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.
- Checkable: passes — It can be checked against evidence.
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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.
- Checkable: passes — It can be checked against evidence.
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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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- 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
“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.
- Based: passes — The paper gives a reason why it holds.
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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- 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.
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.
- 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.
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.
- 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. 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.
- 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.
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.
- Checkable: passes — It can be checked against evidence.
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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.
- Based: fails — The paper may give no reason why it holds.
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.
- 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. 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.
- 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.
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 601–700 of 755
Modelling techniques for biomolecular networksPreprint
Mayer, G. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2003.00327 · Cited by 2
“BioPAX BIOlogical PAthways eXchange, a language for the integration, exchange, [144] visualization and analysis of biological pathway data defined in OWL (Web Ontology Language) / DL [164].”
MethodTouré, V., Flobak, Å., Niarakis, A., Vercruysse, S., & Kuiper, M. T. R. (2020) · Preprints.org · doi:10.20944/preprints202007.0123.v1 · Cited by 1
(2015) · doi:10.18653/v1/w15-38 · Cited by 1
Capturing scientific knowledge in computable formPreprint
Wong, J. V., Franz, M., Siper, M. C., Fong, D., Durupınar, F., Dallago, C., Luna, A., Giorgi, J., Rodchenkov, I. V., Babur, Ö., et al. (2020) · doi:10.31219/osf.io/zep3x · Cited by 1
Self-citationEnhancing Ontology Integration in Medical Texts through Advanced MechanismsPreprint
Kawas, M., Alkhatib, B., & Dashash, M. (2023) · Research Square · doi:10.21203/rs.3.rs-3347581/v1 · Cited by 1
Linkflows: Towards Genuine Semantic Publishing in Science
Bucur, C.-I. (2024) · doi:10.5463/thesis.592 · Cited by 1
Venkatesan, A. (2014) · NORA - Norwegian Open Research Archives · Cited by 1
Database and Visualization for Advanced Systems Biology
Pornputtapong, N. (2014) · Chalmers Publication Library (Chalmers University of Technology)
Computational Methods for Modelling and Analysing Biological Networks
Larjo, A. (2015) · Tampere University Institutional Repository (Tampere University)
Czarnecki, J. (2015) · Birkbeck Institutional Research Online (BiRO) - Theses · doi:10.18743/pub.00040135
Simulation of Gene Regulatory NetworksPreprint
Ycart, B., Pont, F., & Fournié, J. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1310.0730
“These were already under development, and they integrate standard programming tools for the simulation and treatment of gene networks and pathways: BioPAX [22] SBML [52], CellML [78], Biolingua [70].”
MethodKirik, U. (2015) · Lund University Publications (Lund University)
Biological Network Modeling and Analysis
Janowski, S. J., Kaltschmidt, B., & Kaltschmidt, C. (2013) · Springer eBooks · doi:10.1007/978-3-642-41281-3_8
Data Standards in Systems Modeling
Vizcaíno, J. A. (2004) · Dictionary of Bioinformatics and Computational Biology · doi:10.1002/9780471650126.dob0860
Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge
Fuchs, J. E., Bender, A., & Glen, R. C. (2015) · Molecular Informatics · doi:10.1002/minf.201400166
Ramos, F., Hallal, C., Nieto, A., García, D., Berumen-Campos, J., & Escarcega, D. (2012) · Journal of Applied Research and Technology · doi:10.22201/icat.16656423.2012.10.5.370
“Although the three of them are used to describe the same biopathways, their purpose is semantically different: BioPAX and KGML are used for qualitative representations [19], while SBML is used for quantitative modeling [20].”
