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
Items 301–400 of 755
Hierarchical modeling for synthetic biology.
Chandran, D., & Sauro, H. (2012) · ACS Synthetic Biology · doi:10.1021/sb300033q · Cited by 17
BioASF: a framework for automatically generating executable pathway models specified in BioPAX
Haydarlou, R., Jacobsen, A., Bonzanni, N., et al. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw250 · Cited by 17
“The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model.”
MethodThe BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track
Madan, S., Hodapp, S., Senger, P., et al. (2016) · Database · doi:10.1093/database/baw136 · Cited by 17
“The two most common network-modeling languages in systems biology are Biological PAthway eXchange language (BioPAX) (8), a format optimized for database exchange, and Systems Biology Markup Language (SBML) (9), a structured XML-based language.”
MethodSystems psychopharmacology: A network approach to developing novel therapies
Gebicke‐Haerter, P. J. (2016) · World Journal of Psychiatry · doi:10.5498/wjp.v6.i1.66 · Cited by 16
Application of Bioinformatics in Understanding of Plant Stress Tolerance
Upadhyay, J., Joshi, R., Singh, B., Bohra, A., Vijayan, R., Bhatt, M., Bisht, S. P. S., & Wani, S. H. (2017) · Springer eBooks · doi:10.1007/978-3-319-67156-7_14 · Cited by 20
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures
Saqi, M. A. S., Lysenko, A., Guo, Y., Tsunoda, T., & Auffray, C. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby025 · Cited by 16
An integrative modeling framework reveals plasticity of TGF-β signaling
Andrieux, G., Borgne, M. L., & Théret, N. (2014) · BMC Systems Biology · doi:10.1186/1752-0509-8-30 · Cited by 16
“While some limitations in the specifications of Reactome ’ s Bio-PAX2 were previously reported by PID ’ s authors [28], the recent upgrade of BioPAX 2 to BioPAX3 [37] should facilitate data extraction from Reactome into CADBIOM.”
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout
Czauderna, T., Wybrow, M., Marriott, K. G., et al. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-250 · Cited by 16
“However, these approaches can’t translate the widely used KEGG maps into SBGN, and they mostly compute entirely new layouts rather than utilizing lay-out information derived from the original (KEGG, SBML, or BioPAX) map.”
BackgroundInfluentialHahn-Powell, G., Valenzuela-Escárcega, M. A., & Surdeanu, M. (2017) · Annual Meeting of the Association for Computational Linguistics: System Demonstrations (ACL Demo) · doi:10.18653/v1/p17-4018 · Cited by 17
“REACH uses a two-stage bottom-up strategy for event extraction, following biochemical semantics inspired by BioPAX (Demir et al., 2010).”
MethodMelas, I. N., Mitsos, A., Messinis, D. E., Weiß, T. S., Sáez-Rodríguez, J., & Alexopoulos, L. G. (2012) · Molecular BioSystems · doi:10.1039/c2mb05482e · Cited by 15
Accelerating cancer systems biology research through Semantic Web technology
Wang, Z., Sagotsky, J., Taylor, T. J. S., Shironoshita, P., & Deisboeck, T. S. (2012) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1200 · Cited by 15
IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase
Balakrishnan, L., Soman, S., Patil, Y. B., et al. (2013) · Cell Communication & Adhesion · doi:10.3109/15419061.2013.791683 · Cited by 15
“IL-11 signaling pathway information is available in multiple data exchange formats such as PSI-MI 2.5 (Hermjakob et al., 2004), BioPAX level 3 (Demir et al., 2010), and SBML 2.1 (Hucka et al., 2003).”
MethodInfluentialSelf-citationAutomated visualization of rule-based models
Sekar, J. A. P., Tapia, J.-J., & Faeder, J. R. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005857 · Cited by 15
“A number of exchange formats now support rule-based data structures (SBML-Multi [28], BioPax Level 3 [60]) and a number of modeling frameworks integrate BioNetGen rules with higher-order model composition (Virtual Cell [37,38], PySB [56]).”
BackgroundMadan, S., Szostak, J., Elayavilli, R. K., et al. (2019) · Database · doi:10.1093/database/baz084 · Cited by 15
“For dynamic models, systems biology markup language (SBML) is the main format (1) used, and for traditional pathway information, the exchange format BioPAX (2) is useful.”
