{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:25:38Z","timestamp":1767961538992,"version":"3.49.0"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed.<\/jats:p>\n               <jats:p>Results: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.<\/jats:p>\n               <jats:p>Contact: \u00a0lestr@ida.liu.se<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti718","type":"journal-article","created":{"date-parts":[[2005,10,19]],"date-time":"2005-10-19T03:38:37Z","timestamp":1129693117000},"page":"4401-4407","source":"Crossref","is-referenced-by-count":100,"title":["Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX"],"prefix":"10.1093","volume":"21","author":[{"given":"Lena","family":"Str\u00f6mb\u00e4ck","sequence":"first","affiliation":[{"name":"Department of Computer and Information Science, Link\u00f6pings universitet \u00a0 S-581 83 Link\u00f6ping, Sweden"}]},{"given":"Patrick","family":"Lambrix","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Science, Link\u00f6pings universitet \u00a0 S-581 83 Link\u00f6ping, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2005,10,18]]},"reference":[{"key":"2023061007325614100_b1","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1093\/bioinformatics\/17.2.115","article-title":"XML, bioinformatics and data integration","volume":"17","author":"Achard","year":"2001","journal-title":"Bioinformatics"},{"key":"2023061007325614100_b2","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/nar\/29.1.242","article-title":"BIND\u2014the Biomolecular Network Database","volume":"29","author":"Bader","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023061007325614100_b3","article-title":"BioPAX\u2014biological pathways exchange language","author":"BioPAX working group","year":"2004"},{"key":"2023061007325614100_b4","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/nature01626","article-title":"A vision for the future of genomics research: a blueprint for the genomic era","volume":"422","author":"Collins","year":"2003","journal-title":"Nature"},{"key":"2023061007325614100_b5","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1089\/cmb.1995.2.557","article-title":"Challenges in integrating biological data sources","volume":"2","author":"Davidson","year":"1995","journal-title":"J. Comput. Biol."},{"key":"2023061007325614100_b6","article-title":"OWL-QL\u2013a language for deductive query answering on the semantic web","volume-title":"Technical report","author":"Fikes","year":"2003"},{"key":"2023061007325614100_b7","article-title":"Systems biology markup language (SBML) Level 3: proposal: multi-component species features","author":"Finney","year":"2004"},{"key":"2023061007325614100_b8","article-title":"Systems biology markup language (SBML) Level 2: structures and facilities for model definitions","author":"Finney","year":"2003"},{"key":"2023061007325614100_b11","first-page":"148","article-title":"Extended query facilities for racer and an application to software-engineering problems","volume-title":"Proceedings of the 2004 International Workshop on Description Logics (DL-2004)","author":"Haarslev","year":"2004"},{"key":"2023061007325614100_b12","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nbt926","article-title":"The HUPO PSI's molecular interaction format\u2014a community standard for the representation of protein interaction data","volume":"22","author":"Hermjakob","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"2023061007325614100_b13","doi-asserted-by":"crossref","first-page":"D452","DOI":"10.1093\/nar\/gkh052","article-title":"IntAct\u2014an open source molecular interaction database","volume":"32","author":"Hermjakob","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023061007325614100_b14","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"},{"issue":"Database issue","key":"2023061007325614100_b15","doi-asserted-by":"crossref","first-page":"D428","DOI":"10.1093\/nar\/gki072","article-title":"Reactome: a knowledgebase of biological pathways","volume":"33","author":"Joshi-Tope","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023061007325614100_b16","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023061007325614100_b17","doi-asserted-by":"crossref","first-page":"D277","DOI":"10.1093\/nar\/gkh063","article-title":"The KEGG resources for deciphering the genome","volume":"32","author":"Kanehisa","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023061007325614100_b18","first-page":"25","article-title":"The E coli EcoCyc Database: no longer just a metabolic pathway database","volume":"70","author":"Karp","year":"2004","journal-title":"ASM News"},{"key":"2023061007325614100_b19","first-page":"129","article-title":"Ontologies in bioinformatics and systems biology","volume-title":"Artificial Intelligence Methods and Tools for Systems Biology","author":"Lambrix","year":"2004"},{"key":"2023061007325614100_b20","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.pbiomolbio.2004.01.004","article-title":"CellML: its future, present and past","volume":"85","author":"Lloyd","year":"2004","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"2023061007325614100_b22","first-page":"239","article-title":"An evaluation of ontology exchange languages for bioinformatics","volume":"8","author":"McEntire","year":"2000","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"2023061007325614100_b23","first-page":"127","article-title":"Towards the chemical semantic Web","author":"Murray-Rust","year":"2002"},{"key":"2023061007325614100_b24","first-page":"17","article-title":"The knowledge model of Protege-2000: combining interoperability and flexibility","author":"Noy","year":"2000"},{"key":"2023061007325614100_b25","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1101\/gr.1680803","article-title":"Development of human protein reference database as an initial platform for approaching systems biology in humans","volume":"13","author":"Peri","year":"2003","journal-title":"Genome Res."},{"issue":"Database Issue","key":"2023061007325614100_b26","doi-asserted-by":"crossref","first-page":"D449","DOI":"10.1093\/nar\/gkh086","article-title":"The database of interacting proteins: 2004 update","volume":"32","author":"Salvinski","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023061007325614100_b27","article-title":"XML representations of pathway data: a comparison","author":"Str\u00f6mb\u00e4ck","year":"2004"},{"key":"2023061007325614100_b28","first-page":"160","article-title":"An integrated database SPAD (signaling pathway database) for signal transduction and genetic information","author":"Tateishi","year":"1995"},{"key":"2023061007325614100_b29","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/S0014-5793(01)03293-8","article-title":"MINT: a molecular interaction database","volume":"513","author":"Zanzoni","year":"2002","journal-title":"FEBS Lett."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/24\/4401\/50566203\/bioinformatics_21_24_4401.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/24\/4401\/50566203\/bioinformatics_21_24_4401.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T07:33:19Z","timestamp":1686382399000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/24\/4401\/180113"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,10,18]]},"references-count":26,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2005,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti718","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,12,15]]},"published":{"date-parts":[[2005,10,18]]}}}