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.
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Claims the paper makes
25 Not checked yet · 24 No basis given · 21 Own interpretation · 3 Own method
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
plain- Asserted: passes — The authors put it forward as true.
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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
“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
plaindirect- Asserted: passes — The authors put it forward as true.
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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 solves this problem by making pathway data substantially easier to collect, index, interpret and share.”
§ BioPAX – A community standard for pathway data sharing > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
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In 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
plaindirect- Asserted: passes — The authors put it forward as true.
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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
“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
plaindirect- Asserted: passes — The authors put it forward as true.
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In 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
plain- Asserted: passes — The authors put it forward as true.
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In 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
plain- Asserted: passes — The authors put it forward as true.
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In 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
hedged- Asserted: passes — The authors put it forward as true.
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In 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
plain- Asserted: passes — The authors put it forward as true.
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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
“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
plaindirect- Asserted: passes — The authors put it forward as true.
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- 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
plain- Asserted: passes — The authors put it forward as true.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
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Probably 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?
plain- Asserted: passes — The authors put it forward as true.
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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
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
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Probably 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?
plain- Asserted: passes — The authors put it forward as true.
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Probably 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?
plaindirect- Asserted: passes — The authors put it forward as true.
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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
plain- Asserted: passes — The authors put it forward as true.
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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?
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably 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?
plain- Asserted: passes — The authors put it forward as true.
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Probably 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?
plaindirect- Asserted: passes — The authors put it forward as true.
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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?
plain- Asserted: passes — The authors put it forward as true.
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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?
plaindirect- Asserted: passes — The authors put it forward as true.
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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
plaincorrelational- Asserted: passes — The authors put it forward as true.
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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
plain- Asserted: passes — The authors put it forward as true.
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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?
plain- Asserted: passes — The authors put it forward as true.
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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
plain- Asserted: passes — The authors put it forward as true.
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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
plaincorrelational- Asserted: passes — The authors put it forward as true.
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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
plain- Asserted: passes — The authors put it forward as true.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
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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?
plain- Asserted: passes — The authors put it forward as true.
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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
plaindirect- Asserted: passes — The authors put it forward as true.
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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?
plaindirect- Asserted: passes — The authors put it forward as true.
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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
plain- Asserted: passes — The authors put it forward as true.
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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?
plain- Asserted: passes — The authors put it forward as true.
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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?
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
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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?
plaindirect- Asserted: passes — The authors put it forward as true.
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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
plaindirect- Asserted: passes — The authors put it forward as true.
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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
plain- Asserted: passes — The authors put it forward as true.
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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
“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
plaindirect- Asserted: passes — The authors put it forward as true.
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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
“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
plaindirect- Asserted: passes — The authors put it forward as true.
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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
“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
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
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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 (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
plain- Asserted: passes — The authors put it forward as true.
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Probably 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
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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Probably 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
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
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Probably 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
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
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Probably 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
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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- Based: passes — The paper gives a reason why it holds.
Probably 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?
plaindirect- Asserted: passes — The authors put it forward as true.
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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
“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?
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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Probably 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?
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably 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?
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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?
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a 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
“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?
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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- Based: passes — The paper gives a reason why it holds.
Probably 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
Cited by
Sorted by citations
Items 401–500 of 755
Prospects for Declarative Mathematical Modeling of Complex Biological Systems
Mjolsness, E. (2019) · Bulletin of Mathematical Biology · doi:10.1007/s11538-019-00628-7 · Cited by 14
Systems Biology Markup Language (SBML)
Hucka, M. (2013) · Springer eBooks · doi:10.1007/978-1-4419-9863-7_1091 · Cited by 11
Self-citationComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databasesPreprint
Domingo‐Fernándéz, D., Hoyt, C. T., Bobis-Álvarez, C., Marín-Llaó, J., & Hofmann‐Apitius, M. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/353235 · Cited by 9
Enhancing link prediction in biomedical knowledge graphs with BioPathNet
Hu, E. Y., Oleshko, S., Firmani, S., Cheng, H. G., Zhu, Z., Wörheide, M. A., Arnold, M., Colomé‐Tatché, M., Tang, J., Xhonneux, S., et al. (2026) · Nature Biomedical Engineering · doi:10.1038/s41551-025-01598-z · Cited by 23
“C) interactions obtained from Pathway Commons (G2) 59,60 .”
