Cited by 755Bioinformatics and Genomic NetworksBiomedical Text Mining and OntologiesScientific Computing and Data Management

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 access

Demir, Emek, Cary, Michael P, Paley, Suzanne, Fukuda, Ken, Lemer, Christian, Vastrik, Imre, Wu, Guanming, D'Eustachio, Peter, Schaefer, Carl, Luciano, Joanne, Schacherer, Frank, Martinez-Flores, Irma, Hu, Zhenjun, Jimenez-Jacinto, Veronica, Joshi-Tope, Geeta, Kandasamy, Kumaran, Lopez-Fuentes, Alejandra C, Mi, Huaiyu, Pichler, Elgar, Rodchenkov, Igor, Splendiani, Andrea, Tkachev, Sasha, Zucker, Jeremy, Gopinath, Gopal, Rajasimha, Harsha, Ramakrishnan, Ranjani, Shah, Imran, Syed, Mustafa, Anwar, Nadia, Babur, Özgün, Blinov, Michael, Brauner, Erik, Corwin, Dan, Donaldson, Sylva, Gibbons, Frank, Goldberg, Robert, Hornbeck, Peter, Luna, Augustin, Murray-Rust, Peter, Neumann, Eric, Ruebenacker, Oliver, Samwald, Matthias, van Iersel, Martijn, Wimalaratne, Sarala, Allen, Keith, Braun, Burk, Whirl-Carrillo, Michelle, Cheung, Kei-Hoi, Dahlquist, Kam, Finney, Andrew, Gillespie, Marc, Glass, Elizabeth, Gong, Li, Haw, Robin, Honig, Michael, Hubaut, Olivier, Kane, David, Krupa, Shiva, Kutmon, Martina, Leonard, Julie, Marks, Debbie, Merberg, David, Petri, Victoria, Pico, Alex, Ravenscroft, Dean, Ren, Liya, Shah, Nigam, Sunshine, Margot, Tang, Rebecca, Whaley, Ryan, Letovksy, Stan, Buetow, Kenneth H, Rzhetsky, Andrey, Schachter, Vincent, Sobral, Bruno S, Dogrusoz, Ugur, McWeeney, Shannon, Aladjem, Mirit, Birney, Ewan, Collado-Vides, Julio, Goto, Susumu, Hucka, Michael, Le Novère, Nicolas, Maltsev, Natalia, Pandey, Akhilesh, Thomas, Paul, Wingender, Edgar, Karp, Peter D, Sander, Chris, Bader, Gary D·2010·Nature Biotechnology

DOI 10.1038/nbt.1666PMC PMC3001121

Open this paper in CoChat — free account Open PDF

Abstract

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.

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

Crossref · 10.1038/nbt.1666

Cites

85 of 85 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 43 cited sources checked · 0 supported · 0 flagged

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
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
Strength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes

Show all 20 claims

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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“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
- Not checked yetcites [8] Matthews, L. et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37, D619–D622 (2009). source
- Not checked yetcites [9] Schaefer, C.F. et al. PID: the Pathway Interaction Database. Nucleic Acids Res. 37, D674–D679 (2009). source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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, 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably 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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“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
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
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 calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.

53 of 53

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.”

7 of 7

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?

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
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
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’.”
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
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