MethodThe Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine
Touré, V., Dräger, A., Luna, A., Dogrusoz, U., & Rougny, A. (2020) · Systems Medicine · doi:10.1016/b978-0-12-801238-3.11515-6 · Cited by 11
Self-citationOn the Logical Design of a Prototypical Data Lake System for Biological Resources
Che, H., & Duan, Y. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.553904 · Cited by 14
“As a well-accepted exchange language, BioPAX (Biological Pathway Exchange) aims to enable integration, exchange, visualization, and analysis of biological pathway data (Demir et al., 2010).”
BackgroundReNE: A Cytoscape Plugin for Regulatory Network Enhancement
Politano, G. M. M., Benso, A., Savino, A., & Carlo, S. D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115585 · Cited by 15
“Although pathway description languages such as the Biological Pathways Exchange (BioPAX) format [24] and the Systems Biology Markup Language (SBML) [25] have been proposed as standards for pathway data exchange in XML format, each pathway database is constructed based on its own pathway model.”
MethodJiménez-López, J. C., Gachomo, E. W., Sharma, S., & Kotchoni, S. O. (2013) · American Journal of Molecular Biology · doi:10.4236/ajmb.2013.32016 · Cited by 15
“BioPAX [91] has been developed to deliver a compatible standard, faci-”
MethodNetwork-Assisted Disease Classification and Biomarker Discovery
Strunz, S., Wolkenhauer, O., & de la Fuente, A. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3283-2_16 · Cited by 15
Detection of type 2 diabetes related modules and genes based on epigenetic networks
Liu, H., Wang, T., Liu, H., Wei, Y., Zhao, G., Su, J., Wu, Q., Qiao, H., & Zhang, Y. (2014) · BMC Systems Biology · doi:10.1186/1752-0509-8-s1-s5 · Cited by 14
Semantically Linking in Silico Cancer Models
Johnson, D., Connor, A. J., McKeever, S., Wang, Z., Deisboeck, T. S., Quaiser, T., & Shochat, E. (2014) · Cancer Informatics · doi:10.4137/cin.s13895 · Cited by 14
Bohler, A., Eijssen, L., van Iersel, M., Leemans, C., Willighagen, E., Kutmon, M., Jaillard, M., & Evelo, C. T. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0708-8 · Cited by 14
“Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, et al. The BioPAX community standard for pathway data sharing.”
InfluentialSelf-citationDiscovering Medical Knowledge Using Visual Analytics
Sturm, W., Schreck, T., Holzinger, A., & Ullrich, T. (2015) · Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft) · doi:10.2312/vcbm.20151210 · Cited by 14
Bio-Curation for Cellular Signalling: The KAMI Project
Harmer, R., Cornec, Y.-S. L., Légaré, S., & Oshurko, E. (2019) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2019.2906164 · Cited by 14
“Our work also relates to the BioPAX 12 project [22] which aims to represent biological pathways at multiple levels of abstraction.”
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
Schreiber, F., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Novère, N. L., Myers, C., Nickerson, D., Sommer, B., & Walthemath, D. (2016) · Journal of Integrative Bioinformatics · doi:10.2390/biecoll-jib-2016-289 · Cited by 21
“BioPAX (Biological Pathway Exchange), to store biological pathways and support the exchange, integration and analysis of biological pathway data [4].”
BackgroundSelf-citationEnabling Massive XML-Based Biological Data Management in HBase
Liu, J., Liu, Q., Zhang, L., et al. (2019) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2019.2915811 · Cited by 14
“…CellML which is used to describe mathematical models [23], BioPAX (Biological Pathway Exchange) which is used to represent biological pathways [8], BSML (Bioinformatic Sequence Markup Language) which is used to represent sequence data [34], etc. XML model has become a popular choice for…”
MethodPractical resources for enhancing the reproducibility of mechanistic modeling in systems biology
Blinov, M. L., Gennari, J. H., Karr, J. R., Moraru, I. I., Nickerson, D. P., & Sauro, H. M. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.06.001 · Cited by 11
“RDF (Resource Description Framework) -based formats such as BioPAX [12] can be good choices for qualitative and relational information, such as information about transcription factor binding sites and protein e protein interactions.”