MethodAd-hoc Analysis of Genetic Pathways
Müller, D. (2013) · In-memory data management research · doi:10.1007/978-3-319-03035-7_7
Um modelo de qualidade para caracterização e seleção de bancos de dados de biologia molecular
Lichtnow, D. (2012) · Americanae (AECID Library)
Original article The Reactome BioMart
Haw, R., Croft, D. W., Yung, C. K., et al. (2016)
Self-citationData Integration Methods to Interpret Genome-Scale Data from Cancers
Laakso, M. (2012) · Työväentutkimus Vuosikirja
Kim, H., & Anyanwu, K. (2016) · arXiv (Cornell University) · doi:10.48550/arxiv.1602.01040
BioNetLink - An Architecture for Working with Network Data
Klapperstueck, M., & Schreiber, F. (2014) · PubMed · doi:10.2390/biecoll-jib-2014-241
“Such a data source could be, for example, a downloadable data dump file, files using standards such as SBML [9], BioPax [10], or GML [11], or online resources with a query interface.”
MethodData integration in biological research: an
Stefanidakis, M., Jiménez, R. C., Via, A., & Schneider, M. V. (2015)
Онтологии в биоинформатике и системной биологии
Podkolodnyy, N. L., & Podkolodnaya, O. A. (2015)
Flexible Integration and Visualisation of Drosophila Melanogaster Datasets.
van Iersel, M., Dow, J. A. T., & Anwar, N. (2012)
Self-citationLooking into Reactome through Biopax Lens.
Kazemzadeh, L., Deus, H., Dumontier, M. J., et al. (2013) · Research Publications (Maastricht University)
Building executable biological pathway models automatically from BioPAX
Willemsen, T., Feenstra, K. A., & Groth, P. (2013) · VU Research Portal · Cited by 1
INTERPRETABLE MODELS FOR INFORMATION EXTRACTION
Escárcega, V., & Antônio, M. (2016)
Fluck, J., & Zimmermann, M. (2015) · Methods in pharmacology and toxicology · doi:10.1007/978-1-4939-2778-4_5
Integrating translational biomarkers into drug development
Phillips, J. A. (2016) · Cambridge University Press eBooks · doi:10.1017/cbo9780511989421.005
Remli, M. A., & Deris, S. (2013) · Bioinformatics · doi:10.4018/978-1-4666-3604-0.ch091
Bohler (2017) · doi:10.26481/dis.20170216abd
Mapping Genetic Interaction Networks in Yeast
Baryshnikova, A. (2013) · TSpace (University of Toronto)
Signal Transduction Networks Analysis: The Reverse Phase Protein Array
Signore, M., Manganelli, V., & Vitale, I. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.12272-1
Standards and Tools for Model Exchange and Analysis in Systems Biology
Gauges, R. (2011) · heiDOK (Heidelberg University) · doi:10.11588/heidok.00012206
Biological Pathway Data Formats and Standards
Venkata, R. C., & Ghersi, D. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20432-9
Semantic Web Platforms for Bioinformatics and Life Sciences
Picone, M., & Lenzerini, M. (2014) · Advances in information quality and management · doi:10.4018/978-1-4666-5888-2.ch655
Bachman, J. A., Gyori, B. M., & Sorger, P. K. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/225698
Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases
Palli, R., & Thakar, J. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8618-7_18
Semantic Navigation of Disease-Specific Pathways: The Case of Non-small Cell Lung Cancer (NSCLC)
Yang, S. M., & Kim, H. (2018) · Lecture notes in computer science · doi:10.1007/978-3-030-04284-4_27
Integrated Semantic Model for Complex Disease Network
Park, J., Yang, S.-K., & Kim, H. (2018) · Lecture notes in computer science · doi:10.1007/978-3-030-04284-4_28
Mısırlı, G., Taylor, R., Goñi‐Moreno, Á., McLaughlin, J. A., Myers, C. J., Gennari, J. H., Lord, P., & Wipat, A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/499970
An Integrated Approach to Plant Biology via Multi-Analogous Methods
Jan, S., & Ahmad, P. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814872-3.00002-3 · Cited by 1
Knowledge Representation of G-Protein-Coupled Receptor Signal Transduction Pathways
Kertkeidkachorn, N., Zhao, L., Liu, X., et al. (2019) · IEEE International Conference on Semantic Computing (ICSC) · doi:10.1109/icosc.2019.8665519
“To better describe the pathway in general for any biological pathway, there is a huge effort to construct Biological Pathway Exchange (BioPAX) [4].”