Show all 84 references

Sorted by citations

Items 101–200 of 755

INOH: ontology-based highly structured database of signal transduction pathways
Yamamoto, S., Sakai, N., Nakamura, H., Fukagawa, H., Fukuda, K., & Takagi, T. (2011) · Database · doi:10.1093/database/bar052 · Cited by 74
Self-citation
Data Sharing: Convert Challenges into Opportunities
Figueiredo, A. S. (2017) · Frontiers in Public Health · doi:10.3389/fpubh.2017.00327 · Cited by 75
“…scientists can exchange data using standardized data tables for Systems Biology (SBTab) (19), and models using Systems Biology Markup Language (SBML) (20) or Biological Pathway Exchange (BioPax) (21) and can visualize the biological network using Systems Biology Graphical Notation (22) standards.”
Method
Figshare: a universal repository for academic resource sharing?
Thelwall, M. A., & Kousha, K. (2016) · Online Information Review · doi:10.1108/oir-06-2015-0190 · Cited by 75
“For example, identifying diseases from brain scans requires access to large numbers of healthy and diseased examples obtained from organised data sharing (Poline et al. 2012) using common standards (e.g., Demir et al., 2010).”
Background
Case study: the role of mechanistic network models in systems toxicology
Hoeng, J., Talikka, M., Martin, F. P., Sewer, A., Yang, X., Iskandar, A. R., Schlage, W. K., & Peitsch, M. C. (2013) · Drug Discovery Today · doi:10.1016/j.drudis.2013.07.023 · Cited by 70
Modeling and Simulation Using CellDesigner
Matsuoka, Y., Funahashi, A., Ghosh, S., & Kitano, H. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0805-9_11 · Cited by 75
Integrated Enrichment Analysis of Variants and Pathways in Genome-Wide Association Studies Indicates Central Role for IL-2 Signaling Genes in Type 1 Diabetes, and Cytokine Signaling Genes in Crohn's Disease
Carbonetto, P. S., & Stephens, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003770 · Cited by 68
“We aim for a comprehensive evaluation of pathways accessible on the Web in standard, computer-readable formats [63,64,145].”
Background
Challenges in structural approaches to cell modeling
Im, W., Liang, J., Olson, A. J., Zhou, H., Vajda, S., & Vakser, I. A. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.05.024 · Cited by 70
Updates in Rhea—An expert curated resource of biochemical reactions
Morgat, A., Lombardot, T., Axelsen, K. B., Aimo, L., Niknejad, A., Hyka-Nouspikel, N., Coudert, E., Pozzato, M., Pagni, M., Moretti, S., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw990 · Cited by 65
“Reaction data in BioPax2 (24), RXN (25) and CMLReact (26) formats can also be obtained using RESTful web services at http://www.rhea-db. org/webservice.”
Method
The 5-Hydroxytryptamine signaling map: an overview of serotonin-serotonin receptor mediated signaling network
Sahu, A., Gopalakrishnan, L., Gaur, N., Chatterjee, O., Mol, P., Modi, P. K., Dagamajalu, S., Advani, J., Jain, S., & Prasad, T. S. K. (2018) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-018-0482-2 · Cited by 73
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering
McLaughlin, J. A., Beal, J., Mısırlı, G., Grünberg, R., Bartley, B., Scott-Brown, J., Vaidyanathan, P., Fontanarrosa, P., Oberortner, E., Wipat, A., et al. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.01009 · Cited by 69
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data
Kim, S., Cheng, T., He, S., Thiessen, P. A., Li, Q., Gindulytė, A., & Bolton, E. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167514 · Cited by 71
Large-scale automated machine reading discovers new cancer-driving mechanisms
Valenzuela-Escárcega, M. A., Babur, Ö., Hahn-Powell, G., Bell, D., Hicks, T., Noriega-Atala, E., Wang, X., Surdeanu, M., Demir, E., & Morrison, C. T. (2018) · Database · doi:10.1093/database/bay098 · Cited by 73
“The representation of these mentions is constructed internally in a format inspired by the BioPAX standard language (16).”
MethodSelf-citation
A multicellular signal transduction network of AGE/RAGE signaling
Soman, S., Raju, R., Sandhya, V. K., Advani, J., Khan, A. A., Gowda, H., Prasad, T. S. K., Sudhakaran, P. R., Pandey, A., & Adishesha, P. K. (2012) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-012-0181-3 · Cited by 64
Self-citation
Methods for automated genome-scale metabolic model reconstruction
Faria, J. P., Rocha, M., Rocha, I., & Henry, C. S. (2018) · Biochemical Society Transactions · doi:10.1042/bst20170246 · Cited by 64
A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis
Cheng, Y.-K., Beroukhim, R., Levine, R. L., Mellinghoff, I. K., Holland, E. C., & Michor, F. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002337 · Cited by 63
Integrating systems biology models and biomedical ontologies
