{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:36:06Z","timestamp":1763811366791,"version":"3.41.2"},"reference-count":43,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T00:00:00Z","timestamp":1711497600000},"content-version":"vor","delay-in-days":86,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in a format suitable for systems biology applications. Importantly, curation should capture the complexity of molecular interactions in such a format together with annotations of the involved elements and support stable identifiers and versioning. This challenge calls for novel collaborative tools and platforms allowing to improve the quality and the output of the curation process. In particular, community-based curation, an important source of curated knowledge, requires support in role management, reviewing features and versioning. Here, we present Biological Knowledge Curation (BioKC), a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML). BioKC offers a graphical user interface for curation of complex molecular interactions and their annotation with stable identifiers and supporting sentences. With the support of collaborative curation and review, it allows to construct building blocks for systems biology diagrams and computational models. These building blocks can be published under stable identifiers and versioned and used as annotations, supporting knowledge building for modelling activities.<\/jats:p>","DOI":"10.1093\/database\/baae013","type":"journal-article","created":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T19:56:52Z","timestamp":1711569412000},"source":"Crossref","is-referenced-by-count":1,"title":["BioKC: a collaborative platform for curation and annotation of molecular interactions"],"prefix":"10.1093","volume":"2024","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7979-9921","authenticated-orcid":false,"given":"Carlos","family":"Vega","sequence":"first","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, Universit\u00e9 du Luxembourg , 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette 4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1473-370X","authenticated-orcid":false,"given":"Marek","family":"Ostaszewski","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, Universit\u00e9 du Luxembourg , 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette 4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6501-0806","authenticated-orcid":false,"given":"Valentin","family":"Grou\u00e8s","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, Universit\u00e9 du Luxembourg , 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette 4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8278-1618","authenticated-orcid":false,"given":"Reinhard","family":"Schneider","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, Universit\u00e9 du Luxembourg , 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette 4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6532-5880","authenticated-orcid":false,"given":"Venkata","family":"Satagopam","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, Universit\u00e9 du Luxembourg , 7 Avenue des Hauts Fourneaux, Esch-sur-Alzette 4362, Luxembourg"}]}],"member":"286","published-online":{"date-parts":[[2024,3,27]]},"reference":[{"key":"2024062912183183400_R1","doi-asserted-by":"crossref","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":"2024062912183183400_R2","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1146\/annurev.bi.39.070170.002353","article-title":"Computer applications to biochemical kinetics","volume":"39","author":"Garfinkel","year":"1970","journal-title":"Annu. Rev. Biochem."},{"key":"2024062912183183400_R3","first-page":"3","article-title":"The kinetics of the enzyme-substrate compound of peroxidase. 1943","volume":"73","author":"Chance","year":"1999","journal-title":"Adv. Enzymol. Relat. Areas. Mol. Biol."},{"key":"2024062912183183400_R4","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gkab1028","article-title":"The reactome pathway knowledgebase 2022","volume":"50","author":"Gillespie","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024062912183183400_R5","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":"2024062912183183400_R6","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":"2024062912183183400_R7","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":"2024062912183183400_R8","doi-asserted-by":"crossref","first-page":"1475","DOI":"10.1093\/bioinformatics\/btaa850","article-title":"Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps","volume":"37","author":"Balci","year":"2021","journal-title":"Bioinformatics"},{"key":"2024062912183183400_R9","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1093\/bib\/bbz067","article-title":"Closing the gap between formats for storing layout information in systems biology","volume":"21","author":"Hoksza","year":"2020","journal-title":"Brief. Bioinform."},{"key":"2024062912183183400_R10","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nmeth.1931","article-title":"Protein interaction data curation: the International Molecular Exchange (IMEx) consortium","volume":"9","author":"Orchard","year":"2012","journal-title":"Nat. Methods"},{"key":"2024062912183183400_R11","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":"2024062912183183400_R12","doi-asserted-by":"crossref","first-page":"51","DOI":"10.3233\/ISU-2010-0613","article-title":"The anatomy of a nanopublication","volume":"30","author":"Groth","year":"2010","journal-title":"ISU"},{"key":"2024062912183183400_R13","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.jbi.2009.02.001","article-title":"Collaborative text-annotation resource for disease-centered relation extraction from biomedical text","volume":"42","author":"Cano","year":"2009","journal-title":"J. Biomed. Inform."},{"author":"W3C","key":"2024062912183183400_R14","article-title":"RDF 1.1 Concepts and Abstract Syntax"},{"volume-title":"BioKC: a platform for quality controlled curation and annotation of systems biology models","year":"2020","author":"Vega","key":"2024062912183183400_R15"},{"article-title":"BioKB - Text mining and semantic technologies for the biomedical content discovery","year":"2018","author":"Biryukov","key":"2024062912183183400_R16"},{"key":"2024062912183183400_R17","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1093\/bib\/bbs084","article-title":"A survey on annotation tools for the biomedical literature","volume":"15","author":"Neves","year":"2014","journal-title":"Brief. Bioinform."