Track 4 Overview: Extraction of Causal Network Information in Biological Expression Language (BEL)
Fluck, J., Madan, S., Ellendorff, T., et al. (2015) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-116469 · Cited by 8
“Well-known examples of methods to formally represent biological networks are the Systems Biology Markup Language (SBML) [1], the Biological pathway exchange language (BioPAX) [2] and the Biological Expression Language(1) (BEL) [3].”
MethodComputational Synthetic Biology: Progress and the Road Ahead
Myers, C. J. (2015) · IEEE Transactions on Multi-Scale Computing Systems · doi:10.1109/tmscs.2015.2478442 · Cited by 8
Higareda‐Almaraz, J. C., Valtierra-Gutiérrez, I. A., Hernández‐Ortíz, M., Contreras, S., Hernandez, E., & Encarnación‐Guevara, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065433 · Cited by 8
“The PID batch query yielded 64 pathways curated in the Biopax level 3 format [40], which displayed an increased amount of interconnections and crosstalk among their cellular circuits.”
MethodSpecifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
Schreiber, F., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Keating, S. M., Novère, N. L., Myers, C., Nickerson, D., Sommer, B., et al. (2018) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2018-0013 · Cited by 9
“BioPAX (Biological Pathway Exchange) [9] is a format in the Web Ontology Language, to store biological pathways and support the exchange, integration and analysis of biological pathway data.”
BackgroundSelf-citationSpecifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
Schreiber, F., Sommer, B., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., et al. (2019) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2019-0035 · Cited by 15
Self-citationUsing BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data
Agapito, G., & Cannataro, M. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04297-z · Cited by 8
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
Novère, N. G. L., Hucka, M., Anwar, N., Bader, G. D., Demir, E., Moodie, S., & Sorokin, A. (2011) · Standards in Genomic Sciences · doi:10.4056/sigs.2034671 · Cited by 8
“Emek Demir presented the problem of integrating pathways derived from many different data resources , and how Pathway Commons [42,43] aims to tackle the problem with the help of BioPAX [2,44].”
BackgroundSelf-citationMyers, C. J., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Novère, N. G. L., Nickerson, D. P., Schreiber, F., & Waltemath, D. (2017) · Winter Simulation Conference · doi:10.1109/wsc.2017.8247840 · Cited by 10
Self-citationBenchmarking infrastructure for mutation text mining
Klein, A., Riazanov, A., Hindle, M., & Baker, C. J. O. (2014) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-5-11 · Cited by 8
“For example, it is the basis of the BIOPAX [41] format for representing biological pathway data.”
BackgroundExtracting Biological Pathway Models From NLP Event Representations
Spranger, M., Palaniappan, S. K., & Ghosh, S. (2015) · doi:10.18653/v1/w15-3805 · Cited by 8
Construction of Cell Type-Specific Logic Models of Signaling Networks Using CellNOpt
Morris, M. K., Melas, I. N., & Sáez-Rodríguez, J. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-059-5_8 · Cited by 9
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Ramirez-Gaona, M., Marcu, A., Pon, A., Grant, J., Wu, A., & Wishart, D. S. (2017) · Journal of Visualized Experiments · doi:10.3791/54869 · Cited by 8
König, M., Gleeson, P., Golebiewski, M., Gorochowski, T. E., Hucka, M., Keating, S. M., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., et al. (2023) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2023-0004 · Cited by 6
Self-citationPractical Use of BiNoM: A Biological Network Manager Software
Bonnet, É., Calzone, L., Rovera, D., et al. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-450-0_7 · Cited by 7
“Examples of such community standards are the System Biology Markup Language (SBML) [3], a language focused on mathematical modeling, the Biological Pathway Exchange standard (BioPAX) [4], devoted to storing and exchange of pathway information and the Systems Biology Graphical Notation (SBGN), centered on the graphical…”
BackgroundMethodBioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution
Psomopoulos, F. E., Vitsios, D., Baichoo, S., & Ouzounis, C. A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btw813 · Cited by 7
Cheminformatics and Bioinformatics at the Interface with Systems Biology
Kaushik, A. C., Mehmood, A., Wei, D., Nawab, S., Sahi, S., & Kumar, A. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/9781839166037 · Cited by 7
Module Extraction for Efficient Object Queries over Ontologies with Large ABoxes
Xu, J., Shironoshita, P., Visser, U., et al. (2015) · Artificial Intelligence and Applications · doi:10.15764/aia.2015.01002 · Cited by 7
“In recent years, DL ontologies have been increasingly applied in the development of DL-based information systems in diverse areas, including biomedical research [4, 5], health care [6, 7], decision support [8, 9], and many others; see [10] for a review of existing applications.”