MethodInfluentialJo, K., Buitrago, B. S., Kim, M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/614933
“Recently, BioASF [22] suggested a general framework for pathway models specified in BioPAX language [23] that has been used by several pathway databases [24, 25].”
Converting Alzheimer s disease map into a heavyweight ontology: a formal network to integrate dataPreprint
Henry, V., Moszer, I., Dameron, O., Potier, M., Hofmann‐Apitius, M., & Olivier Colliot, A. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1807.10509
“Different RDF schemas were already developed in the field of molecular biology (BioPax [17]) or more specifically for AD biomedical research (neuroRDF [18]).”
BackgroundA Parallel Software Platform for Pathway Enrichment
Agapito, G., & Cannataro, M. (2020) · Lecture notes in computer science · doi:10.1007/978-3-030-39081-5_19
Complex Systems, Data and Inference
Lecca, P. (2020) · SpringerBriefs in statistics · doi:10.1007/978-3-030-41255-5_1
Dasgupta, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.06.981456
Switching On Static Gene Regulatory Networks to Compute Cellular DecisionsPreprint
Pavillet, C. E., Voukantsis, D., & Buffa, F. M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.29.122200
“Although there may never be an Esperanto language, the Biological Pathway Exchange (BioPAX) language (Demir et al., 2010), an OWL-based language represented in the RDF/XML format (Horrocks et al., 2003), represents a community-driven effort to increase uniformity of pathway data.”
BackgroundAutomated Execution of Simulation Studies in Systems Medicine Using SED-ML and COMBINE Archive
Rampadarath, A., & Nickerson, D. P. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11688-5
Centralizing data to unlock whole-cell models
Chew, Y. H., & Karr, J. R. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.06.004
“BioCyc [62], KEGG [64], MetaNetX [65] BioPAX [66], EC, STRENDA [67] Reaction rate constants BRENDA [34], SABIO-RK [35] EC, STRENDA [67]”
MethodManaging biological data in pathways and networks
Kutmon, M. (2015) · doi:10.26481/dis.20150122mk
Self-citationComputational Tools and Resources for Integrative Modeling in Systems Biology
Wierling, C., & Hache, H. (2013) · Springer eBooks · doi:10.1007/978-94-007-6803-1_14
Orsine, L. A., & Donnard, E. R. (2021) · Alfahelix eBooks · doi:10.51780/978-6-599-275326-12
Beard, D. A. (2013) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.718198623.793488366
Remli, M. A., & Deris, S. (2012) · Advances in knowledge acquisition, transfer, and management book series/Advances in knowledge acquisition, transfer and management book series · doi:10.4018/978-1-4666-1993-7.ch018
Neural network modelling of the influence of channelopathies on reflex visual attention
Gravier, A. (2014) · DR-NTU (Nanyang Technological University) · doi:10.32657/10356/65485
Mathematical Models in Biotechnology
Tasseff, R. A., & Varner, J. D. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.09047-6
Data Integration and Visualization
Pettifer, S. R., & Attwood, T. K. (2013) · Springer eBooks · doi:10.1007/978-1-4419-9863-7_1110
New reasons for biologists to write with a formal language
Rodriguez‐Esteban, R. (2022) · Database · doi:10.1093/database/baac039
“Strömb ̈ack,L. and Lambrix,P. (2005) Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX.”
