{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:49:50Z","timestamp":1753876190689,"version":"3.41.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,2,6]],"date-time":"2021-02-06T00:00:00Z","timestamp":1612569600000},"content-version":"vor","delay-in-days":36,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005416","name":"Norges Forskningsr\u00e5d","doi-asserted-by":"publisher","award":["247727\/O70"],"award-info":[{"award-number":["247727\/O70"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Norwegian University of Science and Technology\u2019s Strategic Research Area \"NTNU Health\""},{"name":"ERACoSysMed","award":["COLOSYS"],"award-info":[{"award-number":["COLOSYS"]}]},{"DOI":"10.13039\/501100000921","name":"European Cooperation in Science and Technology","doi-asserted-by":"publisher","award":["CA15205"],"award-info":[{"award-number":["CA15205"]}],"id":[{"id":"10.13039\/501100000921","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,2,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and can be used for connecting biological molecules together to enable the building of regulatory computational models that represent biological systems. However, including a molecular causal interaction in a model requires assessing its relevance to that model, based on the detailed knowledge about the biomolecules, interaction type and biological context. In order to standardize the representation of this knowledge in \u2018causal statements\u2019, we recently developed the Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) guidelines. Here, we introduce causalBuilder: an intuitive web-based curation interface for the annotation of molecular causal interactions that comply with the MI2CAST standard. The causalBuilder prototype essentially embeds the MI2CAST curation guidelines in its interface and makes its rules easy to follow by a curator. In addition, causalBuilder serves as an original application of the Visual Syntax Method general-purpose curation technology and provides both curators and tool developers with an interface that can be fully configured to allow focusing on selected MI2CAST concepts to annotate. After the information is entered, the causalBuilder prototype produces genuine causal statements that can be exported in different formats.<\/jats:p>","DOI":"10.1093\/database\/baaa107","type":"journal-article","created":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T01:51:14Z","timestamp":1607392274000},"source":"Crossref","is-referenced-by-count":2,"title":["CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator"],"prefix":"10.1093","volume":"2021","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4639-4431","authenticated-orcid":false,"given":"Vasundra","family":"Tour\u00e9","sequence":"first","affiliation":[{"name":"Department of Biology, Norwegian University of Science and Technology (NTNU), H\u00f8gskoleringen 5, 7491 Trondheim, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3609-8674","authenticated-orcid":false,"given":"John","family":"Zobolas","sequence":"additional","affiliation":[{"name":"Department of Biology, Norwegian University of Science and Technology (NTNU), H\u00f8gskoleringen 5, 7491 Trondheim, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1171-9876","authenticated-orcid":false,"given":"Martin","family":"Kuiper","sequence":"additional","affiliation":[{"name":"Department of Biology, Norwegian University of Science and Technology (NTNU), H\u00f8gskoleringen 5, 7491 Trondheim, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven","family":"Vercruysse","sequence":"additional","affiliation":[{"name":"Department of Biology, Norwegian University of Science and Technology (NTNU), H\u00f8gskoleringen 5, 7491 Trondheim, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,2,24]]},"reference":[{"key":"2021030607255134500_R1","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btaa622","article-title":"The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)","author":"Tour\u00e9","year":"2020","journal-title":"Bioinformatics"},{"key":"2021030607255134500_R2","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.2002846","article-title":"Biocuration: distilling data into knowledge","volume":"16","author":"International Society for Biocuration","year":"2018","journal-title":"PLoS Biol."},{"key":"2021030607255134500_R3","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gkt1115","article-title":"The MIntAct project\u2014IntAct as a common curation platform for 11 molecular interaction databases","volume":"42","author":"Orchard","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2021030607255134500_R4","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.3-6.v2","article-title":"DataUp: a tool to help researchers describe and share tabular data","volume":"3","author":"Strasser","year":"2014","journal-title":"F1000Research"},{"key":"2021030607255134500_R5","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1109\/WSC.2006.322931","article-title":"Development and implementation of the PSI MI standard for molecular interaction","volume-title":"Proceedings of the 2006 Winter Simulation Conference","author":"Kerrien","year":"2006"},{"key":"2021030607255134500_R6","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":"2021030607255134500_R7","article-title":"Intuitive representation of computable knowledge","author":"Vercruysse","year":"2020","journal-title":"Preprints."},{"key":"2021030607255134500_R8","article-title":"VSM-box: general-purpose interface for biocuration and knowledge representation","author":"Vercruysse","year":"2020","journal-title":"Preprints"},{"key":"2021030607255134500_R9","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The Gene Ontology resource: 20 years and still GOing strong","volume":"47","author":"The Gene OntologyConsortium","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021030607255134500_R10","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.bbapap.2013.02.017","article-title":"Controlled vocabularies and ontologies in proteomics: overview, principles and practice","volume":"1844","author":"Mayer","year":"2014","journal-title":"Biochim. 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