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations
Chandan, K., van Iersel, M., Aladjem, M. I., Kohn, K. W., & Luna, A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr694 · Cited by 7
Self-citationConverting Alzheimer’s Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data
Henry, V., Moszer, I., Dameron, O., Potier, M., Hofmann‐Apitius, M., & Olivier Colliot, A. (2018) · Lecture notes in computer science · doi:10.1007/978-3-030-06016-9_20 · Cited by 7
“Different RDF schemas were already developed in the field of molecular biology (BioPax [17]) or more specifically for AD biomedical research (neuroRDF [18]).”
BackgroundInteractive Multiresolution Visualization of Cellular Network Processes
Ortega, O. O., & Lopez, C. F. (2019) · iScience · doi:10.1016/j.isci.2019.100748 · Cited by 7
Exploring Networks in the STRING and Reactome Database
Koutrouli, M., Hatzis, P., & Pavlopoulos, G. A. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11516-8 · Cited by 9
AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation
Csabai, L., Bohár, B., Türei, D., Prabhu, S. R., Földvári-Nagy, L., Madgwick, M., Fazekas, D., Módos, D., Olbei, M. L., Halka, T., et al. (2023) · Autophagy · doi:10.1080/15548627.2023.2247737 · Cited by 8
“We provide a large range of widely used file formats to choose from during the down-load process, including simple CSV to analyze the data as text file or in Excel as well as in standardized computational file formats such as BioPAX [44] and PSI-MI Tab [45].”
MethodGiannantoni, L., Bardini, R., Savino, A., & Carlo, S. D. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05782-x · Cited by 7
“Some of the COMBINE DSLs specialize in intracellular pathways, such as BioPAX [37], and processes, such as Systems Biology Graphical Notation (SBGN) [38], SBML [31] and CellML [39].”
MethodLeveraging Modeling Approaches: Reaction Networks and Rules
Blinov, M. L., & Moraru, I. I. (2011) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-7210-1_30 · Cited by 7
“Standards like Systems Biology Markup Language (SBML, [37]), Systems Biology Graphical Notations (SBGN, [25]), and Biological PAthway eXchange (BioPAX, [38]) are already widely used to provide exchange of models, visualization schemas, and pathway data, respectively.”
Self-citationMultimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation
Kirik, U., Cifani, P., Albrekt, A.-S., Lindstedt, M., Heyden, A., & Levander, F. (2012) · Journal of Proteome Research · doi:10.1021/pr300038b · Cited by 7
Junker, A., Rohn, H., & Schreiber, F. (2012) · Frontiers in Plant Science · doi:10.3389/fpls.2012.00252 · Cited by 7
“, roles, functions); hard to edit manually Demir et al. (2010)”
BackgroundSig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format
Webb, R. L., & Ma’ayan, A. (2011) · Source Code for Biology and Medicine · doi:10.1186/1751-0473-6-5 · Cited by 7
A Validator and Converter for the Synthetic Biology Open Language
Zundel, Z., Samineni, M., Zhang, Z., et al. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.6b00277 · Cited by 7
The Medical Knowledge Cockpit: Real-time analysis of big medical data enabling precision medicine
Schapranow, M.-P., Kraus, M., Perscheid, C., et al. (2015) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2015.7359783 · Cited by 7
(2017) · doi:10.18653/v1/w17-23 · Cited by 8
Babaiha, N. S., Elsayed, H., Zhang, B., Kaladharan, A., Sethumadhavan, P., Schultz, B. T., Klein, J., Freudensprung, B., Lage‐Rupprecht, V., Kodamullil, A. T., et al. (2023) · Artificial Intelligence in the Life Sciences · doi:10.1016/j.ailsci.2023.100078 · Cited by 7
Bioinformatics Methods for Constructing Metabolic Networks
Petrovskiy, D. V., Malsagova, K. A., Rudnev, V. R., Kulikova, L. I., Pustovoyt, V. I., Balakin, E. I., Yurku, K. A., & Kaysheva, A. L. (2023) · Processes · doi:10.3390/pr11123430 · Cited by 6
MetSim: Integrated Programmatic Access and Pathway Management for Xenobiotic Metabolism Simulators
Groff, L. C., Williams, A. J., Shah, I., et al. (2024) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.3c00398 · Cited by 6
Self-citationRDFBuilder: A tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources
Anguita, A., Martín, L., García-Remesal, M., & Maojo, V. (2013) · Computer Methods and Programs in Biomedicine · doi:10.1016/j.cmpb.2013.04.009 · Cited by 6
Deb, B., George, I. A., Sharma, J. N., & Kumar, P. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9744-2_10 · Cited by 6
SAMMI: a semi-automated tool for the visualization of metabolic networks
Schultz, A., & Akbani, R. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz927 · Cited by 6
Marc, M., Juigné, C., Dameron, O., et al. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac013 · Cited by 6
“It relies on the following ontologies: • Biological Pathway Exchange (BioPAX) is an ontology developed as a standard for representing molecular interactions, including protein-protein interactions (Demir et al. , 2010).”
