Biological Pathway eXchange
Names
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Biological Pathway eXchange
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
BioPAX
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
BioPAX Ontology of Biological Pathways
metasource: Biontology / Bioportal
version: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
BP
metasource: Biontology / Bioportal
version: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
Names
More detailed information about this field from each metasource.
Biological Pathway eXchange
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
BioPAX
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
BioPAX Ontology of Biological Pathways
metasource: Biontology / Bioportalversion: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
BP
metasource: Biontology / Bioportalversion: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
Other names: BioPAX, BioPAX Ontology of Biological Pathways, BP
Names
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Biological Pathway eXchange
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
BioPAX
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
BioPAX Ontology of Biological Pathways
metasource: Biontology / Bioportalversion: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
BP
metasource: Biontology / Bioportalversion: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.
Description
More detailed information about this field from each metasource.
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
The BioPAX ontology (www.biopax.org) is a standard language for formally representing biological pathways. BioPAX Level 3 supports the representation of metabolic pathways, signal transduction pathways, protein-protein interaction networks, gene regulatory networks and genetic interactions.
metasource: Biontology / Bioportalversion: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
Webpage:
http://biopax.org/Webpage
More detailed information about this field from each metasource.
http://biopax.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
www.biopax.org
metasource: Biontology / Bioportalversion: Level3 v1.0 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/BP
Licence:
Name: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain DedicationLicence name
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Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Licence URL
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https://creativecommons.org/publicdomain/zero/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications:
Publications
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The BioPAX community standard for pathway data sharing
PMID: 20829833
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications
More detailed information about this field from each metasource.
The BioPAX community standard for pathway data sharing
PMID: 20829833
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
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The BioPAX community standard for pathway data sharing
PubMed citations: 304.
304 articles citing: The BioPAX community standard for pathway data sharing
Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. PMID:35350714
Author-sourced capture of pathway knowledge in computable form using Biofactoid. PMID:34860157
The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction. PMID:34789143
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Opioid receptors signaling network. PMID:34724150
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
Intelligent host engineering for metabolic flux optimisation in biotechnology. PMID:34673920
Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing. PMID:34668739
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. PMID:34634810
Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data. PMID:34592927
The role of metadata in reproducible computational research. PMID:34553169
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Dissecting immune cell stat regulation network reveals biomarkers to predict ICB therapy responders in melanoma. PMID:34238310
A National, Semantic-Driven, Three-Pillar Strategy to Enable Health Data Secondary Usage Interoperability for Research Within the Swiss Personalized Health Network: Methodological Study. PMID:34185008
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Reactome and the Gene Ontology: Digital convergence of data resources. PMID:33964129
Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review. PMID:33835956
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
GeneWalk identifies relevant gene functions for a biological context using network representation learning. PMID:33526072
Large-scale regulatory and signaling network assembly through linked open data. PMID:33459761
Platelet Proteomes, Pathways, and Phenotypes as Informants of Vascular Wellness and Disease. PMID:33441027
Towards reproducible computational drug discovery. PMID:33430992
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
Multipath: An R Package to Generate Integrated Reproducible Pathway Models. PMID:33371258
KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. PMID:33247931
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR). PMID:33178355
An assembly of galanin-galanin receptor signaling network. PMID:33136286
On the Logical Design of a Prototypical Data Lake System for Biological Resources. PMID:33117777
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. PMID:33015004
Ancestral state reconstruction of metabolic pathways across pangenome ensembles. PMID:32924924
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. PMID:32640021
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. PMID:32371892
Is useful research data usually shared? An investigation of genome-wide association study summary statistics. PMID:32084240
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis. PMID:31888466
Interactive Multiresolution Visualization of Cellular Network Processes. PMID:31884165
SAMMI: a semi-automated tool for the visualization of metabolic networks. PMID:31851289
Hypergraph-based connectivity measures for signaling pathway topologies. PMID:31652258
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. PMID:31604427
The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track. PMID:31603193
PathBank: a comprehensive pathway database for model organisms. PMID:31602464
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz. PMID:31372215
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
Prospects for Declarative Mathematical Modeling of Complex Biological Systems. PMID:31175549
CODA-ML: context-specific biological knowledge representation for systemic physiology analysis. PMID:31138123
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. PMID:31131402
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
Hierarchical sequence labeling for extracting BEL statements from biomedical literature. PMID:30961584
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
Combining relation extraction with function detection for BEL statement extraction. PMID:30624649
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. PMID:30564458
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
Large-scale automated machine reading discovers new cancer-driving mechanisms. PMID:30256986
Comprehensive network map of interferon gamma signaling. PMID:30191398
Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. PMID:30085931
A network map of netrin receptor UNC5B-mediated signaling. PMID:30084000
The 5-Hydroxytryptamine signaling map: an overview of serotonin-serotonin receptor mediated signaling network. PMID:30043327
A network map of thrombopoietin signaling. PMID:30039510
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. PMID:29954318
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. PMID:29872544
A logic-based method to build signaling networks and propose experimental plans. PMID:29777117
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Community-driven roadmap for integrated disease maps. PMID:29688273
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
A graphical and computational modeling platform for biological pathways. PMID:29543794
The BioCyc collection of microbial genomes and metabolic pathways. PMID:29447345
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Data Sharing: Convert Challenges into Opportunities. PMID:29270401
From word models to executable models of signaling networks using automated assembly. PMID:29175850
Automated visualization of rule-based models. PMID:29131816
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China. PMID:29061976
PyBEL: a computational framework for Biological Expression Language. PMID:29048466
Pathway Analysis with Signaling Hypergraphs. PMID:28991726
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. PMID:28365720
Comparison of tissue/disease specific integrated networks using directed graphlet signatures. PMID:28361704
A Web Tool for Generating High Quality Machine-readable Biological Pathways. PMID:28287524
A taxonomy of visualization tasks for the analysis of biological pathway data. PMID:28251869
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
XTalkDB: a database of signaling pathway crosstalk. PMID:27899583
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track. PMID:27694210
An overview of the oxytocin-oxytocin receptor signaling network. PMID:27624619
VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis. PMID:27619687
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). PMID:27554092
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
Signaling network map of the aryl hydrocarbon receptor. PMID:27465749
Where next for the reproducibility agenda in computational biology? PMID:27422148
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language. PMID:27402677
Coreference resolution improves extraction of Biological Expression Language statements from texts. PMID:27374122
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. PMID:27307645
A Six-Stage Workflow for Robust Application of Systems Pharmacology. PMID:27299936
Challenges in structural approaches to cell modeling. PMID:27255863
Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis. PMID:27216817
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. PMID:27141961
An integrated signal transduction network of macrophage migration inhibitory factor. PMID:27139435
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
The systems biology format converter. PMID:27044654
Systems psychopharmacology: A network approach to developing novel therapies. PMID:27014599
Challenges in horizontal model integration. PMID:26968798
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. PMID:26928298
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
The Electron Microscopy eXchange (EMX) initiative. PMID:26873784
Module Extraction for Efficient Object Queries over Ontologies with Large ABoxes. PMID:26848490
Pathway Analysis: State of the Art. PMID:26733877
PaxtoolsR: pathway analysis in R using Pathway Commons. PMID:26685306
Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data. PMID:26632845
NDEx, the Network Data Exchange. PMID:26594663
Datafish Multiphase Data Mining Technique to Match Multiple Mutually Inclusive Independent Variables in Large PACS Databases. PMID:26572132
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
Differential ligand-signaling network of CCL19/CCL21-CCR7 system. PMID:26504105
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. PMID:26454094
Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. PMID:26435758
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. PMID:26424082
Dynamical modeling of uncertain interaction-based genomic networks. PMID:26423606
ReactionFlow: an interactive visualization tool for causality analysis in biological pathways. PMID:26361502
Data integration in biological research: an overview. PMID:26336651
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. PMID:26298294
Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells. PMID:26284497
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
A network map of Interleukin-10 signaling pathway. PMID:26253919
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
Construction of biological networks from unstructured information based on a semi-automated curation workflow. PMID:26200752
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
A knowledgebase resource for interleukin-17 family mediated signaling. PMID:26077014
kpath: integration of metabolic pathway linked data. PMID:26055101
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. PMID:26050742
The role of markup for enabling interoperability in health informatics. PMID:26042043
SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PMID:26030594
GFVO: the Genomic Feature and Variation Ontology. PMID:26019997
Visualisation of BioPAX Networks using BioLayout Express (3D). PMID:25949802
Pathways with PathWhiz. PMID:25934797
KaBOB: ontology-based semantic integration of biomedical databases. PMID:25903923
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. PMID:25887162
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Computational modeling of drug response with applications to neuroscience. PMID:25733952
PathVisio 3: an extendable pathway analysis toolbox. PMID:25706687
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
ReNE: a cytoscape plugin for regulatory network enhancement. PMID:25541727
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Semantically linking in silico cancer models. PMID:25520553
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
Integrated network analysis and effective tools in plant systems biology. PMID:25408696
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. PMID:25326323
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
Integrating biological pathways and genomic profiles with ChiBE 2. PMID:25086704
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Current understanding of the formation and adaptation of metabolic systems based on network theory. PMID:24957641
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. PMID:24911500
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
Signaling hypergraphs. PMID:24857424
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. PMID:24665131
An integrative modeling framework reveals plasticity of TGF-β signaling. PMID:24618419
A network map of the gastrin signaling pathway. PMID:24584707
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. PMID:24573880
Benchmarking infrastructure for mutation text mining. PMID:24568600
Detection of type 2 diabetes related modules and genes based on epigenetic networks. PMID:24565181
Pathway-based drug repositioning using causal inference. PMID:24564553
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
ModeLang: a new approach for experts-friendly viral infections modeling. PMID:24454531
Systems toxicology: from basic research to risk assessment. PMID:24446777
Reverse engineering molecular hypergraphs. PMID:24384702
Ontology of physics for biology: representing physical dependencies as a basis for biological processes. PMID:24295137
Pathway Commons at virtual cell: use of pathway data for mathematical modeling. PMID:24273241
A Signaling Network of Thyroid-Stimulating Hormone. PMID:24255551
The Reactome pathway knowledgebase. PMID:24243840
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
On Crowd-verification of Biological Networks. PMID:24151423
Toward an integrated software platform for systems pharmacology. PMID:24150748
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
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. PMID:24098138
Using biological pathway data with paxtools. PMID:24068901
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
Pattern search in BioPAX models. PMID:24045775
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. PMID:23953132
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis. PMID:23935076
The BioPAX Validator. PMID:23918249
Large-scale gene function analysis with the PANTHER classification system. PMID:23868073
JBioWH: an open-source Java framework for bioinformatics data integration. PMID:23846595
PharmGKB: the Pharmacogenomics Knowledge Base. PMID:23824865
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. PMID:23813008
Analysis and prediction of pathways in HeLa cells by integrating biological levels of organization with systems-biology approaches. PMID:23785426
Representing physiological processes and their participants with PhysioMaps. PMID:23735231
A network perspective on unraveling the role of TRP channels in biology and disease. PMID:23677537
MIMO: an efficient tool for molecular interaction maps overlap. PMID:23672344
Large-scale event extraction from literature with multi-level gene normalization. PMID:23613707
A network map of BDNF/TRKB and BDNF/p75NTR signaling system. PMID:23606317
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. PMID:23547033
An integrated map of corticotropin-releasing hormone signaling pathway. PMID:23504413
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. PMID:23479348
Hierarchical approaches for systems modeling in cardiac development. PMID:23463736
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. PMID:23453054
Precise generation of systems biology models from KEGG pathways. PMID:23433509
Getting more out of biomedical documents with GATE's full lifecycle open source text analytics. PMID:23408875
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
CySBGN: a Cytoscape plug-in to integrate SBGN maps. PMID:23324051
ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. PMID:23311978
Lessons from the gene expression pattern of the rat zona glomerulosa. PMID:23287491
IntPath--an integrated pathway gene relationship database for model organisms and important pathogens. PMID:23282057
Architecture for interoperable software in biology. PMID:23235920
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
Data mining in the MetaCyc family of pathway databases. PMID:23192547
Accelerating cancer systems biology research through Semantic Web technology. PMID:23188758
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. PMID:23175748
Logic modeling and the ridiculome under the rug. PMID:23171629
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
A multicellular signal transduction network of AGE/RAGE signaling. PMID:23161412
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
VANTED v2: a framework for systems biology applications. PMID:23140568
A travel guide to Cytoscape plugins. PMID:23132118
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. PMID:22969728
Evaluation of research in biomedical ontologies. PMID:22962340
Qualitative translation of relations from BioPAX to SBML qual. PMID:22923304
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. PMID:22711793
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. PMID:22693220
A pathway map of prolactin signaling. PMID:22684822
Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. PMID:22672776
A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway. PMID:22649723
Computational tools for metabolic engineering. PMID:22629572
Software support for SBGN maps: SBGN-ML and LibSBGN. PMID:22581176
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. PMID:22548703
Leveling the playing field: bringing development of biomarkers and molecular diagnostics up to the standards for drug development. PMID:22422403
Improving integrative searching of systems chemical biology data using semantic annotation. PMID:22401035
Exploring and linking biomedical resources through multidimensional semantic spaces. PMID:22373409
Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. PMID:22369691
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
graphite - a Bioconductor package to convert pathway topology to gene network. PMID:22292714
Toward interoperable bioscience data. PMID:22281772
Semantically enabling pharmacogenomic data for the realization of personalized medicine. PMID:22256869
A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PMID:22241976
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. PMID:22199389
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826
Leveraging modeling approaches: reaction networks and rules. PMID:22161349
IPAVS: Integrated Pathway Resources, Analysis and Visualization System. PMID:22140115
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. PMID:22135298
Rhea--a manually curated resource of biochemical reactions. PMID:22135291
hiPathDB: a human-integrated pathway database with facile visualization. PMID:22123737
The IntAct molecular interaction database in 2012. PMID:22121220
INOH: ontology-based highly structured database of signal transduction pathways. PMID:22120663
From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. PMID:22103613
WikiPathways: building research communities on biological pathways. PMID:22096230
Software for systems biology: from tools to integrated platforms. PMID:22048662
Controlled vocabularies and semantics in systems biology. PMID:22027554
BioPAX support in CellDesigner. PMID:22021903
The Reactome BioMart. PMID:22012987
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. PMID:21999653
CMLLite: a design philosophy for CML. PMID:21999395
A comprehensive curated resource for follicle stimulating hormone signaling. PMID:21996254
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
NetSlim: high-confidence curated signaling maps. PMID:21959865
Dupuytren's: a systems biology disease. PMID:21943049
Bioinformatics and systems biology of the lipidome. PMID:21939287
Integrating systems biology models and biomedical ontologies. PMID:21835028
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. PMID:21742767
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. PMID:21632604
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. PMID:21624155
Social engineering for virtual 'big science' in systems biology. PMID:21587248
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. PMID:21586134
Signaling gateway molecule pages--a data model perspective. PMID:21505029
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
EcoCyc: a comprehensive database of Escherichia coli biology. PMID:21097882
SPIKE: a database of highly curated human signaling pathways. PMID:21097778
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PMID:21085593
Gramene database in 2010: updates and extensions. PMID:21076153
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). PMID:21051347
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mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
resource metadata
metasource: Fairsharing.org
version: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
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mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
pathway model
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
resource metadata
metasource: Fairsharing.orgversion: FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
mathematical model modeling and simulation pathway model resource metadata
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