{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T23:05:41Z","timestamp":1717023941631},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.lipidmaps.org\" ext-link-type=\"uri\">http:\/\/www.lipidmaps.org<\/jats:ext-link>. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read\/construct\/write access to models in SBML (Systems Biology Markup Language) contained in the local file system.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-3-99","type":"journal-article","created":{"date-parts":[[2009,10,3]],"date-time":"2009-10-03T10:42:31Z","timestamp":1254566551000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["An editor for pathway drawing and data visualization in the Biopathways Workbench"],"prefix":"10.1186","volume":"3","author":[{"given":"Robert W","family":"Byrnes","sequence":"first","affiliation":[]},{"given":"Dawn","family":"Cotter","sequence":"additional","affiliation":[]},{"given":"Andreia","family":"Maer","sequence":"additional","affiliation":[]},{"given":"Joshua","family":"Li","sequence":"additional","affiliation":[]},{"given":"David","family":"Nadeau","sequence":"additional","affiliation":[]},{"given":"Shankar","family":"Subramaniam","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,10,2]]},"reference":[{"issue":"Suppl 1","key":"367_CR1","doi-asserted-by":"publisher","first-page":"S225","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225","volume":"18","author":"PD Karp","year":"2002","unstructured":"Karp PD, Paley S, Romero P: The Pathway Tools Software. Bioinformatics. 2002, 18 (Suppl 1): S225-S232.","journal-title":"Bioinformatics"},{"key":"367_CR2","doi-asserted-by":"publisher","first-page":"W633","DOI":"10.1093\/nar\/gki391","volume":"33","author":"B Miecnik","year":"2005","unstructured":"Miecnik B, Scheideier M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z: Pathway Explorer: web service for visualizing high-throughput expression data on biological pathways. Nucl Acids Res. 2005, 33: W633-W637. 10.1093\/nar\/gki391","journal-title":"Nucl Acids Res"},{"key":"367_CR3","doi-asserted-by":"publisher","first-page":"2841","DOI":"10.1093\/bioinformatics\/bth278","volume":"20","author":"A Ludermann","year":"2004","unstructured":"Ludermann A, Weicht D, Selbig J, Kopka J: PaVESy: Pathway Visualization and Editing System. Bioinformatics. 2004, 20: 2841-2844. 10.1093\/bioinformatics\/bth278","journal-title":"Bioinformatics"},{"key":"367_CR4","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1147\/rd.506.0561","volume":"50","author":"A Sorokin","year":"2006","unstructured":"Sorokin A, Paly K, Selkov A, Demin O, Dronov S, Ghazai P, Goryanin I: The Pathway Editor: A tool for managing complex biological networks. IBM J Res & Dev. 2006, 50: 561-573.","journal-title":"IBM J Res & Dev"},{"key":"367_CR5","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1093\/bib\/bbl012","volume":"7","author":"V Shulaev","year":"2006","unstructured":"Shulaev V: Metabolomics technology and bioinformatics. Briefings in Bioinformatics. 2006, 7: 128-139. 10.1093\/bib\/bbl012","journal-title":"Briefings in Bioinformatics"},{"key":"367_CR6","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1186\/1471-2105-7-109","volume":"7","author":"BH Junker","year":"2006","unstructured":"Junker BH, Klukas C, Schreiber F: VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006, 7: 109-121. 10.1186\/1471-2105-7-109","journal-title":"BMC Bioinformatics"},{"key":"367_CR7","doi-asserted-by":"publisher","first-page":"W466","DOI":"10.1093\/nar\/gkl308","volume":"34","author":"M Baitaluk","year":"2006","unstructured":"Baitaluk M, Sedova M, Ray A, Gupta A: Biological Networks: visualization and analysis tool for system for systems biology. Nucleic Acids Res. 2006, 34: W466-W471. 10.1093\/nar\/gkl308","journal-title":"Nucleic Acids Res"},{"key":"367_CR8","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1038\/nrd1776","volume":"4","author":"M Wenk","year":"2005","unstructured":"Wenk M: The emerging field of lipidomics. Nat Rev Drug Discov. 2005, 4: 594-610. 