Hoehndorf, R., Dumontier, M., Gennari, J. H., Wimalaratne, S., de Bono, B., Cook, D. L., & Gkoutos, G. V. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-124 · Cited by 60
“The Model Format Ontology (MFO) [12,51] further provides structural restrictions and constraints for the SBML and the BioPAX standard [7] is based on an ontology for representing pathways and reactions.”
BackgroundMethodSelf-citation
Automated assembly of molecular mechanisms at scale from text mining and curated databases
Bachman, J. A., Gyori, B. M., & Sorger, P. K. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211325 · Cited by 64
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases
Domingo‐Fernándéz, D., Hoyt, C. T., Bobis-Álvarez, C., Marín-Llaó, J., & Hofmann‐Apitius, M. (2018) · npj Systems Biology and Applications · doi:10.1038/s41540-018-0078-8 · Cited by 61
Precise generation of systems biology models from KEGG pathways
Wrzodek, C., Büchel, F., Ruff, M., Dräger, A., & Zell, A. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-15 · Cited by 60
“In systems biology, two wide-spread formats for modeling and exchanging pathways are the Systems Biology Markup Language (SBML) [5] and Biological Pathway Exchange (BioPAX) [6].”
Method
Integrated network analysis and effective tools in plant systems biology
Fukushima, A., Kanaya, S., & Nishida, K. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00598 · Cited by 61
Using Biological Pathway Data with Paxtools
Demir, E., Babur, Ö., Rodchenkov, I. V., Aksoy, B. A., Fukuda, K., Gross, B. E., Sumer, O., Bader, G. D., & Sander, C. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003194 · Cited by 60
“BioPAX (Biological Pathway Exchange) [9] a standard language developed by a community of pathway data providers, tool developers and scientists enables data exchange between data providers and acts as a common interface for software tools to access pathway data from multiple sources.”
BackgroundSelf-citation
Recent advances in modeling languages for pathway maps and computable biological networks
Slater, T. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2013.12.011 · Cited by 59
“17 Demir, E. et al. (2010) The BioPAX community standard for pathway data sharing.”
Background
A roadmap for the functional annotation of protein families: a community perspective
de Crécy‐Lagard, V., Amorín, R., Arighi, C. N., Babor, J. T., Bateman, A. G., Blaby, I. K., Blaby, C., Bridge, A. J., Burley, S. K., Cleveland, S., et al. (2022) · Database · doi:10.1093/database/baac062 · Cited by 58
“The BioPAX standardized language for sharing pathway data (77) is an example in this regard.”
Self-citation
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
Kuperstein, I., Cohen, D., Pook, S. L., Viara, E., Calzone, L., Barillot, E., & Zinovyev, A. Y. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-100 · Cited by 61
“These challenges inspired the creation of tools like CellDesigner [16], SBGN standard for graphical representation of biological diagrams [17] and SBML [18] and BioPAX standards for exchanging the content of biological pathway databases [19].”
Method
Platelet Proteomes, Pathways, and Phenotypes as Informants of Vascular Wellness and Disease
Aslan, J. E. (2021) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.120.314647 · Cited by 56
Improving Collaboration by Standardization Efforts in Systems Biology
Dräger, A., & Palsson, B. Ã. (2014) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2014.00061 · Cited by 60
“BioPAX The motivation for the creation of the BioPAX5 format (Biological Pathway Exchange) was the aim to unify the various co-existing pathway encoding formats of numerous online databases (Demir et al., 2010).”
Influential
Knowledge management for Systems Biology a general and visually driven framework applied to translational medicine
Maier, D., Kalus, W., Wolff, M., Kalko, S. G., Roca, J., de Mas, I. M., Turan, N., Cascante, M., Francesco Falciani, B., Ibáñez-Hernández, M. Á., et al. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-38 · Cited by 53
“Future directions include: support of additional structured languages for import and export such as BioPAX [48]and CellML [49]; development of a workflow framework for data analysis and integration of algorithmic methods for semantic mapping.”
Method
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., Okamoto, S., Kawano, S., Kim, J.-D., Wang, Y., et al. (2014) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-5-5 · Cited by 56
“PSICQUIC RDF output is based on the popular BioPAX format [21] for interactions and pathways.”
MethodSelf-citation
An overview of the oxytocin-oxytocin receptor signaling network
Chatterjee, O., Patil, K., Sahu, A., Gopalakrishnan, L., Mol, P., Advani, J., Mukherjee, S., Christopher, R., & Prasad, T. S. K. (2016) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-016-0353-7 · Cited by 55