},{"key":"2024062912183183400_R18","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1093\/bib\/bbz130","article-title":"An extensive review of tools for manual annotation of documents","volume":"22","author":"Neves","year":"2021","journal-title":"Brief. Bioinform."},{"key":"2024062912183183400_R19","doi-asserted-by":"crossref","first-page":"bau067","DOI":"10.1093\/database\/bau067","article-title":"Assisting manual literature curation for protein-protein interactions using BioQRator","volume":"2014","author":"Kwon","year":"2014","journal-title":"Database"},{"key":"2024062912183183400_R20","doi-asserted-by":"crossref","first-page":"W523","DOI":"10.1093\/nar\/gky428","article-title":"ezTag: tagging biomedical concepts via interactive learning","volume":"46","author":"Kwon","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2024062912183183400_R21","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1093\/bioinformatics\/bts435","article-title":"MyMiner: a web application for computer-assisted biocuration and text annotation","volume":"28","author":"Salgado","year":"2012","journal-title":"Bioinformatics"},{"key":"2024062912183183400_R22","doi-asserted-by":"crossref","first-page":"bau033","DOI":"10.1093\/database\/bau033","article-title":"tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles","volume":"2014","author":"Cejuela","year":"2014","journal-title":"Database"},{"key":"2024062912183183400_R23","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1038\/nbt1111","article-title":"Using process diagrams for the graphical representation of biological networks","volume":"23","author":"Kitano","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2024062912183183400_R24","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2024062912183183400_R25","doi-asserted-by":"crossref","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":"2024062912183183400_R26","doi-asserted-by":"crossref","DOI":"10.1186\/1752-0509-7-100","article-title":"NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps","volume":"7","author":"Kuperstein","year":"2013","journal-title":"BMC Syst. Biol."},{"key":"2024062912183183400_R27","doi-asserted-by":"crossref","first-page":"W225","DOI":"10.1093\/nar\/gkz440","article-title":"BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data","volume":"47","author":"Kolpakov","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2024062912183183400_R28","doi-asserted-by":"crossref","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":"2024062912183183400_R29","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/bib\/bby087","article-title":"Harmonizing semantic annotations for computational models in biology","volume":"20","author":"Neal","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2024062912183183400_R30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bib\/bbab049","article-title":"SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks","volume":"22","author":"Rougny","year":"2021","journal-title":"Brief. Bioinform."},{"key":"2024062912183183400_R31","first-page":"pp. 102","article-title":"brat: a web-based tool for NLP-assisted text annotation","author":"Stenetorp","year":"2012"},{"key":"2024062912183183400_R32","first-page":"pp. 1","article-title":"WebAnno: a flexible, web-based and visually supported system for distributed annotations","author":"Yimam","year":"2013"},{"key":"2024062912183183400_R33","first-page":"63","article-title":"FoLiA: a practical XML format for linguistic annotation - a descriptive and comparative study","volume":"3","author":"van Gompel","year":"2014","journal-title":"Comput. Linguist. Neth. J."},{"key":"2024062912183183400_R34","doi-asserted-by":"crossref","first-page":"D689","DOI":"10.1093\/nar\/gkj092","article-title":"BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems","volume":"34","author":"Le Novere","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2024062912183183400_R35","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2012-13-7-r62","article-title":"CIDeR: multifactorial interaction networks in human diseases","volume":"13","author":"Lechner","year":"2012","journal-title":"Genome Biol"},{"key":"2024062912183183400_R36","doi-asserted-by":"crossref","first-page":"i44","DOI":"10.1093\/bioinformatics\/btt227","article-title":"A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text","volume":"29","author":"Miwa","year":"2013","journal-title":"Bioinformatics"},{"key":"2024062912183183400_R37","doi-asserted-by":"crossref","first-page":"D580","DOI":"10.1093\/nar\/gkr1097","article-title":"Identifiers.org and MIRIAM Registry: community resources to provide persistent identification","volume":"40","author":"Juty","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2024062912183183400_R38","doi-asserted-by":"crossref","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":"2024062912183183400_R39","doi-asserted-by":"crossref","DOI":"10.3389\/fbinf.2023.1197310","article-title":"A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance","volume":"3","author":"Mazein","year":"2023","journal-title":"Front. bioinform."},{"key":"2024062912183183400_R40","article-title":"COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms","volume":"17","author":"Ostaszewski","year":"2021","journal-title":"Mol. Syst. Biol."},{"key":"2024062912183183400_R41","doi-asserted-by":"crossref","first-page":"5712","DOI":"10.1093\/bioinformatics\/btaa622","article-title":"The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)","volume":"36","author":"Tour\u00e9","year":"2021","journal-title":"Bioinformatics"},{"key":"2024062912183183400_R42","doi-asserted-by":"crossref","DOI":"10.1515\/jib-2020-0015","article-title":"SBML Level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2","volume":"17","author":"Zhang","year":"2020","journal-title":"J. Integrative Bioinform."},{"key":"2024062912183183400_R43","doi-asserted-by":"crossref","DOI":"10.15252\/msb.202211325","article-title":"Automated assembly of molecular mechanisms at scale from text mining and curated databases","volume":"19","author":"Bachman","year":"2023","journal-title":"Mol. Syst. Biol."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae013\/58365253\/baae013.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae013\/58365253\/baae013.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,29]],"date-time":"2024-06-29T12:25:26Z","timestamp":1719663926000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baae013\/7636031"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,1]]},"references-count":43,"URL":"https:\/\/doi.org\/10.1093\/database\/baae013","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2024,1,1]]},"published":{"date-parts":[[2024,1,1]]},"article-number":"baae013"}}