10.1038\/nrd1776","journal-title":"Nat Rev Drug Discov"},{"key":"367_CR9","first-page":"169","volume":"432","author":"K Schmelzer","year":"2007","unstructured":"Schmelzer K, Fahy E, Subramaniam S, Dennis E: The LIPID MAPS initiative in lipidomics. Meth Enzymol. 2007, 432: 169-181.","journal-title":"Meth Enzymol"},{"key":"367_CR10","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/S0076-6879(07)32011-9","volume":"432","author":"E Fahy","year":"2007","unstructured":"Fahy E, Cotter D, Byrnes RW, Sud M, Maer A, Li J, Nadeau D, Zhau Y, Subramaniam S: Bioinformatics for lipidomics. Meth Enzymol. 2007, 432: 247-273. full_text","journal-title":"Meth Enzymol"},{"key":"367_CR11","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093\/nar\/28.1.27","journal-title":"Nucleic Acids Res"},{"key":"367_CR12","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1016\/j.jala.2007.04.002","volume":"12","author":"RW Byrnes","year":"2007","unstructured":"Byrnes RW, Fahy E, Subramaniam S: A laboratory information management system for high throughput experimental lipidomics: Minimal information required for the analysis of lipidomics experiments (MIALE). J Assoc Laboratory Automation. 2007, 12: 230-238. 10.1016\/j.jala.2007.04.002.","journal-title":"J Assoc Laboratory Automation"},{"key":"367_CR13","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1194\/jlr.M600027-JLR200","volume":"47","author":"CH Raetz","year":"2006","unstructured":"Raetz CH, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC, Ribeiro RA, Murphy RC, Ulevitch RJ, Fearns C, Riechart D, Glass CK, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry RC, Buczynski MW, Cooper JA, Deems RA, Dennis EA: Purification and properties of Escherichia coli Kdo2-lipid A, a defined endotoxin that activates macrophages via TLR-4. J Lipid Res. 2006, 47: 1097-1111. 10.1194\/jlr.M600027-JLR200","journal-title":"J Lipid Res"},{"key":"367_CR14","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1074\/mcp.M400129-MCP200","volume":"3","author":"PL Ross","year":"2004","unstructured":"Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 2004, 3: 1154-1169. 10.1074\/mcp.M400129-MCP200","journal-title":"Mol Cell Proteomics"},{"key":"367_CR15","unstructured":"LIPID Metabolites and Pathways Strategy. http:\/\/www.lipidmaps.org"},{"key":"367_CR16","unstructured":"LIPID Metabolites and Pathways Strategy Pathway Editor download page and tutorial. http:\/\/www.lipidmaps.org\/pathways\/pathwayeditor.html"},{"key":"367_CR17","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","volume":"24","author":"BJ Bornstein","year":"2008","unstructured":"Bornstein BJ, Keating SM, Jouraku A, Hucka M: LibSBML: an API Library for SBML. Bioinformatics. 2008, 24: 880-881. 10.1093\/bioinformatics\/btn051","journal-title":"Bioinformatics"},{"key":"367_CR18","unstructured":"The Systems Biology Markup Language. http:\/\/sbml.org\/Main_Page"},{"key":"367_CR19","volume-title":"Design Patterns: Elements of Reusable Object-Oriented Software","author":"E Gamma","year":"1995","unstructured":"Gamma E, Helm R, Johnson R, Vlissides J: Design Patterns: Elements of Reusable Object-Oriented Software. 1995, Addison-Wesley: Reading, Massachusetts"},{"key":"367_CR20","doi-asserted-by":"publisher","first-page":"D527","DOI":"10.1093\/nar\/gkl838","volume":"35","author":"M Sud","year":"2007","unstructured":"Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Murphy RC, Raetz CR, Russell DW, Subramaniam S: LMSD: LIPID MAPS structure database. Nucleic Acids Res. 2007, 35: D527-532. 10.1093\/nar\/gkl838","journal-title":"Nucleic Acids Res"},{"key":"367_CR21","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1194\/jlr.E400004-JLR200","volume":"46","author":"E Fahy","year":"2005","unstructured":"Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH, Murphy RC, Raetz CR, Russell DW, Seyama Y, Shaw W: A comprehensive classification system for lipids. J Lipid Res. 2005, 46: 839-862. 10.1194\/jlr.E400004-JLR200","journal-title":"J Lipid Res"},{"key":"367_CR22","doi-asserted-by":"publisher","first-page":"D26","DOI":"10.1093\/nar\/gkl993","volume":"35","author":"D Maglott","year":"2007","unstructured":"Maglott D, Ostell J, Pruitt KD, Tatusova T: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2007, 35: D26-D31. 