BackgroundSelf-citationA network map of the gastrin signaling pathway
Subbannayya, Y., Anuja, K., Advani, J., et al. (2014) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-014-0224-z · Cited by 14
Self-citationPathway Commons at Virtual Cell: use of pathway data for mathematical modeling
Blinov, M. L., Schaff, J. C., Ruebenacker, O., Wei, X., Vasilescu, D. D., Gao, F., Morgan, F., Ye, L., Lakshminarayana, A., Moraru, I. I., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt660 · Cited by 14
“However, there is no standard mechanism for using these data (stored in BioPAX format) to annotate and build quantitative mathematical models.”
BackgroundSelf-citationGraph databases in systems biology: a systematic review
Mazein, I., Rougny, A., Mazein, A., Henkel, R., Gütebier, L., Michaelis, L., Ostaszewski, M., Schneider, R., Satagopam, V., Jensen, L. J., et al. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae561 · Cited by 15
“Its content is represented using mainly the BioPAX language [18] with visualization available in SBGN [17].”
Signalling pathway database usability: lessons learned
Tieri, P., & Nardini, C. (2013) · Molecular BioSystems · doi:10.1039/c3mb70242a · Cited by 13
Ontology-supported research on vaccine efficacy, safety and integrative biological networks
He, Y. O. (2014) · Expert Review of Vaccines · doi:10.1586/14760584.2014.923762 · Cited by 13
“Some common formats, such as BioPAX [55] , are used for data exchange.”
BackgroundMethodA knowledge representation meta-model for rule-based modelling of signalling networks
Basso-Blandin, A., Fontana, W., & Harmer, R. (2016) · Electronic Proceedings in Theoretical Computer Science · doi:10.4204/eptcs.204.5 · Cited by 13
“Indeed, our approach is, by design, particularly attuned to the representation of signalling networks and, as such, is less constrained than BioPAX which, as a framework of far broader applicability, has to bear a far stronger semantic burden.”
MethodInformation content and scalability in signal transduction network reconstruction formats
Rother, M. B., Münzner, U., Thieme, S., & Krantz, M. (2013) · Molecular BioSystems · doi:10.1039/c3mb00005b · Cited by 13
Uncovering influence links in molecular knowledge networks to streamline personalized medicine
Shin, D., Arthur, G., Popescu, M., Korkin, D., & Shyu, C. (2014) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2014.08.003 · Cited by 13
“For example, for an enzyme E and a biochemical reaction BR (RDF protein and RDF interaction respectively in RIIG terminology, see Definitions 9–12 in SM), the ‘‘CONTROLLER’’ RDF object property of the Biopax 2 ontology [62] can be used to express the influence of E on active state of BR using an RDF triple t = hE, CON…”
ModelBricks—modules for reproducible modeling improving model annotation and provenance
Cowan, A. E., Mendes, P., & Blinov, M. L. (2019) · npj Systems Biology and Applications · doi:10.1038/s41540-019-0114-3 · Cited by 15
Self-citationGupta, M., Singh, D. B., Shukla, R., & Misra, K. (2013) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2013.0007 · Cited by 13
“Biological pathway exchange (BioPAX) was used to exchange SBML format with owl format (Demir et al., 2010).”
NAViGaTOR: Large Scalable and Interactive Navigation and Analysis of Large Graphs
Djebbari, A., Ali, M. A. M., Otasek, D., Kotlyar, M., Fortney, K., Wong, S., Hrvojic, A., & Jurišica, I. (2011) · Internet Mathematics · doi:10.1080/15427951.2011.604289 · Cited by 13
“…provides (1) the ability to process large data sets representing graphs from different file formats (e.g., PSI-MI XML [Kerrien et al. 07], BioPAX OWL [Demir et al. 10, Antoniou and Harmelen 09], GML [Himsolt 96], MITAB [Ker-rien et al. 07], tab-delimited), (2) tools to manipulate, modify, and…”
BackgroundSignaling network map of the aryl hydrocarbon receptor
Yelamanchi, S. D., Solanki, H. S., Radhakrishnan, A., et al. (2016) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-016-0341-y · Cited by 12
AOPWIKI-EXPLORER: An interactive graph-based query engine leveraging large language models
Kumar, S., Deepika, D., Slater, K., et al. (2024) · Computational Toxicology · doi:10.1016/j.comtox.2024.100308 · Cited by 12
CMLLite: a design philosophy for CML
Townsend, J. A., & Murray‐Rust, P. (2011) · Journal of Cheminformatics · doi:10.1186/1758-2946-3-39 · Cited by 12
“BioPAX [25].”
