{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:53:31Z","timestamp":1760709211119,"version":"3.37.3"},"reference-count":15,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,12,13]],"date-time":"2016-12-13T00:00:00Z","timestamp":1481587200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,12,13]],"date-time":"2016-12-13T00:00:00Z","timestamp":1481587200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Metabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload. How do we enable scientists to rapidly construct personalized multi-pathway diagrams that depict a desired collection of interacting pathways that emphasize particular pathway interactions?<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts. The user specifies a set of pathways of interest for the collage from a Pathway\/Genome Database. Layouts for the individual pathways are generated by the Pathway Tools software, and are sent to a Javascript Pathway Collage application implemented using Cytoscape.js. That application allows the user to re-position pathways; define connections between pathways; change visual style parameters; and paint metabolomics, gene expression, and reaction flux data onto the collage to obtain a desired multi-pathway diagram. We demonstrate the use of pathway collages in two application areas: a metabolomics study of pathogen drug response, and an <jats:italic>Escherichia coli<\/jats:italic> metabolic model.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Pathway collages enable facile construction of personalized multi-pathway diagrams.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1382-1","type":"journal-article","created":{"date-parts":[[2016,12,13]],"date-time":"2016-12-13T10:59:34Z","timestamp":1481626774000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Pathway collages: personalized multi-pathway diagrams"],"prefix":"10.1186","volume":"17","author":[{"given":"Suzanne","family":"Paley","sequence":"first","affiliation":[]},{"given":"Paul E.","family":"O\u2019Maille","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Weaver","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5876-6418","authenticated-orcid":false,"given":"Peter D.","family":"Karp","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,12,13]]},"reference":[{"issue":"5","key":"1382_CR1","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1093\/bib\/bbv079","volume":"17","author":"PD Karp","year":"2015","unstructured":"Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R. Pathway Tools version 19.0 update: Software for pathway\/genome informatics and systems biology. Brief Bioinform. 2015; 17(5):877\u201390. doi:10.1093\/bib\/bbv079.","journal-title":"Brief Bioinform"},{"issue":"Suppl 6 Proceed","key":"1382_CR2","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1753-6561-9-S6-S4","volume":"9","author":"F Paduano","year":"2015","unstructured":"Paduano F, Forbes AG. Extended linesets: a visualization technique for the interactive inspection of biological pathways. BMC Proc. 2015; 9(Suppl 6 Proceedings of the 5th Symposium on Biological Data S4):S4. doi:10.1186\/1753-6561-9-S6-S4. eCollection 2015","journal-title":"BMC Proc"},{"key":"1382_CR3","unstructured":"Example Pathway Collage. http:\/\/biocyc.org\/pathway-collage-info. 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Bioinformatics. 2011; 27(3):431\u20132.","journal-title":"Bioinformatics"},{"issue":"2","key":"1382_CR8","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","volume":"32","author":"M Franz","year":"2016","unstructured":"Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD. Cytoscape.js: a graph theory library for visualisation and analysis. Bioinformatics. 2016; 32(2):309\u201311. doi:10.1093\/bioinformatics\/btv557.","journal-title":"Bioinformatics"},{"key":"1382_CR9","unstructured":"Cytoscape.js. http:\/\/js.cytoscape.org\/. Accessed 29 Nov 2016."},{"key":"1382_CR10","doi-asserted-by":"publisher","first-page":"bat061","DOI":"10.1093\/database\/bat061","volume":"2013","author":"M Travers","year":"2013","unstructured":"Travers M, Paley SM, Shrager J, Holland TA, Karp PD. Groups: knowledge spreadsheets for symbolic biocomputing. Database. 2013; 2013:bat061. doi:10.1093\/database\/bat061.","journal-title":"Database"},{"key":"1382_CR11","unstructured":"How to Use a Pathway Tools Website. http:\/\/biocyc.org\/PToolsWebsiteHowto.shtml#smarttables. Accessed 29 Nov 2016."},{"key":"1382_CR12","unstructured":"SmartTable for Pathway Collage. http:\/\/biocyc.org\/group?id=biocyc14-61-3670184769. Accessed 29 Nov 2016."},{"key":"1382_CR13","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1146\/annurev.pharmtox.48.113006.094715","volume":"48","author":"R Kaddurah-Daouk","year":"2008","unstructured":"Kaddurah-Daouk R, Kristal BS, Weinshilboum RM. Metabolomics: a global biochemical approach to drug response and disease. Annu Rev Pharmacol Toxicol. 2008; 48:653\u201383.","journal-title":"Annu Rev Pharmacol Toxicol"},{"key":"1382_CR14","unstructured":"Example Pathway Collage. http:\/\/biocyc.org\/cytoscape-js\/ovsubset.html?graph=hpy-metab-example. 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