10.1093\/nar\/gkl993","journal-title":"Nucleic Acids Res"},{"key":"367_CR23","unstructured":"Java bindings for Open GL. https:\/\/jogl.dev.java.net"},{"key":"367_CR24","unstructured":"JFreeChart. http:\/\/www.jfree.org\/jfreechart"},{"key":"367_CR25","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"9","author":"M Hucka","year":"2003","unstructured":"Hucka M, Bolouri H, Finney A, Sauro H, Doyle JHK, Arkin A, Bornstein B, Bray D, Cornish-Bowden A, Cuellar A, Dronov S, Ginkel M, Gor V, Goryanin I, Hedley W, Hodgmean T, Hunter P, Juty N, Kasberger J, Kremling A, Kummer U, Le Novere N, Loew L, Lucio D, Mendes P, Mjolsness E, Nakayama Y, Nelson M, Nielsen P, Sakurada T, Schaff J, Shapiro B, Shimizu T, Spence H, Stelling J, Takashi K, Tomita M, Wagner J, Wang J: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 9: 524-532. 10.1093\/bioinformatics\/btg015.","journal-title":"Bioinformatics"},{"key":"367_CR26","doi-asserted-by":"publisher","first-page":"1963","DOI":"10.1093\/bioinformatics\/btn319","volume":"24","author":"FT Bergmann","year":"2008","unstructured":"Bergmann FT, Sauro HM: Comparing simulation results of SBML capable simulators. Bioinformatics. 2008, 24: 1963-5. 10.1093\/bioinformatics\/btn319","journal-title":"Bioinformatics"},{"key":"367_CR27","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1038\/nbt1156","volume":"23","author":"N Le Novere","year":"2005","unstructured":"Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro BE, Snoep JL, Spence HD, Wanner BL: Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol. 2005, 23: 1509-15. 10.1038\/nbt1156","journal-title":"Nat Biotechnol"},{"key":"367_CR28","unstructured":"The Systems Biology Ontology. http:\/\/www.ebi.ac.uk\/sbo\/"},{"key":"367_CR29","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/1752-0509-1-58","volume":"1","author":"C Laibe","year":"2007","unstructured":"Laibe C, Le Novere N: MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Systems Biology. 2007, 1: 58- 10.1186\/1752-0509-1-58","journal-title":"BMC Systems Biology"},{"key":"367_CR30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0076-6879(07)32001-6","volume":"432","author":"J Krank","year":"2007","unstructured":"Krank J, Murphy RC, Barkley RM, Duchoslav E, McAnoy A: Qualitative analysis and quantitative assessment of changes in neutral glycerol lipid molecular species within cells. Meth Enzymol. 2007, 432: 1-20. full_text","journal-title":"Meth Enzymol"},{"key":"367_CR31","doi-asserted-by":"publisher","first-page":"10241","DOI":"10.1074\/jbc.M709006200","volume":"283","author":"R Harkewicz","year":"2008","unstructured":"Harkewicz R, Hartvigsen K, Almazan F, Dennis EA, Witztum JL, Miller YI: Cholesteryl ester hydroperoxides are biologically active components of minimally oxidized LDL. J Biol Chem. 2008, 283: 10241-10251. 10.1074\/jbc.M709006200","journal-title":"J Biol Chem"},{"key":"367_CR32","unstructured":"Biological Pathways Exchange. http:\/\/www.biopax.org"},{"key":"367_CR33","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"The Gene Ontology Consortium","year":"2000","unstructured":"The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet. 2000, 25: 25-29. 10.1038\/75556","journal-title":"Nature Genet"},{"key":"367_CR34","unstructured":"The Gene Ontology. http:\/\/www.geneontology.org\/index.shtml"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-99.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:22:55Z","timestamp":1630466575000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-3-99"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10,2]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["367"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-3-99","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10,2]]},"assertion":[{"value":"6 March 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 October 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 October 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"99"}}