Self-citationSystems Toxicology from Genes to Organs
Jack, J., Wambaugh, J. F., & Shah, I. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-059-5_17 · Cited by 12
Self-citationIntelligent host engineering for metabolic flux optimisation in biotechnology
Munro, L. J., & Kell, D. B. (2021) · Biochemical Journal · doi:10.1042/bcj20210535 · Cited by 12
Joint learning-based causal relation extraction from biomedical literature
Li, D., Wu, P., Dong, Y., Gu, J., Qian, L., & Zhou, G. (2023) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2023.104318 · Cited by 11
Transforming semi-structured life science diagrams into meaningful domain ontologies with DiDOn
Keet, C. M. (2012) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2012.01.004 · Cited by 12
Reverse Engineering Molecular Hypergraphs
Rahman, A., Poirel, C. L., Badger, D. J., et al. (2013) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2013.71 · Cited by 12
“Many databases and interaction storage formats support hyper-edges of different types, either explicitly or implicitly [7], [25].”
BackgroundBenis, N., Wells, J. M., Smits, M. A., Kar, S. K., van der Hee, B., dos Santos, V. A. P. M., Diez, M. S., & Schokker, D. (2019) · BMC Genomics · doi:10.1186/s12864-019-6390-x · Cited by 12
Open modeling and exchange (OMEX) metadata specification version 1.0
Neal, M. L., Gennari, J. H., Waltemath, D., Nickerson, D. P., & König, M. (2020) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2020-0020 · Cited by 12
“Other formats for storing knowledge terms might include the Synthetic Biology Open Language (SBOL [15]) , BioPax [16], BpForms [17], BcForms [17], the Web Ontology Language (OWL, https://www.w3.org/TR/owl2-overview/ , or the Open Biomedical Ontology (OBO) format [18].”
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
Rougny, A., Touré, V., Albanese, J. S., Waltemath, D., Shirshov, D., Sorokin, A., Bader, G. D., Blinov, M. L., & Mazein, A. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab049 · Cited by 10
“This general approach could be employed to efficiently query models expressed in other such XML-based standard formats (e.g. SBML), and queries could be direcyly written for standard formats that support query languages (e.g. SPARQL queries for BioPAX RDF/XML files) or structured databases (e.g. SQL queries for Reacto…”
InfluentialSelf-citationGolebiewski, M., Bader, G. D., Gleeson, P., Gorochowski, T. E., Keating, S., König, M., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., et al. (2024) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2024-0015 · Cited by 12
Self-citationDynamical modeling of uncertain interaction-based genomic networks
Mohsenizadeh, D. N., Jianping Hua, A., Bittner, M. L., & Dougherty, E. R. (2015) · BMC Bioinformatics · doi:10.1186/1471-2105-16-s13-s3 · Cited by 11
“…centered around biological interactions is currently being curated into well organized public databases, such as PID [1], Reactome [2,3], and Pathway Commons [4], where the interactions and their associated physical entities are defined and shared via a standard language such as Bio-PAX [5].”
BackgroundCapturing cooperative interactions with the PSI-MI format
Roey, K. V., Orchard, S. E., Kerrien, S., Dumousseau, M., Ricard‐Blum, S., Hermjakob, H., & Gibson, T. J. (2013) · Database · doi:10.1093/database/bat066 · Cited by 11
The Electron Microscopy eXchange (EMX) initiative
Marabini, R., Ludtke, S. J., Murray, S. C., Chiu, W., de la Rosa-Trevin, J. M., Patwardhan, A., Heymann, J. B., & Carazo, J. M. (2016) · Journal of Structural Biology · doi:10.1016/j.jsb.2016.02.008 · Cited by 11
kpath: integration of metabolic pathway linked data
Navas‐Delgado, I., García-Godoy, M. J., López-Camacho, E., Rybiński, M., Reyes‐Palomares, A., Medina, M. Á., & Aldana-Montes, J. F. (2015) · Database · doi:10.1093/database/bav053 · Cited by 11
“Users can run SPARQL queries, defined or parameterized queries using the Bioqueries platform (37) and retrieve the results in different standard formats, such as different serializations of the RDF graphs (RDF/XML, N-Triples, Turtle) or JSON, using the local vocabulary or BioPAX Level 3 (38).”