BackgroundComputing optimal factories in metabolic networks with negative regulation
Krieger, S., & Kececioglu, J. D. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac231 · Cited by 6
García-Godoy, M. J., Navas‐Delgado, I., & Aldana-Montes, J. F. (2011) · Semantic Web Applications and Tools for Life Sciences · doi:10.1145/2166896.2166906 · Cited by 6
“To do this, we have used Relfinder [38] that extracts and visualizes the objects from RDF data.”
MethodOSNAP! Introducing the open semantic network analysis platform
Radics, P. J., Polys, N. F., Neuman, S. P., et al. (2015) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.2077834 · Cited by 6
Architecture for interoperable software in biology
Bare, J. C., & Baliga, N. S. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs074 · Cited by 6
“Toward the more structured end of this spectrum are Semantic Web formats including Gene Ontology [27] and BioPAX [28].”
BackgroundGFVO: the Genomic Feature and Variation Ontology
Baran, J., Durgahee, B. S. B., Eilbeck, K. L., Antezana, E., Hoehndorf, R., & Dumontier, M. (2015) · PeerJ · doi:10.7717/peerj.933 · Cited by 5
Modeling biological complexity using Biology System Description Language (BiSDL)
Muggianu, F., Benso, A., Bardini, R., Hu, E., Politano, G. M. M., & Carlo, S. D. (2018) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2018.8621533 · Cited by 7
Wang, J., Li, F., Xu, Y., Zheng, X., Zhang, C., Hu, C., Xu, Y., Mi, W., Li, X., & Zhang, Y. (2021) · Journal of Translational Medicine · doi:10.1186/s12967-021-02962-8 · Cited by 6
Multipath: An R Package to Generate Integrated Reproducible Pathway Models
Hammoud, Z., & Krämer, F. (2020) · Biology · doi:10.3390/biology9120483 · Cited by 6
“In this paper, we present the R package Multipath that creates these multilayer extendable models from BioPAX-encoded pathway files [2], and extract influencing knowledge from external databases.”
MethodHumanMine: advanced data searching, analysis and cross-species comparison
Lyne, R., Bazaga, A., Butano, D., et al. (2022) · Database · doi:10.1093/database/baac054 · Cited by 6
“InterMine is able to integrate data from a wide variety of sources in various biological formats, including GFF3, FASTA, VCF, OBO, BioPAX (18), GAF, PSI (19) and Chado (20) and includes a powerful identifier resolution system such that any outdated identifiers from a dataset are mapped to the current ones.”
BackgroundInfluentialSemantic Breakthrough in Drug Discovery
Chen, B., Wang, H., Ding, Y., & Wild, D. J. (2015) · Synthesis lectures on data, semantics and knowledge · doi:10.1007/978-3-031-79456-8 · Cited by 8
Jo, K., Santos-Buitrago, B., Kim, M., et al. (2020) · Methods · doi:10.1016/j.ymeth.2020.05.008 · Cited by 6
Logic modeling and the ridiculome under the rug
Blinov, M. L., & Moraru, I. I. (2012) · BMC Biology · doi:10.1186/1741-7007-10-92 · Cited by 6
“A lot of information has been already assembled and curated into what we call canonical prior knowledge (well characterized fully referenced data stored in electronic exchange formats such as BioPAX [13]), which can be used as a starting point for models.”