GeneWalk identifies relevant gene functions for a biological context using network representation learning
Ietswaart, R., Gyori, B. M., Bachman, J. A., Sorger, P. K., & Churchman, L. S. (2021) · Genome biology · doi:10.1186/s13059-021-02264-8 · Cited by 51
A National, Semantic-Driven, Three-Pillar Strategy to Enable Health Data Secondary Usage Interoperability for Research Within the Swiss Personalized Health Network: Methodological Study
Gaudet-Blavignac, C., Raisaro, J. L., Touré, V., Österle, S., Crameri, K., & Lovis, C. (2021) · JMIR Medical Informatics · doi:10.2196/27591 · Cited by 54
“The reasons for choosing RDF technologies are summarized in Textbox 4 [43-47].”
Background
Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis
Stoll, G., Surdez, D., Tirode, F., Laud, K., Barillot, E., Zinovyev, A. Y., & Delattre, O. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt678 · Cited by 57
“Annotations from the fact-sheet can be read using the BiNoM plugin (BioPAX (38) annotation file is available at http://bioinfo-out.”
Method
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data
Kolpakov, F., Akberdin, I. R., Kashapov, T. A., Kiselev, L., Kolmykov, S. K., Kondrakhin, Y. V., Kutumova, E. O., Mandrik, N., Pintus, S. S., Ryabova, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz440 · Cited by 54
Combining computational models, semantic annotations and simulation experiments in a graph database
Henkel, R., Wolkenhauer, O., & Waltemath, D. (2015) · Database · doi:10.1093/database/bau130 · Cited by 50
“Many of these aspects have already been described in standard formats, including model structure (27–29), simulation descriptions (30), simulation results (31) and semantic annotations (32, 33, 34).”
Background
Signaling hypergraphs
Ritz, A., Tegge, A. N., Kim, H., Poirel, C. L., & Murali, T. M. (2014) · Trends in biotechnology · doi:10.1016/j.tibtech.2014.04.007 · Cited by 54
Simulation Frameworks for Morphogenetic Problems
Tanaka, S. (2015) · Computation · doi:10.3390/computation3020197 · Cited by 47
“The standard language (ontology) BioPAX (Biological Pathway Exchange) [137] focuses more on reaction network visualization and qualitative analysis.”
Background
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
Bonnet, É., Calzone, L., Rovera, D., Stoll, G., Barillot, E., & Zinovyev, A. Y. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-18 · Cited by 56
“The BioPAX format was primarily conceived as a standard facilitating the exchange of data between various database systems [8].”
BackgroundMethod
Tools for visualization and analysis of molecular networks, pathways, and -omics data
Habermann, B. H., Villaveces, J. M., & Koti, P. S. (2015) · Advances and Applications in Bioinformatics and Chemistry · doi:10.2147/aabc.s63534 · Cited by 54
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway
Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B., Thomas, J. K., Sharma, J. N., Rahiman, B. A., Gowda, H., et al. (2011) · Database · doi:10.1093/database/bar021 · Cited by 49
Self-citation
Domain‐mediated protein interaction prediction: From genome to network
Reimand, J., Hui, S., Jain, S., Law, B., & Bader, G. D. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.04.027 · Cited by 53
“Some describe highly structured biological pathway mechanisms, such as the BioPAX pathway representation standard [65].”
BackgroundSelf-citation
The pangenome of the genus C lostridium
Udaondo, Z., Duque, E., & Ramos, J. L. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13732 · Cited by 50
Towards quantitative measures in applied ontologyPreprint
Hoehndorf, R., Dumontier, M., & Gkoutos, G. V. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1202.3602 · Cited by 49
How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine
Waltemath, D., & Wolkenhauer, O. (2016) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2016.2555481 · Cited by 49
“Currently, COMBINE covers standards for models (CellML [30], SBML [31]), synthetic designs (SBOL [32]), and pathways (BioPAX [33]); for simulation descriptions”
Leveling the Playing Field: Bringing Development of Biomarkers and Molecular Diagnostics up to the Standards for Drug Development
Poste, G. H., Carbone, D. P., Parkinson, D. R., Verweij, J., Hewitt, S. M., & Jessup, J. M. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-2206 · Cited by 49
“BIOPAX (48) or SMBL (49), respectively.”
PathMe: merging and exploring mechanistic pathway knowledge
Domingo‐Fernándéz, D., Mubeen, S., Marín-Llaó, J., Hoyt, C. T., & Hofmann‐Apitius, M. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2863-9 · Cited by 51
Updates in Rhea—a manually curated resource of biochemical reactions