MethodComparison of tissue/disease specific integrated networks using directed graphlet signatures
Sonmez, A. B., & Can, T. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1525-z · Cited by 11
“It is also closely integrated with BioPAX [4], which is an ontological model for integration and exchange of heterogenous biological pathway data.”
BackgroundData Mining in the MetaCyc Family of Pathway Databases
Karp, P. D., Paley, S., & Altman, T. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-107-3_12 · Cited by 11
“BioPAX Files: BioPAX [6] is an XML-based standard format that facilitates the exchange of pathway-related information.”
BackgroundSelf-citationPathway analysis with signaling hypergraphs
Ritz, A., & Murali, T. M. (2014) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/2649387.2649450 · Cited by 11
“The NCI-PID pathways are freely available in BioPAX format [7], and we processed them using an in-house parser built upon PaxTools [6].”
MethodTowards the Collaborative Curation of the Registry underlying identifiers.org
Juty, N., Novère, N. G. L., Hermjakob, H., & Laibe, C. (2013) · Database · doi:10.1093/database/bat017 · Cited by 10
“For example, such harmonization is undertaken by Pathway Commons (14) when the system processes BioPAX (15) files coming from multiple sources.”
Comprehensive pathway enrichment analysis workflows: COVID-19 case study
Agapito, G., Pastrello, C., & Jurišica, I. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa377 · Cited by 12
“BiP[31]performsPEAusingpathwaysencodedinBiologicalPath-way Exchange (BioPAX) format [32].”
Gopinath, G., Hari, K., Jain, R., Mammel, M. K., Kothary, M. H., Franco, A. A., Grim, C., Jarvis, K. G., Sathyamoorthy, V., Hu, L., et al. (2013) · Food Microbiology · doi:10.1016/j.fm.2013.01.001 · Cited by 11
“, 2011) for analysis of nucleotide sequences, UniPROT (UniProt Consortium, 2011) for protein sequences and structure analyses, BioPAX (Demir et al., 2010) for the analysis of biological pathways and molecular interactions, and Gene Ontology (Ashburner et al.”
BackgroundMethodSelf-citationRole of a Web-based Software Platform for Systems Biology
Turenne, N. (2011) · Journal of Computer Science & Systems Biology · doi:10.4172/jcsb.1000101e · Cited by 11
“BioPAX is a protocol for the specification and representation of cell signalling pathways, gene-regulatory networks, protein-protein interactions and other types of biomolecular interaction data [24].”
BackgroundStaal, Y. C. M., Pennings, J. L. A., Hessel, E. V. S., & Piersma, A. H. (2017) · Applied In Vitro Toxicology · doi:10.1089/aivt.2017.0019 · Cited by 10
“Biological Pathways Exchange (BioPAX) 20 is an ontology for analysis and visualization of biological pathway data in various forms, ranging from metabolic pathways to gene regulations.”
Human-like layout algorithms for signalling hypergraphs: outlining requirements
Siebenhaller, M., Nielsen, S. S., McGee, F., et al. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby099 · Cited by 11
Palaniappan, S. K., Yachie‐Kinoshita, A., & Ghosh, S. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20287-2 · Cited by 12
Engel, S. R., Aleksander, S., Nash, R. S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.16.613348 · Cited by 11
“BioPAX provides a standardized format for representing biological pathways, allowing researchers to integrate pathway information from different sources and databases.”
InfluentialOMEX metadata specification (version 1.2)
Gennari, J. H., König, M., Misirli, G., Neal, M. L., Nickerson, D. P., & Waltemath, D. (2021) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2021-0020 · Cited by 11
“Other formats for storing knowledge terms might include the Synthetic Biology Open Language (SBOL [16]) , BioPax [17], BpForms [18], BcForms [18], the Web Ontology Language (OWL, https://www.w3.org/TR/owl2-overview/ , or the Open Biomedical Ontology (OBO) format [19].”
