S. O., Solit, D. B., et al. (2015) · eLife · doi:10.7554/elife.04640 · Cited by 99
Self-citationComputational tools for metabolic engineering
Copeland, W. B., Bartley, B., Chandran, D., Galdzicki, M., Kim, K. H., Sleight, S. C., Maranas, C. D., & Sauro, H. M. (2012) · Metabolic Engineering · doi:10.1016/j.ymben.2012.03.001 · Cited by 100
“The Biological Pathway Exchange Language (BioPAX; Demir et al., 2010) defines the semantics for pathway representation, which allows databases and software tools to exchange information regarding the qualitative functional relationships of networks.”
BackgroundISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Thomas, D., Gaheen, S., Harper, S. L., Fritts, M. J., Klaessig, F., Hahn-Dantona, E. A., Paik, D. S., Pan, S., Stafford, G. A., Freund, E. T., et al. (2013) · BMC Biotechnology · doi:10.1186/1472-6750-13-2 · Cited by 99
Functional and genomic context in pathway analysis of GWAS data
Mooney, M. A., Nigg, J. T., McWeeney, S. K., & Wilmot, B. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.07.004 · Cited by 101
Self-citationA Six‐Stage Workflow for Robust Application of Systems Pharmacology
Gadkar, K., Kirouac, D., Mager, D., van der Graaf, P., & Ramanujan, S. (2016) · CPT: Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12071 · Cited by 93
Pathway-based drug repositioning using causal inference
Li, J., & Lu, Z. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s16-s3 · Cited by 95
He, Y. O., Xiang, Z., Zheng, J., et al. (2018) · Journal of Biomedical Semantics · doi:10.1186/s13326-017-0169-2 · Cited by 96
“…[5]; (3) Data exchange, e.g., BioPAX for representing molecular and cellular pathways and facilitating the exchange of biological pathway data [6]; (4) Data integration, e.g., the Ontology for Biomedical Investigations (OBI) [7] for integrative representations of data in various areas of…”
BackgroundThe Biomolecular Interaction Network Database in PSI-MI 2.5
Isserlin, R., El-Badrawi, R. A., & Bader, G. D. (2011) · Database · doi:10.1093/database/baq037 · Cited by 96
“Binding sites can be mapped to PSI-MI participant features, but actions and states are not covered by PSI-MI—though they are covered by the BioPAX pathway exchange language (36).”
BackgroundSelf-citationNetworks and Graphs Discovery in Metabolomics Data Analysis and Interpretation
Amara, A., Frainay, C., Jourdan, F., Naake, T., Neumann, S., Novoa‐del‐Toro, E. M., Salek, R. M., Salzer, L., Scharfenberg, S., & Witting, M. A. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.841373 · Cited by 106
“An alternative to SBML to represent metabolism knowledge is the BioPAX standard (Demir et al., 2010), oriented towards a semantic description of biological processes for indexing, sharing, and integration purposes, rather than quantitative modeling (Strömbäck and Lambrix, 2005).”
MethodTowards a detailed atlas of protein–protein interactions
Mosca, R., Pons, T., Ceol, A. G. M., Valencia, A., & Aloy, P. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.07.005 · Cited by 91
SPIKE: a database of highly curated human signaling pathways
Paz, A., Brownstein, Z., Ber, Y., Bialik, S., David, E. M., Sagir, D., Ulitsky, I., Elkon, R., Kimchi, A., Avraham, K. B., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1167 · Cited by 93
Immune digital twins for complex human pathologies: applications, limitations, and challenges
Niarakis, A., Laubenbacher, R., An, G. C., Ilan, Y., Fisher, J., Flobak, Å., Reiche, K., Martínez, M. R., Geris, L., Ladeira, L., et al. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00450-5 · Cited by 104
“…Markup Language (SBML) 31 for mathematical model exchange, Systems Biology Graphical Notation (SBGN) 32 for model visualisation, Biological Pathway Exchange (BioPaX) 33 for pathway descriptions, and Simulation Experiment Description Markup Language (SED-ML) 34 for simulation speci fi cations.”