Morgat, A., Axelsen, K. B., Lombardot, T., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku961 · Cited by 48
“Rhea RESTful web services allow reactions to be retrieved in BioPAX level 2 (22), CMLReact (cmlreact) (24) or RXN CTfile (rxn) (23) formats by querying for their D ow naded rom http/academ ic.”
BackgroundMethod
IntPath--an integrated pathway gene relationship database for model organisms and important pathogens
Zhou, H., Jin, J., Zhang, H., Yi, B., Woźniak, M., & Wong, L. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-s2-s2 · Cited by 48
“Retrieving gene relationships from BioPAX files is mainly by using the Paxtools Java programming library [15] in combination with our own simple Java program.”
Method
Standardization in Synthetic Biology
Müller, K. M., & Arndt, K. M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-412-4_2 · Cited by 48
Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis
Lee, S., Mardinoğlu, A., Zhang, C., Lee, D., & Nielsen, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw462 · Cited by 49
“Identifying signaling hubs, based on an integrated network and a curated metabolic model In order to establish a comprehensive signaling network, six BioPAX (23)-formatted databases were integrated by using the Java library Paxtools (24) (the first step in Supplementary Figure S1).”
Method
Modelling the Structure and Dynamics of Biological Pathways
O’Hara, L., Livigni, A., Theo, T., Boyer, B., Angus, T., Wright, D., Chen, S.-H., Raza, S., Barnett, M. W., Digard, P., et al. (2016) · PLoS Biology · doi:10.1371/journal.pbio.1002530 · Cited by 49
“In mEPN, we currently list 40 types of processes that one might wish to define when constructing a pathway, including all of those associated with the BioPAX level 3 pathway exchange language [30].”
Background
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences
Ravikumar, K. E., Rastegar-Mojarad, M., & Liu, H. (2016) · Database · doi:10.1093/database/baw156 · Cited by 48
“We have standards for representing biological cascades/ pathways such as Systems Biology Ontology (29, 30), Biological pathway exchange language (BioPAX) (31), Systems Biology Mark Up Language (SBML) (32), and Systems Biology Graphical Notation (SBGN) (33).”
Method
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference
Alaimo, S., Bonnici, V., Cancemi, D., Ferro, A., Giugno, R., & Pulvirenti, A. (2015) · BMC Systems Biology · doi:10.1186/1752-0509-9-s3-s4 · Cited by 45
“We retrieve all pathways by downloading Bio-Pax [72] level 3 XML files from the Pathway-Commons web service, using PC2 [73] for the remote connection to the public database.”
Method
FAIRification of health-related data using semantic web technologies in the Swiss Personalized Health Network
Touré, V., Krauss, P., Gnodtke, K., Buchhorn, J., Unni, D. R., Horki, P., Raisaro, J. L., Kalt, K., Teixeira, D., Crameri, K., et al. (2023) · Scientific Data · doi:10.1038/s41597-023-02028-y · Cited by 46
Best Practices for Making Reproducible Biochemical Models
Porubsky, V. L., Goldberg, A. P., Rampadarath, A. K., Nickerson, D. P., Karr, J. R., & Sauro, H. M. (2020) · Cell Systems · doi:10.1016/j.cels.2020.06.012 · Cited by 45
“OpenCOR is a modeling environment, which can be used to simulate models described using CellML (Garny and Hunter, 2015).”
Background
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
Hoehndorf, R., Dumontier, M., & Gkoutos, G. V. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts350 · Cited by 46
“CTD uses MeSH identifiers to refer to drugs and diseases, and we do not add new classes but directly use the classes in our OWL representation of MeSH.”
Method
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps
Balcı, H., Siper, M. C., Saleh, N., et al. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa850 · Cited by 46
“With widely accepted standard formats such as BioPAX (Demir et al., 2010), SBGN (Le Novère et al., 2009) and SBML (Hucka et al., 2003), pathway databases such as Pathway Commons (Rodchenkov et al., 2020), Reactome (Croft et al., 2011) and WikiPathways (Slenter et al., 2018) are able to make this…”
MethodSelf-citation
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks
Csabai, L., Fazekas, D., Kadlecsik, T., Szalay-Bekő, M., Bohár, B., Madgwick, M., Módos, D., Olbei, M. L., Gul, L., Sudhakar, P., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab909 · Cited by 43
“SignaLink3 can be downloaded in many widely used formats such as CSV, PSIMITAB (41) or BioPAX (42).”
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies
Subramanian, S. L., Kitchen, R. R., Alexander, R. P., Carter, B. S., Cheung, K., Laurent, L. C., Pico, A. R., Roberts, L. R., Roth, M. E., Rozowsky, J. S., et al. (2015) · Journal of Extracellular Vesicles · doi:10.3402/jev.v4.27497 · Cited by 45