MethodA Profile of Today's SBML-Compatible Software
Hucka, M., Bergmann, F., Keating, S., & Smith, L. P. (2011) · IEEE International Conference on e-Science Workshops · doi:10.1109/esciencew.2011.28 · Cited by 10
Self-citationAn introduction to and survey of biological network visualization
Ehlers, H., Brich, N., Krone, M., Nöllenburg, M., Yu, J., Natsukawa, H., Yuan, X., & Wu, H. (2024) · Computers & Graphics · doi:10.1016/j.cag.2024.104115 · Cited by 13
A quick guide to biomolecular network studies: Construction, analysis, applications, and resources
Tang, H., Zhong, F., & Xie, H. (2012) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2012.06.085 · Cited by 10
Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration
Santra, T., Kölch, W., & Kholodenko, B. Ν. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003385 · Cited by 10
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory
Splendiani, A., Gündel, M., Austyn, J. M., Cavalieri, D., Scognamiglio, C., & Brandizi, M. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr051 · Cited by 10
“When data integration was carried out within homogenous research communities, those languages could rely on a shared understanding of their concepts and the semantic challenges of data integration were addressed through the definition of ‘exchange languages’ [21, 22].”
MethodSelf-citationRepresenting physiological processes and their participants with PhysioMaps
Cook, D. L., Neal, M. L., Hoehndorf, R., et al. (2013) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-4-s1-s2 · Cited by 10
“Similarly, for Reactome, the BioPAX formalism [6] provides the basis for a node-and-arc representation of processes.”
Methodcd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats
Balaur, I., Roy, L., Mazein, A., et al. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz969 · Cited by 10
Towards modelling emergence in plant systems
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6 · Cited by 10
“…formats for model description and analysis, such as CellML, an XML-based format for the encoding of mathematical models, Systems Biology Graphical Notation (SBGN), Systems Biology Markup Language (SBML), and BioPAX (Demir et al., 2010), a language for the representation of biological pathways.”
MethodSystems Biology in ELIXIR: modelling in the spotlight
dos Santos, V. A. P. M., Anton, M., Szomolay, B., Ostaszewski, M., Arts, I. C. W., Benfeitas, R., Angel, V. D. D., Domínguez-Romero, E., Ferk, P., Fey, D., et al. (2022) · F1000Research · doi:10.12688/f1000research.126734.1 · Cited by 12
Self-citationHeterogeneous Networks on Multiple Levels
Schreiber, F., Kerren, A., Börner, K., et al. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-06793-3_9 · Cited by 10
“To support exchange between tools and databases, a few standard representations are widely used such as SBML [26] and BioPAX [14].”
MethodFinding gene regulatory network candidates using the gene expression knowledge base
Venkatesan, A., Tripathi, S., de Galdeano, A. S., Blondé, W., Lægreid, A., Mironov, V., & Kuiper, M. T. R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0386-y · Cited by 10
“A small number of additional terms (1 or 2 per ontology) from BioPAX [53], ChEBI [54], IAO [55], PSI-MOD [56], and OBI [57] are used to provide an interface between the SIO terms and the data, when needed.”
MethodPathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways
Fried, J. Y., van Iersel, M., Aladjem, M. I., Kohn, K. W., & Luna, A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt146 · Cited by 11
Self-citationModeLang: A New Approach for Experts-Friendly Viral Infections Modeling
Wąsik, S., Prejzendanc, T., & Błażewicz, J. (2013) · Computational and Mathematical Methods in Medicine · doi:10.1155/2013/320715 · Cited by 10
“Example languages in this group are ACE View [37], Sydney OWL Syntax [38], Rabbit [39], Lite Natural Language [40], CLOnE [41], or BioPAX [42] that can be used to store biological pathways.”
MethodCoreference resolution improves extraction of Biological Expression Language statements from texts
Choi, M., Liu, H., Baumgartner, W. A., et al. (2016) · Database · doi:10.1093/database/baw076 · Cited by 10
“There is also much interest in standard representations of biological networks, such as the Biological pathway exchange language (4), the Systems Biology Markup Language (5) and the Biological Expression Language (BEL) (6).”
BackgroundMısırlı, G., Taylor, R., Goñi‐Moreno, Á., et al. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00532 · Cited by 10
The role of metadata in reproducible computational research
Leipzig, J., Nüst, D., Hoyt, C. T., Soiland-Reyes, S., Ram, K., & Greenberg, J. (2020) · Patterns · doi:10.1016/j.patter.2021.100322 · Cited by 129
From knowledge to models: Automated modeling in systems and synthetic biology
Gyori, B. M., & Bachman, J. A. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.100362 · Cited by 10
Heuristic shortest hyperpaths in cell signaling hypergraphs
Krieger, S., & Kececioglu, J. D. (2022) · Algorithms for Molecular Biology · doi:10.1186/s13015-022-00217-9 · Cited by 10
“The NCI-PID and Reactome pathways were downloaded in the BioPAX format [30] from Pathway Commons, and processed using a parser from Franzese et al. [22] built on PaxTools [31].”