Self-citationLuciano, J., Andersson, B., Batchelor, C. R., Bodenreider, O., Clark, T., Denney, C. K., Domarew, C., Gambet, T., Harland, L., Anja Jentzsch, D., et al. (2011) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-2-s2-s1 · Cited by 90
“Already, OWL ontologies have been developed to support drug, pharmacogenomics and clinical trials [15][16][17], provide a mechanism for the integration and exchange of biological pathways [18,19], and are increasingly being used in health care and life sciences applications [20].”
BackgroundSelf-citationEngel, S. R., Aleksander, S., Nash, R. S., et al. (2024) · Genetics · doi:10.1093/genetics/iyae185 · Cited by 90
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013
Pyysalo, S., Ohta, T., Rak, R., Rowley, A. G. D., Chun, H.-W., Jung, S.-J., Choi, S.-P., Tsujii, J., & Ananiadou, S. (2015) · BMC Bioinformatics · doi:10.1186/1471-2105-16-s10-s2 · Cited by 89
“By contrast to the disease-oriented focus of the CG task, the goals of the PC task are defined by a specific category of knowledge representation, namely formal models of biomolecular pathways such as the Systems Biology Markup Language (SBML) [9,10] and the Biological Pathway Exchange (BioPAX) language [11,12].”
MethodA pathway map of prolactin signaling
Radhakrishnan, A., Raju, R., Tuladhar, N., et al. (2012) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-012-0168-0 · Cited by 90
Self-citationCommunity-driven roadmap for integrated disease maps
Ostaszewski, M., Gebel, S., Kuperstein, I., Mazein, A., Zinovyev, A. Y., Doğrusöz, U., Hasenauer, J., Fleming, R. M. T., Novère, N. G. L., Gawron, P., et al. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby024 · Cited by 86
A network map of BDNF/TRKB and BDNF/p75NTR signaling system
Sandhya, V. K., Raju, R., Verma, R., Advani, J., Sharma, R., Radhakrishnan, A., Nanjappa, V., Jayasuryan, N., Somani, B. L., Mukherjee, K. K., et al. (2013) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-013-0200-z · Cited by 88
Self-citationCritical assessment of genome-scale metabolic networks: the need for a unified standard
Ravikrishnan, A., & Raman, K. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv003 · Cited by 87
Software support for SBGN maps: SBGN-ML and LibSBGN
van Iersel, M., Villéger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F., Luna, A., Demir, E., Sorokin, A., Doğrusöz, U., Matsuoka, Y., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts270 · Cited by 90
Self-citationMaize Metabolic Network Construction and Transcriptome Analysis
Monaco, M. K., Sen, T. Z., Dharmawardhana, P. D., Ren, L., Schaeffer, M. L., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L. C., Gardiner, J. M., et al. (2013) · The Plant Genome · doi:10.3835/plantgenome2012.09.0025 · Cited by 84
“For advanced users working on network modeling, we provide pathway data dumps in the standardized BioPax levels 2 and 3 (Demir et al., 2010) and systems biology markup language (SBML) (Hucka et al., 2003) formats.”
MethodSelf-citationKaBOB: ontology-based semantic integration of biomedical databases
Livingston, K., Bada, M. A., Baumgartner, W. A., et al. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0559-3 · Cited by 83
“Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, et al. The BioPAX community standard for pathway data sharing.”
BackgroundNine quick tips for pathway enrichment analysis
Chicco, D., & Agapito, G. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010348 · Cited by 99
“To perform pathway enrichment by employing more than a single database, users can employ cPEA [48], a software tool able to deal with several pathway databases using the BioPAX language [61] to store and represent pathways.”
MethodBioinformatic approaches for functional annotation and pathway inference in metagenomics data
Filippo, C. D., Ramazzotti, M., Fontana, P., & Cavalieri, D. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs070 · Cited by 84
“A number of alternative schemes, mostly implemented in specialized XML (eXtensible Markup Language), have been proposed to code increased levels of complexity (SBML [5], SBGN [6], BioPax [7], CellML [8], KGML [3], BCML [9]).”