“Such knowledge is naturally represented in a machine-readable form using the network-based RDF formalism, as evidenced by databases such as WikiPathways (21) and BioPAX (22) that are now available in RDF form.”
MethodSelf-citation
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources
Bleda, M., Tárraga, J., de Maria, A., Salavert, F., García‐Alonso, L., Celma, M., Martin, A., Dopazo, J., & Medina, I. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks575 · Cited by 39
“BioPAX data exchange format enables the integration of diverse pathway resources.”
Background
A taxonomy of visualization tasks for the analysis of biological pathway data
Murray, P., McGee, F., & Forbes, A. G. (2017) · BMC Bioinformatics · doi:10.1186/s12859-016-1443-5 · Cited by 44
“For instance, the BioPax [2] specification contains a “Trans-port” class, which is one of four types of “Conversion,” which in turn is one of five different types of “Interaction,” which, finally, is one of four types of “Entity.””
BackgroundMethod
A review of bioinformatics tools and web servers in different microarray platforms used in cancer research
Hephzibah Cathryn, R., Kumar, S. U., Younes, S. N., Zayed, H., & Doss, C. G. P. (2022) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2022.05.002 · Cited by 45
PyBEL: a computational framework for Biological Expression Language
Hoyt, C. T., Konotopez, A., & Ebeling, C. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx660 · Cited by 43
ReactionFlow: an interactive visualization tool for causality analysis in biological pathways
Dang, T. N., Murray, P., Aurisano, J., & Forbes, A. G. (2015) · BMC Proceedings · doi:10.1186/1753-6561-9-s6-s6 · Cited by 39
“Both of these tools load pathway data that is represented in a standardized format, such as BioPAX [15].”
Dupuytren's: a systems biology disease
Rehman, S., Goodacre, R., Day, P. J., Bayat, A., & Westerhoff, H. V. (2011) · Arthritis Research & Therapy · doi:10.1186/ar3438 · Cited by 44
“Emerging standard languages, such as the Systems Biology Markup Language (SBML) [92], Cell Markup Language (CellML) [93], Cell System Markup Language (CSML) [94], Biological Pathway Exchange (BioPAX) [95] and Systems Biology Graphical Notation (SBGN) [96], and modelling tools such as COmplex PAthway SImulator (COPASI)…”
Method
Proteogenomic convergence for understanding cancer pathways and networks
Boja, E. S., & Rodriguez, H. (2014) · Clinical Proteomics · doi:10.1186/1559-0275-11-22 · Cited by 42
“gov), as well as data analyses and computational modeling [106,141-143].”
Method
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language
Hoyt, C. T., Domingo‐Fernándéz, D., Aldisi, R. S., Xu, L., Kolpeja, K., Spalek, S., Wollert, E., Bachman, J. A., Gyori, B. M., Greene, P., et al. (2019) · Database · doi:10.1093/database/baz068 · Cited by 42
Network analysis has diverse roles in drug discovery
Hasan, S., Bonde, B. K., Buchan, N. S., & Hall, M. D. (2012) · Drug Discovery Today · doi:10.1016/j.drudis.2012.05.006 · Cited by 42
PathBank 2.0—the pathway database for model organism metabolomics
Wishart, D. S., Kruger, R., Sivakumaran, A., Harford, K., Sanford, S., Doshi, R., Khetarpal, N., Fatokun, O., Doucet, D., Zubkowski, A., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1041 · Cited by 46
“…pathway and pathway component descriptions and its compatibility with several common machine readable or data exchange formats including BioPAX ( 18 ), SBML ( 19 ), PWML ( 8 ,9 ), SBGN ( 20 ), PNG and SVG. Additional details regarding PathBank’s (version 1.0) distinguishing features with regard…”
BackgroundInfluential
Differential ligand-signaling network of CCL19/CCL21-CCR7 system
Raju, R., Gadakh, S., Gopal, P., George, B., Advani, J., Soman, S., Prasad, T. S. K., & Girijadevi, R. (2015) · Database · doi:10.1093/database/bav106 · Cited by 43
Social engineering for virtual 'big science' in systems biology
Kitano, H., Ghosh, S., & Matsuoka, Y. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.574 · Cited by 40
A standard-enabled workflow for synthetic biology
Myers, C. J., Beal, J., Gorochowski, T. E., Kuwahara, H., Madsen, C. K., McLaughlin, J. A., Mısırlı, G., Nguyen, T., Oberortner, E., Samineni, M., et al. (2017) · Biochemical Society Transactions · doi:10.1042/bst20160347 · Cited by 39
“While some are SBOL repositories, others store their information in other formats such as GenBank or BioPAX [54], another COMBINE standard.”
BackgroundMethod
hiPathDB: a human-integrated pathway database with facile visualization
Yu, N., Seo, J.-W., Rho, K., Jang, Y., Park, J., Kim, W., & Lee, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1127 · Cited by 40