BackgroundSelf-citationLou, P., Wang, C., Guo, R. R., Yao, L., Zhang, G., Yang, J., Yuan, Y., Dong, Y., Gao, Z., Gong, T., et al. (2022) · Scientific Data · doi:10.1038/s41597-022-01505-0 · Cited by 6
Path-based reasoning for biomedical knowledge graphs with BioPathNetPreprint
Hu, Y., Oleshko, S., Firmani, S., Zhu, Z., Cheng, H., Wörheide, M. A., Arnold, M., Colomé‐Tatché, M., Tang, J., Xhonneux, S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.17.599219 · Cited by 7
“Additionally, we utilized a BRG containing regulatory relationships between gene-gene (G-G), gene-chemical (G-C), and chemical-771 chemical (C-C) obtained from Pathway Commons (G2)[52, 53].”
Cheminformatics for genome-scale metabolic reconstructions
May, J. W. (2015) · Apollo (University of Cambridge) · doi:10.17863/cam.15987 · Cited by 6
“The BioPax [25] standard is also notable but is mainly used for the exchange of pathway information.”
BackgroundMethodLabbassi, S., Tahiri, A., Mimouni, A., et al. (2024) · Genetic Resources and Crop Evolution · doi:10.1007/s10722-024-02047-7 · Cited by 5
“Data concerning the genetic diversity of wild and cultivated plants holds significant value in the species identification, conservation efforts, and breeding programs (Demir et al. 2010).”
KGG: a fully automated workflow for creating disease-specific knowledge graphs
Karki, R., Gadiya, Y., Zaliani, A., Pokharel, B. K., Babaiha, N. S., Ostaszewski, M., Hofmann‐Apitius, M., & Gribbon, P. M. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf383 · Cited by 5
“The advent of systems biology has led to a number of tools and frameworks such as CellDesigner (Funahashi et al. 2006), OpenBEL (Slater 2014), BioPAX (Demir et al. 2010), and SBML (Hucka et al. 2003) for modeling complex biological phenomena.”
Building immune digital twins: An international and transdisciplinary community effort
Niarakis, A., An, G. C., Ladeira, L., Hiroi, N. F., Papadopoulou, A., Crawley, F. P., Nikaein, N., Calzone, L., Tsirvouli, E., Balcı, H., et al. (2025) · ImmunoInformatics · doi:10.1016/j.immuno.2025.100060 · Cited by 5
Self-citationOrganic Synthesis as Artificial Intelligence Planning
Masoumi, A., Soutchanski, M., & Marrella, A. (2013) · Cited by 5
Agapito, G., Pastrello, C., Niu, Y., & Jurišica, I. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac368 · Cited by 5
Understanding molecular signaling cascades in neural disease using multi-resolution models
Viswan, N. A., & Bhalla, U. S. (2023) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2023.102808 · Cited by 5
The BioRECIPE Knowledge Representation Format
Holtzapple, E., Zhou, G. Y., Luo, H., et al. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00096 · Cited by 5
Leveraging public AI tools to explore systems biology resources in mathematical modeling
Kannan, M., Bridgewater, G., Zhang, M., & Blinov, M. L. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00496-z · Cited by 5
“The BioPAX and SBGN fi les of the EGFR pathway (Supplementary Notes 2 and 4, respectively) were downloaded from the Reactome database (https://reactome.org/ content/detail/R-HSA-177922).”
InfluentialSelf-citationBioPARKIN — Biology-related Parameter Identification in Large Kinetic Networks
Dierkes, T., Wade, M., Nowak, U., et al. (2011) · Cited by 5
Ontologies in bioinformatics and systems biology
Podkolodnyy, N. L., & Podkolodnaya, O. A. (2016) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vj15.090 · Cited by 5
Karki, R., Kodamullil, A. T., Hoyt, C. T., & Hofmann‐Apitius, M. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3101-1 · Cited by 5
Large-scale regulatory and signaling network assembly through linked open data
Lefebvre, M., Gaignard, A., Folschette, M., et al. (2020) · Database · doi:10.1093/database/baaa113 · Cited by 5
“In particular, PC leverages the BioPAX ontology (17) to provide a standard and uniform view of these multiple and diverse databases.”