BackgroundBiological network extraction from scientific literature: state of the art and challenges
Li, C., Liakata, M., & Rebholz‐Schuhmann, D. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt006 · Cited by 80
“Qualitative models are encoded usually in some logical formalism such as Prolog, whereas quantitative models are usually encoded according to standards such as the Systems Biology Markup Language (SBML) [5], CellML [6] and BioPAX [7], and then kept in special repositories [8, 9].”
MethodKotlyar, M., Pastrello, C., Ahmed, Z., Chee, J., Varyova, Z., & Jurišica, I. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1034 · Cited by 83
“Data from these databases are downloaded in BioPAX (54) Level 3 format and converted to extended binary SIF format (SIFnx) using the function ‘toSifnx’ from the package PaxtoolsR (55) v1.”
MethodSoftware platforms to facilitate reconstructing genome‐scale metabolic networks
Hamilton, J. J., & Reed, J. L. (2013) · Environmental Microbiology · doi:10.1111/1462-2920.12312 · Cited by 76
Cohen, P. R. (2015) · Physical Biology · doi:10.1088/1478-3975/12/4/045008 · Cited by 82
Babur, Ö., Melrose, A. R., Cunliffe, J. M., Klimek, J. E., Pang, J., Sepp, A.-L. I., Zilberman‐Rudenko, J., Yunga, S. T., Zheng, T. J., Parra‐Izquierdo, I., et al. (2020) · Blood · doi:10.1182/blood.2020005496 · Cited by 84
Self-citationGu, Z., Liu, J., Cao, K., Zhang, J., & Wang, J. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-56 · Cited by 79
“Demir E, Cary MP, Paley S, et al: The BioPAX community standard for pathway data sharing.”
BackgroundEvaluation of research in biomedical ontologies
Hoehndorf, R., Dumontier, M., & Gkoutos, G. V. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs053 · Cited by 86
Sharing Structure and Function in Biological Design with SBOL 2.0
Roehner, N., Beal, J., Clancy, K., Bartley, B., Mısırlı, G., Grünberg, R., Oberortner, E., Pocock, M., Bissell, M. G., Madsen, C. K., et al. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00215 · Cited by 78
Biomedical Event Extraction using Abstract Meaning Representation
Rao, S., Marcu, D., Knight, K. K., & Daumé, H. (2017) · doi:10.18653/v1/w17-2315 · Cited by 82
“We use the BioPax (Biological Pathway Exchange) database (Demir et al., 2010) as our knowledge base of protein relations and we use the PubMed central articles as our unannotated text corpus.”
MethodKirouac, D. C., Sáez-Rodríguez, J., Swantek, J. L., Burke, J. M., Lauffenburger, D. A., & Sorger, P. K. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-29 · Cited by 82
“Standardized languages do exist (BioPAX, CellML, SBML, and PSI-MI) but none is as-yet universal [24].”
BackgroundHarmonizing semantic annotations for computational models in biology
Neal, M. L., König, M., Nickerson, D., Mısırlı, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., et al. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bby087 · Cited by 74
“However, this specification is still under development, and several implementation details must be resolved before it can be completed, including how annotations should be implemented in BioPAX [97] and SBOL documents.”