MethodThe role of markup for enabling interoperability in health informatics
McKeever, S., & Johnson, D. (2015) · Frontiers in Physiology · doi:10.3389/fphys.2015.00152 · Cited by 10
“Other examples of open semantic standards and ontologies include MAGE-TAB 18 (Rayner et al., 2006) (MicroArray and Gene Expression Tabular), ISA-TAB 19 (Sansone et al., 2012), BioPAX 20 (Biological Pathway Exchange) (Demir et al., 2010), and the Gene Ontology (GO) (Ashburner et al., 2000) to name but a few.”
BackgroundBEL Networks Derived from Qualitative Translations of BioNLP Shared Task Annotations
Fluck, J., Klenner, A., Madan, S., et al. (2013) · Cited by 10
Krämer, F., & Beißbarth, T. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6622-6_6 · Cited by 10
Ontology‐Driven Formal Conceptual Data Modeling for Biological Data Analysis
Keet, C. M. (2013) · doi:10.1002/9781118617151.ch06 · Cited by 10
“1)—such as the PRO protein ontology [51] and Biopax [19].”
MethodInfluentialToward Genome‐Scale Models of Signal Transduction Networks
Münzner, U., Lubitz, T., Klipp, E., & Krantz, M. (2017) · Systems Biology · doi:10.1002/9783527696130.ch8 · Cited by 10
Community-driven roadmap for integrated disease mapsPreprint
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) · doi:10.31219/osf.io/hcuqa · Cited by 10
Extracting reaction networks from databases—opening Pandora’s box
Fearnley, L. G., Davis, M. J., Ragan, M. A., & Nielsen, L. K. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbt058 · Cited by 9
“[21], Biological Pathway Exchange (BioPAX) [22]”
Bio-Curation for Cellular Signalling: The KAMI Project
Harmer, R., Cornec, Y.-S. L., Légaré, S., et al. (2017) · Lecture notes in computer science · doi:10.1007/978-3-319-67471-1_1 · Cited by 9
Pathway Curation Support as an Information Extraction Task
Ohta, T., Pyysalo, S., Ananiadou, S., & Tsujii, J. (2011) · Cited by 8
JBioWH: an open-source Java framework for bioinformatics data integration
Vera, R., Pérez‐Riverol, Y., Perez, S., Ligeti, B., Kertész‐Farkas, A., & Pongor, S. (2013) · Database · doi:10.1093/database/bat051 · Cited by 9
“The BioWarehouse includes data from 10 databases [GeneBank (27), Uniprot (18), NCBI Taxonomy (28), Gene Ontology (29), BioCyc and MetaCyc (37), BioPad (38), CMR (39), Enzyme (40) and KEGG (22)].”
MethodPathPPI: an integrated dataset of human pathways and protein-protein interactions
Tang, H., Zhong, F., Liu, W., He, F., & Xie, H. (2015) · Science China Life Sciences · doi:10.1007/s11427-014-4766-3 · Cited by 9
Lang, P. F., Chebaro, Y., Zheng, X., Sekar, J. A. P., Shaikh, B., Natale, D., & Karr, J. R. (2019) · Genome Biology · doi:10.1186/s13059-020-02025-z · Cited by 7
Yan, G., Luna, A., Wang, H., Bozorgui, B., Li, X., Sanchez, M., Dereli, Z., Kahraman, N., Kara, G., Chen, X., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2022.111304 · Cited by 18
Self-citationHierarchical approaches for systems modeling in cardiac development
Gould, R. A., Aboulmouna, L., Varner, J. D., & Butcher, J. T. (2013) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1217 · Cited by 11
Rodchenkov, I. V., Demir, E., Sander, C., & Bader, G. D. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt452 · Cited by 9
“Summary: BioPAX is a community-developed standard language for biological pathway data.”
BackgroundSelf-citationComputational modeling of drug response with applications to neuroscience
Herwig, R. (2014) · Dialogues in Clinical Neuroscience · doi:10.31887/dcns.2014.16.4/rherwig · Cited by 8
“tejidos de los pacientes en varios niveles moleculares y ha dado lugar a un cambio de paradigma en la medicina hacia terapias personalizadas .”
Background
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