“Even though the Biological Pathways Exchange (BioPAX) and Systems Biology Markup Language (SBML) have been proposed as standards for pathway data exchange in the XML format (9,10), pathway integration is still a non-trivial task since each pathway database was constructed based on its own pathway model.”
Background
NetSlim: high-confidence curated signaling maps
Raju, R., Nanjappa, V., Balakrishnan, L., Radhakrishnan, A., Thomas, J. K., Sharma, J. N., Mi, T., Palapetta, S. M., Subbannayya, T., Sekhar, N. R., et al. (2011) · Database · doi:10.1093/database/bar032 · Cited by 41
Self-citation
Data quality issues in big data
Rao, D. L., Gudivada, V. N., & Raghavan, V. V. (2015) · IEEE International Conference on Big Data (BigData) · doi:10.1109/bigdata.2015.7364065 · Cited by 40
“BioPAX [22] is such a standard to enable integration, exchange, visualization and analysis.”
Background
Integration, visualization and analysis of human interactome
Pastrello, C., Pasini, E., Kotlyar, M., Otasek, D., Wong, S., Sangrar, W., Rahmati, S., & Jurišica, I. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.01.151 · Cited by 41
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
Miwa, M., Ohta, T., Rak, R., Rowley, A. G. D., Kell, D. B., Pyysalo, S., & Ananiadou, S. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt227 · Cited by 38
A graphical and computational modeling platform for biological pathways
Livigni, A., O’Hara, L., Polak, M. E., Angus, T., Wright, D. W., Smith, L. B., & Freeman, T. C. (2018) · Nature Protocols · doi:10.1038/nprot.2017.144 · Cited by 36
“…various models have been constructed that are based on this approach 2,10–15 , and there is a growing number of software tools that support model creation (using SBGN-compliant languages), e.g., CellDesigner 16,17 , NaviCell 11 , KEGG Mapper 18 , ReactomeFiViz 19 , iPath 20 and SBGN-Ed 21 .”
Method
Challenges and Limitations of Biological Network Analysis
Milano, M., Agapito, G., & Cannataro, M. (2022) · BioTech · doi:10.3390/biotech11030024 · Cited by 38
“BioPAX (Biological Pathway Exchange) [12] aims to simplify the integration and exchange of data stored in biological pathway databases through a unique way to represent data.”
Background
rBiopaxParser—an R package to parse, modify and visualize BioPAX data
Krämer, F., Bayerlová, M., Klemm, F., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts710 · Cited by 38
Closing the gap between formats for storing layout information in systems biology
Hoksza, D., Gawron, P., Ostaszewski, M., Hasenauer, J., & Schneider, R. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz067 · Cited by 38
“The most frequently used community-driven formats to encode molecular networks are the Systems Biology Markup Language (SBML) [6] and the Biological Pathway Exchange format (BioPAX) [7].”
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms
Suthers, P. F., Foster, C., Sarkar, D., Wang, L., & Maranas, C. D. (2020) · Metabolic Engineering · doi:10.1016/j.ymben.2020.11.013 · Cited by 39
Computer-aided design for metabolic engineering
Fernández‐Castané, A., Fehér, T., Carbonell, P., Pauthenier, C., & Faulon, J. (2014) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2014.03.029 · Cited by 39
Signaling gateway molecule pages—a data model perspective
Dinasarapu, A. R., Saunders, B., Ozerlat, I., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr190 · Cited by 37
“The channel function is defined with the channel ions, ionic conductance, channel blockers and thermodynamic data on channel gating.”
Background
Strategies for Pathway Analysis Using GWAS and WGS Data
White, M. J., Yaspan, B. L., Veatch, O. J., Goddard, P. C., Risse-Adams, O. S., & Contreras, M. G. (2018) · Current Protocols in Human Genetics · doi:10.1002/cphg.79 · Cited by 37
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
Waltemath, D., Golebiewski, M., Blinov, M. L., Gleeson, P., Hermjakob, H., Hucka, M., Inau, E. T., Keating, S., König, M., Krebs, O., et al. (2020) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2020-0005 · Cited by 38
“Core COMBINE standards are BioPAX [5], CellML [6, 7], the Simulation Experiment Markup Language (SED-ML) [8], the Systems Biology Graphical Notation (SBGN) [9], the Systems Biology Markup Language (SBML) [10], the Synthetic Biology Open Language (SBOL) [11], SBOL Visual [12] and NeuroML [13].”
Self-citation
Opioid receptors signaling network
Gopalakrishnan, L., Chatterjee, O., Ravishankar, N., Suresh, S., Raju, R., Mahadevan, A., & Prasad, T. S. K. (2021) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-021-00653-z · Cited by 36
The Reactome BioMart
Haw, R., Croft, D. W., Yung, C. K., Ndegwa, N., D’Eustachio, P., Hermjakob, H., & Stein, L. D. (2011) · Database · doi:10.1093/database/bar031 · Cited by 37
Self-citation
Data management strategies for multinational large-scale systems biology projects