Self-citationCritical assessment of human metabolic pathway databases: a stepping stone for future integration
Stobbe, M. D., Houten, S. M., Jansen, G. A., van Kampen, A. H. C., & Moerland, P. D. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-165 · Cited by 72
Metadata
- Authors
- Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, Ö., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Ruebenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K.-H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Le Novère, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C., & Bader, G. D.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- SRI International (US)
- National Institute of Advanced Industrial Science and Technology (JP)
- Université Libre de Bruxelles (BE)
- Ontario Institute for Cancer Research (CA)
- National Institutes of Health (US)
- Boston University (US)
- Johns Hopkins University (US)
- University of Toronto (CA)
- Rothamsted Research (GB)
- Cell Signaling Technology (United States) (US)
- Broad Institute (US)
- Center for Food Safety and Applied Nutrition (US)
- Oregon Health & Science University (US)
- Environmental Protection Agency (US)
- Argonne National Laboratory (US)
- UConn Health (US)
- Harvard University (US)
- National Institute of Standards and Technology (US)
- University of Auckland (NZ)
- Syngenta (United States) (US)
- Yale University (US)
- Loyola Marymount University (US)
- St. John's University (US)
- Stanford University (US)
- Columbia University (US)
- SRA International (United States) (US)
- University of Ottawa (CA)
- Vertex Pharmaceuticals (United States) (US)
- Medical College of Wisconsin (US)
- Cornell University (US)
- Cold Spring Harbor Laboratory (US)
- Takeda Oncology (United States) (US)
- Virginia Tech (US)
- European Bioinformatics Institute (GB)
- Kyoto University Institute for Chemical Research (JP)
- California Institute of Technology (US)
- University of Göttingen (DE)
- Corresponding author
- Bader, Gary D
- ORCID
- Demir, Emek
- Cary, Michael P
- Paley, Suzanne
- Fukuda, Ken
- Wu, Guanming
- Mi, Huaiyu
- Splendiani, Andrea
- Tkachev, Sasha
- Zucker, Jeremy
- Gopinath, Gopal
- Rajasimha, Harsha
- Shah, Imran
- Syed, Mustafa
- Anwar, Nadia
- Babur, Özgün
- Blinov, Michael
- Goldberg, Robert
- Hornbeck, Peter
- Luna, Augustin
- Neumann, Eric
- Wimalaratne, Sarala
- Cheung, Kei-Hoi
- Dahlquist, Kam
- Gillespie, Marc
- Gong, Li
- Haw, Robin
- Kane, David
- Kutmon, Martina
- Merberg, David
- Petri, Victoria
- Shah, Nigam
- Whaley, Ryan
- Buetow, Kenneth H
- Rzhetsky, Andrey
- McWeeney, Shannon
- Aladjem, Mirit
- Birney, Ewan
- Goto, Susumu
- Hucka, Michael
- Pandey, Akhilesh
- Thomas, Paul
- Wingender, Edgar
- Karp, Peter D
- Sander, Chris
- Bader, Gary D
- Venue
- Nature Biotechnology
- Published
- 2010-09
- Volume
- 28
- Issue
- 9
- Pages
- 935-942
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3001121
- OpenAlex
- W1969709265
- Semantic Scholar
- 1876dd0e382dd215782af61d09157646fc8eb204
- Cited by
- 745
- References
- 84
- Citations by year
- 2026: 27 · 2025: 13 · 2024: 32 · 2023: 35 · 2022: 41 · 2021: 46 · 2020: 44 · 2019: 43 · 2018: 45 · 2017: 35 · 2016: 57 · 2015: 74 · 2014: 49 · 2013: 78 · 2012: 62
- FWCI
- 26.30
- Type
- journal article
- Language
- en
- Update notices
- Open access
- bronze
- doi.org
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
- Rothamsted Repository (Rothamsted Repository) (submittedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Arrow@dit (Dublin Institute of Technology) (submittedVersion)
- ARAN (University of Galway Research Repository) (Ollscoil na Gaillimhe – University of Galway) (submittedVersion, cc-by-nc-nd)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- Research Publications (Maastricht University) (submittedVersion)
- Funders
- U.S. Department of Energy (FG02-04ER63931, DE‐FG02‐)
- Genome Canada
- Ontario Genomics
- Ontario Genomics Institute
- National Institutes of Health (5r13gm076939-03)
- Biotechnology and Biological Sciences Research Council (BB/F010516/1)
- National Human Genome Research Institute (P41HG004118, U54HG004028)
- National Cancer Institute (P30CA069533)
- National Institute of General Medical Sciences (R13 GM076939, 1R13GM076939, R01GM071962, R01GM070923, U24GM077678)
- National Institute of Allergy and Infectious Diseases (U54AI081680)
- National Center for Research Resources (R01RR022971)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- BioPAX, data exchange standards, pathway databases, metabolic pathways, signaling pathways, molecular interactions, gene regulatory networks, data interoperability
- MeSH terms
- Programming Languages, Software, Signal Transduction, Computational Biology, Databases as Topic, Information Dissemination, Metabolic Networks and Pathways
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-09, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-09 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