BackgroundPyBioPAX: biological pathway exchange in Python
Gyori, B. M., & Hoyt, C. T. (2022) · The Journal of Open Source Software · doi:10.21105/joss.04136 · Cited by 5
“BioPAX (Demir et al., 2010) is a widely used pathway exchange format that is formally defined in the BioPAX Language Specification.”
MethodModelling Methodologies for Systems Biology
Singh, V. (2014) · Springer eBooks · doi:10.1007/978-94-017-9514-2_3 · Cited by 5
A Modular Inference System for Probabilistic Description Logics
Cota, G., Riguzzi, F., Zese, R., et al. (2018) · Lecture notes in computer science · doi:10.1007/978-3-030-00461-3_6 · Cited by 5
“Test 1 The first test considers 4 real world KBs of various complexity as in [27]: (1) BRCA [11], which models the risk factors of breast cancer; (2) an extract of DBPedia(8) [13], containing structured information from Wikipedia, usually those contained in the information box on the righthand side of pages; (3) Biopa…”
BackgroundMochão, H., Barahona, P., & Costa, R. S. (2020) · Database · doi:10.1093/database/baaa093 · Cited by 5
“For storing mathematical models, SBML is the most common standard, and it is based on XML. CellML (19), also based on XML, Biological Pathway Exchange (20) and MATLAB are other popular languages to store and deal with computational models in systems biology.”
Li, M., He, Q., Yang, C., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-07827-4 · Cited by 5
“BioPAX [10] is a pathway exchange language for biological pathway data.”
BackgroundIntegrating Military Systems using Semantic Web Technologies and Lightweight Agents
Halvorsen, J., & Hansen, B. J. (2011) · Cited by 5
HINO: a BFO-aligned ontology representing human molecular interactions and pathwaysPreprint
He, Y. O., & Xiang, Z. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1311.3355 · Cited by 5
Two Decades of Biological Pathway Databases: Results and Challenges
Rahmati, S., Pastrello, C., Rossos, A. E. M., & Jurišica, I. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20496-2 · Cited by 5
CHEMINFORMATICS TOOLS FOR ENABLING METABOLOMICS
Djoumbou-Feunang, Y. (2017) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3vd6pj8b · Cited by 5
A resource for the comparison and integration of heterogeneous microbiome networksPreprint
Hu, Z., Kishore, D., Wang, Y., Bîrzu, G., DeLisi, C., Korolev, K. S., & Segrè, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.07.503059 · Cited by 6
“…for interactions and networks, including the HUPO PSI's molecular interaction format (PSI-MI) [81], Biological Pathways Exchange format (BioPAX) [82], and Systems Biology Markup Language (SBML) [83], as well as ones for the metadata in the metagenomic studies, such as the minimum information…”
BackgroundSelf-citationUpdates implemented in version 4 of the GlyCosmos Glycoscience Portal
Lee, S., Ono, T., Masaaki, S., Fujita, A., Matsubara, M., Zappa, A., Yamada, I., & Aoki-Kinoshita, K. F. (2024) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-024-05692-0 · Cited by 3
A Practical Guide to Reproducible Modeling for Biochemical Networks
Porubsky, V. L., & Sauro, H. M. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3008-2_5 · Cited by 4
Data integration strategies for whole-cell modeling
Tummler, K., & Klipp, E. (2024) · FEMS Yeast Research · doi:10.1093/femsyr/foae011 · Cited by 4
“T he COMBINE standards ( https://co.mbine .org/) comprise a series of modeling formats , i.e . next to SBML also BioPax (Demir et al. 2010 ) as a language to integrate , analyze , and exchange pathway data, CellML (Clerx et al. 2020 ) to store and exchange computer-based mathematical models, Synthetic Biology Open Lan…”
BackgroundIntegrating Human Genome Variation Data: An Information System Approach
Martín, A., & Celma, M. (2011) · International Workshop on Database and Expert Systems Applications (DEXA) · doi:10.1109/dexa.2011.45 · Cited by 4
“These proposals cover partial aspects of the domain and they are difficult to integrate [8] [9] [10].”
BackgroundReverse engineering molecular hypergraphs
Rahman, A., Poirel, C. L., Badger, D. J., & Murali, T. M. (2012) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/2382936.2382945 · Cited by 4
“Many databases and interaction storage formats support hyperedges of different types, either explicitly or implicitly [6, 20].”
BackgroundA dedicated database system for handling multi-level data in systems biology
Pornputtapong, N., Wanichthanarak, K., Nilsson, A., Nookaew, I., & Nielsen, J. C. O. (2014) · Source Code for Biology and Medicine · doi:10.1186/1751-0473-9-17 · Cited by 6
“The major design of the conceptual data structure that characterizes data in systems biology was adapted from the BioPAX ontology.”
BackgroundInfluentialControlled annotations for systems biology.
Juty, N., Laibe, C., & Novère, N. L. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-450-0_12 · Cited by 4
Genome-scale model management and comparison.
Pabinger, S., & Trajanoski, Z. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-299-5_1 · Cited by 4
Ontologies in bioinformatics and systems biology
Podkolodnyy, N. L., & Podkolodnaya, O. A. (2016) · Russian Journal of Genetics Applied Research · doi:10.1134/s2079059716070091 · Cited by 4
“org), a format for the description and integration of information about molecular interactions and biological processes (Demir et al., 2010).”
BackgroundStandards, Platforms, and Applications
Gu, S., & Sauro, H. M. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-405926-9.00008-3 · Cited by 4
Hierarchical sequence labeling for extracting BEL statements from biomedical literature
Liu, S., Shao, Y., Qian, L., et al. (2019) · BMC Medical Informatics and Decision Making · doi:10.1186/s12911-019-0758-3 · Cited by 4
Belz, A., Hoile, R., Ford, E. M., & Mullick, A. (2019) · Workshop on Noisy User-generated Text (W-NUT) · doi:10.18653/v1/d19-5526 · Cited by 4
“Structured information resources in health informatics range from ordered lists of terms, glos-saries and medical thesauri (MeSH 5 , UMLS (Bo-denreider, 2004)), to ontologies like SNOMED CT (Donnelly, 2006) and BioPax (Demir et al., 2010).”
BackgroundSpecifications of standards in systems and synthetic biology: status and developments in 2021
Schreiber, F., Gleeson, P., Golebiewski, M., Gorochowski, T., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., Sommer, B., et al. (2021) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2021-0026 · Cited by 6
Self-citationSemantic Breakthrough in Drug Discovery
Chen, B., Wang, H., Ding, Y., & Wild, D. J. (2014) · Synthesis lectures on the semantic web · doi:10.2200/s00600ed1v01y201409web009 · Cited by 5
A parallel software pipeline to select relevant genes for pathway enrichment
Agapito, G., & Cannataro, M. (2022) · Proceedings - Euromicro Workshop on Parallel and Distributed Processing/Proceedings · doi:10.1109/pdp55904.2022.00041 · Cited by 4
Graph algorithms for predicting subcellular localization at the pathway level
Magnano, C. S., & Gitter, A. (2022) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789811270611_0014 · Cited by 4
“Pathways were downloaded from Pathway Commons, and localization information was retrieved from BioPax pathway representations using the PyBioPax package v0.”
Nezamuldeen, L., & Jafri, M. S. (2023) · Biology · doi:10.3390/biology12101344 · Cited by 5
“With reference to the available PPI databases, such as BioPAX [2], Pathway Commons [3], and CausalPath [4], discovering the most recent form of interactions between proteins and other elements remains difficult [5].”
MethodNishida, K., Maruyama, J., Kaizu, K., Takahashi, K., & Yugi, K. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00342-8 · Cited by 4
Current Challenges in Modeling Cellular Metabolism
Sonnenschein, N., Zhuang, K. H., Machado, D., & Herrgård, M. J. (2016) · Frontiers research topics · doi:10.3389/978-2-88919-754-5 · Cited by 4
Henry, V., Saïs, F., Inizan, O., et al. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03637-9 · Cited by 4
“Other bio-ontologies present a more generic paradigm, such as Biology Pathway Exchange (BioPAX) ontology [18], offering a language to represent pathways at the molecular and cellular level.”
BackgroundMethodInfluentialOverview: Standards for Modeling in Systems Medicine
Dräger, A., & Waltemath, D. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816077-0.00001-7 · Cited by 3
Ancestral state reconstruction of metabolic pathways across pangenome ensembles
Psomopoulos, F. E., van Helden, J., Médigue, C., Chasapi, A., & Ouzounis, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000429 · Cited by 4
“The metabolic pathway under study is represented by a BioPAX file [27].”
Influential
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 ›
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