BackgroundScientific evidence and sources of knowledge for pharmacogenomics
Whirl‐Carrillo, M., Klein, C., & Klein, T. E. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-824453-1.00012-9
Self-citationIntegrative Data Analysis and Exploratory Data Mining in Biological Knowledge Graphs
Brandizi, M., Singh, A., Parsons, J. D., Rawlings, C., & Hassani‐Pak, K. (2022) · Springer eBooks · doi:10.1007/978-981-16-6795-4_8
(2022) · Elsevier eBooks · doi:10.1016/b978-0-12-822952-1.00029-2
Predicting transcription factor activity using prior biological informationPreprint
Estabrook, J., Yashar, W. M., Holly, H. D., Somers, J., Nikolova, O. H., Barbur, Ö., Braun, T. P., & Demir, E. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.16.520295
Self-citationCreating PROV-DM Graphs from Model Databases
Wilsdorf, P., & Uhrmacher, A. M. (2022) · Winter Simulation Conference · doi:10.1109/wsc57314.2022.10015331
“For BioModels, these include, e.g., the OWL-based BioPAX exchange format (Demir et al. 2010) or Scilab (Campbell et al. 2010), which can all be autogenerated by the Systems Biology Format Converter (Rodriguez et al. 2016) from an SBML specification (often done in older database entries).”
MethodReview: Towards modelling emergence in plant systems — R2/PR12
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr12
Author comment: Towards modelling emergence in plant systems — R2/PR11
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr11
Recommendation: Towards modelling emergence in plant systems — R1/PR9
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr9
Review: Towards modelling emergence in plant systems — R1/PR7
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr7
Author comment: Towards modelling emergence in plant systems — R1/PR6
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr6
Decision: Towards modelling emergence in plant systems — R0/PR5
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr5
Review: Towards modelling emergence in plant systems — R0/PR3
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr3
Author comment: Towards modelling emergence in plant systems — R0/PR1
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr1
RIMBO - An Ontology for Model Revision Databases
Kronström, F., Gower, A. H., Tiukova, I., & King, R. D. (2023) · Lecture notes in computer science · doi:10.1007/978-3-031-45275-8_35 · Cited by 1
The Perspective of Physiome Modelling in Systems Biology: New Horizon
Parvatikar, P., Bagali, S., Kanthe, P. S., Patil, A. V., & Das, K. K. (2023) · BENTHAM SCIENCE PUBLISHERS eBooks · doi:10.2174/9789815165616123010008
RNA interaction format: a general data format for RNA interactions
Schäfer, R. A., Rabsch, D., Scholz, G. E., Stadler, P. F., Hess, W. R., Backofen, R., Fallmann, J., & Voß, B. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad665
“…XML-based formats which can represent biological networks include the Proteomics Standard Initiative Molecular Interactions interchange format (PSI-MI; Hermjakob et al. 2004), the Chemical Markup Language (CML; Murray-Rust et al. 2001), BioPAX (Demir et al. 2010), and GraphML (Brandes et al. 2002).”
Recommendation: Towards modelling emergence in plant systems — R3/PR17
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr17
Decision: Towards modelling emergence in plant systems — R3/PR18
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr18
Author comment: Towards modelling emergence in plant systems — R3/PR16
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr16
Decision: Towards modelling emergence in plant systems — R2/PR15
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr15
Review: Towards modelling emergence in plant systems — R2/PR13
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr13
Recommendation: Towards modelling emergence in plant systems — R2/PR14
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr14
Decision: Towards modelling emergence in plant systems — R1/PR10
Tomkins, M. (2023) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr10
Review: Towards modelling emergence in plant systems — R1/PR8
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr8
Review: Towards modelling emergence in plant systems — R0/PR2
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr2
Recommendation: Towards modelling emergence in plant systems — R0/PR4
Tomkins, M. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2023.6.pr4
Standards and Modals for Biological Data: BioPax
Agapito, G. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00002-6
Li, M., He, Q., Yang, C., et al. (2021) · Figshare · doi:10.6084/m9.figshare.17037237
Wang, J., Li, F., Xu, Y., Zheng, X., Zhang, C., Hu, C., Xu, Y., Mi, W., Li, X., & Zhang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14936500
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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