Wruck, W., Peuker, M., & Regenbrecht, C. (2012) · Briefings Bioinform. · doi:10.1093/bib/bbs064 · Cited by 36
“MIBBI is complemented by many other standards, e.g. protein standards initiative—molecular interactions (PSI-MI) [30] in the proteomics area, mass Spectrometry Markup Language [31] in the mass spectrometry area, BioPax [32] as exchange format for pathway data, SBML [33] for the description of systems biology models in…”
XTalkDB: a database of signaling pathway crosstalk
Sam, S. A., Teel, J., Tegge, A. N., Bharadwaj, A., & Murali, T. M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1037 · Cited by 36
“We are examining approaches such as BioPAX (32) and the Biological Expression Language (BEL) (33).”
Method
Network‐Based Approaches for Pathway Level Analysis
Nguyen, T., Mitrea, C., & Drăghici, S. (2018) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.42 · Cited by 37
“Some attempts exist to use BIO-PAX (Demir et al., 2010) as the lingua franca for this domain.”
Background
Enabling Web-scale data integration in biomedicine through Linked Open Data
Kamdar, M. R., Fernández, J. D., Polleres, A., Tudorache, T., & Musen, M. A. (2019) · npj Digital Medicine · doi:10.1038/s41746-019-0162-5 · Cited by 36
Data Integration in Bioinformatics: Current Efforts and Challenges
Zhang, Z., Vladimir, B., Yu, J. M., Cheung, K., & Jeffrey, P. (2011) · InTech eBooks · doi:10.5772/21654 · Cited by 39
Self-citation
The systems biology format converter
Rodríguez, N., Pettit, J., Pezze, P. D., Li, L., Henry, A., van Iersel, M., Jalowicki, G., Kutmon, M., Natarajan, K. N., Tolnay, D., et al. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1000-2 · Cited by 35
“…equations [8]; – BioPAXModel for BioPax, format to exchange descriptions of biomolecular pathways, including reaction and interaction networks [9]; – DotModel for the Dot format, that encodes graph descriptions used by the open source graph visualisation software GraphViz [10] to generate…”
MethodSelf-citation
An integrated signal transduction network of macrophage migration inhibitory factor
Subbannayya, T., Variar, P., Advani, J., Nair, B. G., Shankar, S., Gowda, H., Saussez, S., Chatterjee, A., & Prasad, T. S. K. (2016) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-016-0326-x · Cited by 34
Synthetic Biology Open Language (SBOL) Version 2.3
Madsen, C., Goñi‐Moreno, Á., Umesh, P., et al. (2019) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2019-0025 · Cited by 34
Hypergraph-based connectivity measures for signaling pathway topologies
Franzese, N., Groce, A., Murali, T. M., et al. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007384 · Cited by 34
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review
Baltoumas, F. A., Zafeiropoulou, S., Karatzas, E., Koutrouli, M., Thanati, F., Voutsadaki, K., Gkonta, M., Hotova, J., Kasionis, I., Hatzis, P., et al. (2021) · Biomolecules · doi:10.3390/biom11081245 · Cited by 36
“Gene format), and (iii) machine-readable formats (GPML, RDF, BioPAX, XGMML, SBGN, SBML) for further pathway analysis by various tools, such as PathVisio [214] and Cytoscape [39].”
BackgroundInfluential
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination
Perfetto, L., Acencio, M. L., Bradley, G., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz132 · Cited by 32
Self-citation
ANAP: An Integrated Knowledge Base for Arabidopsis Protein Interaction Network Analysis
Wang, C., Marshall, A., Zhang, D., et al. (2012) · PLANT PHYSIOLOGY · doi:10.1104/pp.111.192203 · Cited by 33
“The importance of data integration is now being fully appreciated, and there is a general emphasis toward the development of standards for large data sets with deﬁned speciﬁc formats, which include PSI-MI (Kaiser, 2002) for protein interactions and BioPAX (Demir et al., 2010) and SBML (Hucka et al., 2003) for pathway…”
Odin’s Runes: A Rule Language for Information Extraction
Valenzuela-Escárcega, M. A., Hahn-Powell, G., & Surdeanu, M. (2016) · Language Resources and Evaluation Conference (LREC) · doi:10.63317/23ofday96scm · Cited by 33
“Example 6: A formalized taxonomy of biochemical entities and interactions inspired by BioPAX (Demir et al., 2010).”
Background

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
Publisher: Springer Science and Business Media LLC
Published: 2010-09
Volume: 28
Issue: 9
Pages: 935-942
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/nbt.1666
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: erratum (2010-12-07)
erratum (2012-04-10)
Open access: bronze
doi.org
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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

The BioPAX community standard for pathway data sharing

Abstract

Overview

AI snapshot

TL;DR

Key findings

Methods

Limitations

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks