{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T13:52:39Z","timestamp":1774619559128,"version":"3.50.1"},"reference-count":104,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,12,30]],"date-time":"2020-12-30T00:00:00Z","timestamp":1609286400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Regulation Ensemble Effort for the Knowledge Commons","award":["CA15205"],"award-info":[{"award-number":["CA15205"]}]},{"name":"ERACoSysMed","award":["COLOSYS"],"award-info":[{"award-number":["COLOSYS"]}]},{"name":"The Norwegian University of Science and Technology\u2019s Strategic Research Area \u2018NTNU Health\u2019"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. Logical regulatory networks can be used to predict biological and cellular behaviors by system perturbations and in silico simulations. Today, broad sets of causal interactions are available in a variety of biological knowledge resources. However, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. It can therefore be challenging to efficiently explore various resources of causal interaction and maintain an overview of recorded contextual information that ensures valid use of the data. This review lists the different types of public resources with causal interactions, the different views on biological processes that they represent, the various data formats they use for data representation and storage, and the data exchange and conversion procedures that are available to extract and download these interactions. This may further raise awareness among the targeted audience, i.e. logical modelers and other scientists interested in molecular causal interactions, but also database managers and curators, about the abundance and variety of causal molecular interaction data, and the variety of tools and approaches to convert them into one interoperable resource.<\/jats:p>","DOI":"10.1093\/bib\/bbaa390","type":"journal-article","created":{"date-parts":[[2020,12,2]],"date-time":"2020-12-02T13:09:22Z","timestamp":1606914562000},"source":"Crossref","is-referenced-by-count":17,"title":["The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4639-4431","authenticated-orcid":false,"given":"Vasundra","family":"Tour\u00e9","sequence":"first","affiliation":[{"name":"Department of Biology of the Norwegian University of Science and Technology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3357-425X","authenticated-orcid":false,"given":"\u00c5smund","family":"Flobak","sequence":"additional","affiliation":[{"name":"Residential Oncologist and an Associate Professor"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9687-7426","authenticated-orcid":false,"given":"Anna","family":"Niarakis","sequence":"additional","affiliation":[{"name":"Department of Biology, Univ Evry, University of Paris-Saclay, affiliated with the laboratory GenHotel in Genopole campus, and a delegate at the Lifeware Group, INRIA Saclay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3136-7353","authenticated-orcid":false,"given":"Steven","family":"Vercruysse","sequence":"additional","affiliation":[{"name":"Researcher in computer science and computational biology and focuses on building a bridge between human and computer understanding"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1171-9876","authenticated-orcid":false,"given":"Martin","family":"Kuiper","sequence":"additional","affiliation":[{"name":"systems biology at the Department of Biology of the Norwegian University of Science and Technology"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,12,30]]},"reference":[{"key":"2021072117054998500_ref1","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1080\/00221309.2014.977216","article-title":"Causal inference from descriptions of experimental and non-experimental research: public understanding of correlation-versus-causation","volume":"142","author":"Bleske-Rechek","year":"2015","journal-title":"J Gen Psychol"},{"key":"2021072117054998500_ref2","volume-title":"A Treatise of Human Nature","author":"David","year":"1740"},{"key":"2021072117054998500_ref3","article-title":"The minimum information about a molecular interaction causal statement (MI2CAST)","author":"Tour\u00e9","year":"2020","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref4","doi-asserted-by":"crossref","first-page":"055001","DOI":"10.1088\/1478-3975\/9\/5\/055001","article-title":"Boolean modeling in systems biology: an overview of methodology and applications","volume":"9","author":"Wang","year":"2012","journal-title":"Phys Biol"},{"key":"2021072117054998500_ref5","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.biosystems.2009.04.008","article-title":"Logical modelling of regulatory networks with GINsim 2.3","volume":"97","author":"Naldi","year":"2009","journal-title":"Biosystems"},{"key":"2021072117054998500_ref6","first-page":"180","article-title":"Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits. Chaos Interdiscip. J","volume":"11","author":"Thomas","year":"2001","journal-title":"Nonlinear Sci"},{"key":"2021072117054998500_ref7","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/0022-5193(73)90208-7","article-title":"The logical analysis of continuous, non-linear biochemical control networks","volume":"39","author":"Glass","year":"1973","journal-title":"J Theor Biol"},{"key":"2021072117054998500_ref8","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.aar3641","article-title":"Cooperation between T cell receptor and toll-like receptor 5 signaling for CD4+ T cell activation","volume":"12","author":"Rodr\u00edguez-Jorge","year":"2019","journal-title":"Sci Signal"},{"key":"2021072117054998500_ref9","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.biosystems.2005.10.004","article-title":"A network model for the control of the differentiation process in Th cells","volume":"84","author":"Mendoza","year":"2006","journal-title":"Biosystems"},{"key":"2021072117054998500_ref10","doi-asserted-by":"crossref","first-page":"5792","DOI":"10.1073\/pnas.1610622114","article-title":"Logical modeling of lymphoid and myeloid cell specification and transdifferentiation","volume":"114","author":"Collombet","year":"2017","journal-title":"Proc Natl Acad Sci"},{"key":"2021072117054998500_ref11","doi-asserted-by":"crossref","first-page":"2407","DOI":"10.1158\/0008-5472.CAN-19-3147","article-title":"Hybrid epithelial\u2013mesenchymal phenotypes are controlled by microenvironmental factors","volume":"80","author":"Selvaggio","year":"2020","journal-title":"Cancer Res"},{"key":"2021072117054998500_ref12","doi-asserted-by":"crossref","first-page":"16308","DOI":"10.1073\/pnas.0806447105","article-title":"Network model of survival signaling in large granular lymphocyte leukemia","volume":"105","author":"Zhang","year":"2008","journal-title":"Proc Natl Acad Sci"},{"key":"2021072117054998500_ref13","doi-asserted-by":"crossref","first-page":"e1004426","DOI":"10.1371\/journal.pcbi.1004426","article-title":"Discovery of drug synergies in gastric cancer cells predicted by logical Modeling","volume":"11","author":"Flobak","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"2021072117054998500_ref14","doi-asserted-by":"crossref","first-page":"8033","DOI":"10.1038\/ncomms9033","article-title":"Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data","volume":"6","author":"Terfve","year":"2015","journal-title":"Nat Commun"},{"key":"2021072117054998500_ref15","doi-asserted-by":"crossref","first-page":"4473","DOI":"10.1093\/bioinformatics\/btaa484","article-title":"Automated inference of Boolean models from molecular interaction maps using CaSQ","volume":"36","author":"Aghamiri","year":"2020","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref16","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1186\/1471-2105-8-462","article-title":"Dynamic simulation of regulatory networks using SQUAD","volume":"8","author":"Di Cara","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2021072117054998500_ref17","doi-asserted-by":"crossref","first-page":"D548","DOI":"10.1093\/nar\/gkv1048","article-title":"SIGNOR: a database of causal relationships between biological entities","volume":"44","author":"Perfetto","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref18","first-page":"D504","article-title":"SIGNOR 2.0, the SIGnaling network open resource 2.0: 2019 update","volume":"48","author":"Licata","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref19","doi-asserted-by":"crossref","first-page":"3779","DOI":"10.1093\/bioinformatics\/btz132","article-title":"CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination","volume":"35","author":"Perfetto","year":"2019","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref20","doi-asserted-by":"crossref","first-page":"D527","DOI":"10.1093\/nar\/gkx876","article-title":"DISNOR: a disease network open resource","volume":"46","author":"Lo Surdo","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref21","first-page":"D845","article-title":"The DisGeNET knowledge platform for disease genomics: 2019 update","volume":"48","author":"Pi\u00f1ero","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref22","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1752-0509-7-7","article-title":"SignaLink 2\u2014a signaling pathway resource with multi-layered regulatory networks","volume":"7","author":"Fazekas","year":"2013","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref23","doi-asserted-by":"crossref","first-page":"W601","DOI":"10.1093\/nar\/gkt392","article-title":"A new reference implementation of the PSICQUIC web service","volume":"41","author":"Del-Toro","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref24","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","article-title":"The BioPAX community standard for pathway data sharing","volume":"28","author":"Demir","year":"2010","journal-title":"Nat Biotechnol"},{"key":"2021072117054998500_ref25","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref26","doi-asserted-by":"crossref","first-page":"e9110","DOI":"10.15252\/msb.20199110","article-title":"SBML level 3: an extensible format for the exchange and reuse of biological models","volume":"16","author":"Keating","year":"2020","journal-title":"Mol Syst Biol"},{"key":"2021072117054998500_ref27","article-title":"Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. Database","volume":"2015","author":"Bou\u00e9","year":"2015","journal-title":"J Biol Databases Curation"},{"key":"2021072117054998500_ref28","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1752-0509-5-168","article-title":"A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue","volume":"5","author":"Schlage","year":"2011","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref29","first-page":"s12","article-title":"Construction of a computable network model of tissue repair and angiogenesis in the lung","author":"S Park","year":"2013","journal-title":"J Clin Toxicol"},{"key":"2021072117054998500_ref30","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1186\/1479-5876-12-185","article-title":"A vascular biology network model focused on inflammatory processes to investigate atherogenesis and plaque instability","volume":"12","author":"De Le\u00f3n","year":"2014","journal-title":"J Transl Med"},{"key":"2021072117054998500_ref31","doi-asserted-by":"crossref","first-page":"97","DOI":"10.4137\/BBI.S11154","article-title":"Construction of a computable network model for DNA damage, autophagy, cell death, and senescence","volume":"7","author":"Gebel","year":"2013","journal-title":"Bioinforma Biol Insights"},{"key":"2021072117054998500_ref32","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1186\/1752-0509-5-105","article-title":"Construction of a computable cell proliferation network focused on non-diseased lung cells","volume":"5","author":"Westra","year":"2011","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref33","doi-asserted-by":"crossref","first-page":"167","DOI":"10.4137\/BBI.S11509","article-title":"A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue","volume":"7","author":"Westra","year":"2013","journal-title":"Bioinforma Biol Insights"},{"key":"2021072117054998500_ref34","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1093\/bioinformatics\/btx660","article-title":"PyBEL: a computational framework for biological expression language","volume":"34","author":"Hoyt","year":"2018","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref35","doi-asserted-by":"crossref","first-page":"D793","DOI":"10.1093\/nar\/gkq1167","article-title":"SPIKE: a database of highly curated human signaling pathways","volume":"39","author":"Paz","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref36","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1186\/1752-0509-6-96","article-title":"The cell collective: toward an open and collaborative approach to systems biology","volume":"6","author":"Helikar","year":"2012","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref37","first-page":"D407","article-title":"BioModels\u201415 years of sharing computational models in life science","volume":"48","author":"Malik-Sheriff","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref38","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1093\/bioinformatics\/btw682","article-title":"PyBoolNet: a python package for the generation, analysis and visualization of boolean networks","volume":"33","author":"Klarner","year":"2017","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref39","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/1752-0509-7-135","article-title":"SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools","volume":"7","author":"Chaouiya","year":"2013","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref40","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nbt.1558","article-title":"The systems biology graphical notation","volume":"27","author":"Nov\u00e8re","year":"2009","journal-title":"Nat Biotechnol"},{"key":"2021072117054998500_ref41","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref42","doi-asserted-by":"crossref","first-page":"D661","DOI":"10.1093\/nar\/gkx1064","article-title":"WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research","volume":"46","author":"Slenter","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref43","doi-asserted-by":"crossref","first-page":"D488","DOI":"10.1093\/nar\/gkv1024","article-title":"WikiPathways: capturing the full diversity of pathway knowledge","volume":"44","author":"Kutmon","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref44","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1038\/s41588-019-0500-1","article-title":"Gene ontology causal activity modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems","volume":"51","author":"Thomas","year":"2019","journal-title":"Nat Genet"},{"key":"2021072117054998500_ref45","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"2021072117054998500_ref46","first-page":"16","article-title":"Systems biology graphical notation: process description language level 1 version 2.0","author":"Rougny","year":"2019","journal-title":"J Integr Bioinform"},{"key":"2021072117054998500_ref47","doi-asserted-by":"crossref","first-page":"D284","DOI":"10.1093\/nar\/gki078","article-title":"The PANTHER database of protein families, subfamilies, functions and pathways","volume":"33","author":"Mi","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref48","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/s41596-019-0128-8","article-title":"Protocol update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)","volume":"14","author":"Mi","year":"2019","journal-title":"Nat Protoc"},{"key":"2021072117054998500_ref49","first-page":"D498","article-title":"The reactome pathway knowledgebase","volume":"48","author":"Jassal","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref50","doi-asserted-by":"crossref","first-page":"e160","DOI":"10.1038\/oncsis.2015.19","article-title":"Atlas of cancer signalling network: a systems biology resource for integrative analysis of cancer data with Google maps","volume":"4","author":"Kuperstein","year":"2015","journal-title":"Oncogenesis"},{"key":"2021072117054998500_ref51","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1093\/bib\/bby024","article-title":"Community-driven roadmap for integrated disease maps","volume":"20","author":"Ostaszewski","year":"2018","journal-title":"Brief Bioinform"},{"key":"2021072117054998500_ref52","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41540-018-0059-y","article-title":"Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms","volume":"4","author":"Mazein","year":"2018","journal-title":"Npj Syst. Biol. Appl."},{"key":"2021072117054998500_ref53","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","article-title":"CellDesigner: a process diagram editor for gene-regulatory and biochemical networks","volume":"1","author":"Funahashi","year":"2003","journal-title":"BIOSILICO"},{"key":"2021072117054998500_ref54","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/s41597-020-0477-8","article-title":"COVID-19 disease map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms","volume":"7","author":"Ostaszewski","year":"2020","journal-title":"Sci Data"},{"key":"2021072117054998500_ref55","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1007\/s12035-013-8489-4","article-title":"Integrating pathways of Parkinson\u2019s disease in a molecular interaction map","volume":"49","author":"Fujita","year":"2014","journal-title":"Mol Neurobiol"},{"key":"2021072117054998500_ref56","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1111\/cea.13211","article-title":"AsthmaMap: an expert-driven computational representation of disease mechanisms","volume":"48","author":"Mazein","year":"2018","journal-title":"Clin Exp Allergy"},{"key":"2021072117054998500_ref57","article-title":"Computational systems biology approach for the study of rheumatoid arthritis: from a molecular map to a dynamical model","volume":"4","author":"Singh","year":"2018","journal-title":"Genomics Comput Biol"},{"key":"2021072117054998500_ref58","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baaa017","article-title":"RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis","volume":"2020","author":"Singh","year":"2020","journal-title":"Database"},{"key":"2021072117054998500_ref59","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/npjsba.2016.20","article-title":"MINERVA\u2014a platform for visualization and curation of molecular interaction networks","volume":"2","author":"Gawron","year":"2016","journal-title":"Npj Syst Biol Appl"},{"key":"2021072117054998500_ref60","article-title":"The atlas of inflammation-resolution (AIR)","author":"Serhan","year":"2020","journal-title":"bioRxiv"},{"key":"2021072117054998500_ref61","doi-asserted-by":"crossref","first-page":"e201800029","DOI":"10.26508\/lsa.201800029","article-title":"Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma","volume":"1","author":"Zhou","year":"2018","journal-title":"Life Sci Alliance"},{"key":"2021072117054998500_ref62","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.4049\/jimmunol.1502513","article-title":"An interactive macrophage signal transduction map facilitates comparative analyses of high-throughput data","volume":"198","author":"Wentker","year":"2017","journal-title":"J Immunol"},{"key":"2021072117054998500_ref63","doi-asserted-by":"crossref","first-page":"e0146759","DOI":"10.1371\/journal.pone.0146759","article-title":"Comprehensive map of molecules implicated in obesity","volume":"11","author":"Jagannadham","year":"2016","journal-title":"PLoS One"},{"key":"2021072117054998500_ref64","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s12918-015-0181-z","article-title":"The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms","volume":"9","author":"Tripathi","year":"2015","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref65","doi-asserted-by":"crossref","first-page":"5041","DOI":"10.18632\/oncotarget.3238","article-title":"Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies","volume":"6","author":"Tortolina","year":"2015","journal-title":"Oncotarget"},{"key":"2021072117054998500_ref66","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/1752-0509-6-52","article-title":"AlzPathway: a comprehensive map of signaling pathways of Alzheimer\u2019s disease","volume":"6","author":"Mizuno","year":"2012","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref67","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1186\/1752-0509-7-115","article-title":"Translation of SBGN maps: process description to activity flow","volume":"7","author":"Vogt","year":"2013","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref68","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1093\/bioinformatics\/btq407","article-title":"Editing, validating and translating of SBGN maps","volume":"26","author":"Czauderna","year":"2010","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref69","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.4077","article-title":"OmniPath: guidelines and gateway for literature-curated signaling pathway resources","volume":"13","author":"T\u00fcrei","year":"2016","journal-title":"Nat Methods"},{"key":"2021072117054998500_ref70","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1093\/bioinformatics\/btz968","article-title":"Bringing data from curated pathway resources to Cytoscape with OmniPath","volume":"36","author":"Ceccarelli","year":"2020","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref71","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2105-10-S10-S11","article-title":"BioGateway: a semantic systems biology tool for the life sciences","volume":"10","author":"Antezana","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2021072117054998500_ref72","doi-asserted-by":"crossref","first-page":"2422","DOI":"10.12688\/f1000research.9656.2","article-title":"Identifying ELIXIR Core data resources","volume":"5","author":"Durinx","year":"2017","journal-title":"F1000Research"},{"key":"2021072117054998500_ref73","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1093\/bioinformatics\/btz835","article-title":"The Cytoscape BioGateway app: explorative network building from an RDF store","volume":"36","author":"Holm\u00e5s","year":"2020","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref74","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.cels.2015.10.001","article-title":"NDEx, the network data exchange","volume":"1","author":"Pratt","year":"2015","journal-title":"Cell Syst"},{"key":"2021072117054998500_ref75","first-page":"D489","article-title":"Pathway commons 2019 update: integration, analysis and exploration of pathway data","volume":"48","author":"Rodchenkov","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref76","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1186\/s12859-019-2863-9","article-title":"PathMe: merging and exploring mechanistic pathway knowledge","volume":"20","author":"Domingo-Fern\u00e1ndez","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2021072117054998500_ref77","first-page":"631812","article-title":"Integration of structured biological data sources using biological expression language","author":"Hoyt","year":"2019","journal-title":"bioRxiv"},{"key":"2021072117054998500_ref78","doi-asserted-by":"crossref","first-page":"4501","DOI":"10.1093\/bioinformatics\/btz289","article-title":"INDRA-IPM: interactive pathway modeling using natural language with automated assembly","volume":"35","author":"Todorov","year":"2019","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref79","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41540-019-0118-z","article-title":"From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL","volume":"5","author":"Liu","year":"2019","journal-title":"Npj Syst Biol Appl"},{"key":"2021072117054998500_ref80","doi-asserted-by":"crossref","first-page":"3670","DOI":"10.1093\/bioinformatics\/btx425","article-title":"CausalR: extracting mechanistic sense from genome scale data","volume":"33","author":"Bradley","year":"2017","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref81","doi-asserted-by":"crossref","first-page":"3066","DOI":"10.1093\/bioinformatics\/btv305","article-title":"CoRegNet: reconstruction and integrated analysis of co-regulatory networks","volume":"31","author":"Nicolle","year":"2015","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref82","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1186\/1471-2105-14-340","article-title":"Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data","volume":"14","author":"Catlett","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2021072117054998500_ref83","first-page":"258855","article-title":"Causal interactions from proteomic profiles: molecular data meets pathway knowledge","author":"Babur","year":"2018","journal-title":"bioRxiv"},{"key":"2021072117054998500_ref84","article-title":"CaNDis: a web server for investigation of causal relationships between diseases, drugs and drug targets","author":"\u0160krlj","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref85","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.jbi.2014.08.010","article-title":"SAGA: a hybrid search algorithm for Bayesian network structure learning of transcriptional regulatory networks","volume":"53","author":"Adabor","year":"2015","journal-title":"J Biomed Inform"},{"key":"2021072117054998500_ref86","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2105-7-S1-S7","article-title":"ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context","volume":"7","author":"Margolin","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2021072117054998500_ref87","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/1752-0509-6-54","article-title":"Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks","volume":"6","author":"Martin","year":"2012","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref88","doi-asserted-by":"crossref","first-page":"2975","DOI":"10.1038\/s41598-020-59669-x","article-title":"Challenges and opportunities with causal discovery algorithms: application to Alzheimer\u2019s pathophysiology","volume":"10","author":"Shen","year":"2020","journal-title":"Sci Rep"},{"key":"2021072117054998500_ref89","doi-asserted-by":"crossref","first-page":"D619","DOI":"10.1093\/nar\/gkw1033","article-title":"Genenames.Org: the HGNC and VGNC resources in 2017","volume":"45","author":"Yates","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref90","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"The UniProt Consortium","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref91","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/978-1-60761-987-1_18","article-title":"Cytoscape: software for visualization and analysis of biological networks","volume":"696","author":"Kohl","year":"2011","journal-title":"Data Min Proteomics Stand Appl"},{"key":"2021072117054998500_ref92","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1021\/acs.jproteome.7b00370","article-title":"Proteomics standards initiative: fifteen years of progress and future work","volume":"16","author":"Deutsch","year":"2017","journal-title":"J Proteome Res"},{"key":"2021072117054998500_ref93","doi-asserted-by":"crossref","first-page":"e737168","DOI":"10.1155\/2015\/737168","article-title":"Computational modelling approaches on epigenetic factors in neurodegenerative and autoimmune diseases and their mechanistic analysis","volume":"2015","author":"Khanam Irin","year":"2015","journal-title":"J Immunol Res"},{"issue":"2004","key":"2021072117054998500_ref94","article-title":"OWL web ontology language overview","volume":"10","author":"McGuinness","year":"2004","journal-title":"W3C Recomm"},{"key":"2021072117054998500_ref95","article-title":"diatomsRcool","author":"Mungall","year":"2020"},{"key":"2021072117054998500_ref96","doi-asserted-by":"crossref","first-page":"19","DOI":"10.3389\/fbioe.2015.00019","article-title":"Promoting coordinated development of community-based information standards for Modeling in biology: the COMBINE initiative","volume":"3","author":"Hucka","year":"2015","journal-title":"Front Bioeng Biotechnol"},{"key":"2021072117054998500_ref97","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1186\/1752-0509-6-133","article-title":"CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms","volume":"6","author":"Terfve","year":"2012","journal-title":"BMC Syst Biol"},{"key":"2021072117054998500_ref98","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","article-title":"BoolNet\u2014an R package for generation, reconstruction and analysis of Boolean networks","volume":"26","author":"M\u00fcssel","year":"2010","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref99","doi-asserted-by":"crossref","first-page":"W150","DOI":"10.1093\/nar\/gkq352","article-title":"VISIBIOweb: visualization and layout services for BioPAX pathway models","volume":"38","author":"Dilek","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2021072117054998500_ref100","first-page":"17","article-title":"Rule-based modelling of cellular signalling. CONCUR 2007\u2014Concurr","author":"Danos","year":"2007","journal-title":"Theory"},{"key":"2021072117054998500_ref101","first-page":"822668","article-title":"Assembling a phosphoproteomic knowledge base using ProtMapper to normalize phosphosite information from databases and text mining","author":"Bachman","year":"2019","journal-title":"bioRxiv"},{"key":"2021072117054998500_ref102","article-title":"Setting the basis of best practices and standards for curation and annotation of logical models in biology\u2014highlights of the [BC]2 2019 CoLoMoTo\/SysMod workshop","author":"Niarakis","year":"2020","journal-title":"Brief Bioinform"},{"key":"2021072117054998500_ref103","doi-asserted-by":"crossref","first-page":"2636","DOI":"10.1093\/bioinformatics\/btz959","article-title":"The ELIXIR Core data resources: fundamental infrastructure for the life sciences","volume":"36","author":"Drysdale","year":"2020","journal-title":"Bioinformatics"},{"key":"2021072117054998500_ref104","doi-asserted-by":"crossref","first-page":"D841","DOI":"10.1093\/nar\/gkr1088","article-title":"The IntAct molecular interaction database in 2012","volume":"40","author":"Kerrien","year":"2012","journal-title":"Nucleic Acids Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/4\/bbaa390\/39165031\/bbaa390.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/4\/bbaa390\/39165031\/bbaa390.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,14]],"date-time":"2023-10-14T12:34:22Z","timestamp":1697286862000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaa390\/6055722"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,30]]},"references-count":104,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2021,7,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaa390","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,7]]},"published":{"date-parts":[[2020,12,30]]},"article-number":"bbaa390"}}