{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T01:30:45Z","timestamp":1767922245212,"version":"3.49.0"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The increasing availability and diversity of omics data in the post-genomic era offers new perspectives in most areas of biomedical research. Graph-based biological networks models capture the topology of the functional relationships between molecular entities such as gene, protein and small compounds and provide a suitable framework for integrating and analyzing omics-data. The development of software tools capable of integrating data from different sources and to provide flexible methods to reconstruct, represent and analyze topological networks is an active field of research in bioinformatics.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>BisoGenet is a multi-tier application for visualization and analysis of biomolecular relationships. The system consists of three tiers. In the data tier, an in-house database stores genomics information, protein-protein interactions, protein-DNA interactions, gene ontology and metabolic pathways. In the middle tier, a global network is created at server startup, representing the whole data on bioentities and their relationships retrieved from the database. The client tier is a Cytoscape plugin, which manages user input, communication with the Web Service, visualization and analysis of the resulting network.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>BisoGenet is able to build and visualize biological networks in a fast and user-friendly manner. A feature of Bisogenet is the possibility to include coding relations to distinguish between genes and their products. This feature could be instrumental to achieve a finer grain representation of the bioentities and their relationships. The client application includes network analysis tools and interactive network expansion capabilities. In addition, an option is provided to allow other networks to be converted to BisoGenet. This feature facilitates the integration of our software with other tools available in the Cytoscape platform. BisoGenet is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/bio.cigb.edu.cu\/bisogenet-cytoscape\/\" ext-link-type=\"uri\">http:\/\/bio.cigb.edu.cu\/bisogenet-cytoscape\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-91","type":"journal-article","created":{"date-parts":[[2010,2,17]],"date-time":"2010-02-17T19:15:47Z","timestamp":1266434147000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":269,"title":["BisoGenet: a new tool for gene network building, visualization and analysis"],"prefix":"10.1186","volume":"11","author":[{"given":"Alexander","family":"Martin","sequence":"first","affiliation":[]},{"given":"Maria E","family":"Ochagavia","sequence":"additional","affiliation":[]},{"given":"Laya C","family":"Rabasa","sequence":"additional","affiliation":[]},{"given":"Jamilet","family":"Miranda","sequence":"additional","affiliation":[]},{"given":"Jorge","family":"Fernandez-de-Cossio","sequence":"additional","affiliation":[]},{"given":"Ricardo","family":"Bringas","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,2,17]]},"reference":[{"key":"3548_CR1","doi-asserted-by":"publisher","first-page":"D54","DOI":"10.1093\/nar\/gki031","volume":"33","author":"D Maglott","year":"2005","unstructured":"Maglott D, Ostell J, Pruitt KD, Tatusova T: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2005, 33: D54-D58. 10.1093\/nar\/gki031","journal-title":"Nucleic Acids Res"},{"key":"3548_CR2","doi-asserted-by":"publisher","first-page":"D707","DOI":"10.1093\/nar\/gkm988","volume":"36","author":"P Flicek","year":"2008","unstructured":"Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, et al.: Ensembl 2008. Nucl Acids Res 2008, 36: D707-D714. 10.1093\/nar\/gkm988","journal-title":"Nucl Acids Res"},{"key":"3548_CR3","first-page":"D449","volume-title":"Nucleic Acids Res","author":"L Salwinski","year":"2004","unstructured":"Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, (32 Database):D449-D451. 10.1093\/nar\/gkh086"},{"key":"3548_CR4","doi-asserted-by":"publisher","first-page":"D418","DOI":"10.1093\/nar\/gki051","volume":"33","author":"C Alfarano","year":"2005","unstructured":"Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, et al.: The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33: D418-D424. 10.1093\/nar\/gki051","journal-title":"Nucleic Acids Res"},{"key":"3548_CR5","first-page":"D411","volume-title":"Nucleic Acids Res","author":"GR Mishra","year":"2006","unstructured":"Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, et al.: Human protein reference database--2006 update. Nucleic Acids Res 2006, (34 Database):D411-D414. 10.1093\/nar\/gkj141"},{"key":"3548_CR6","first-page":"D535","volume-title":"Nucleic Acids Res","author":"C Stark","year":"2006","unstructured":"Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, (34 Database):D535-D539. 10.1093\/nar\/gkj109"},{"key":"3548_CR7","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/S0014-5793(01)03293-8","volume":"513","author":"A Zanzoni","year":"2002","unstructured":"Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G: MINT: a Molecular INTeraction database. FEBS Lett 2002, 513: 135\u2013140. 10.1016\/S0014-5793(01)03293-8","journal-title":"FEBS Lett"},{"key":"3548_CR8","doi-asserted-by":"publisher","first-page":"D561","DOI":"10.1093\/nar\/gkl958","volume":"35","author":"S Kerrien","year":"2007","unstructured":"Kerrien S, Alam-Faruque Y, Aranda B, .Bancarz I, Bridge A, Derow C, et al.: IntAct - Open Source Resource for Molecular Interaction Data. Nucleic Acids Res 2007, 35: D561-D565. 10.1093\/nar\/gkl958","journal-title":"Nucleic Acids Res"},{"key":"3548_CR9","doi-asserted-by":"publisher","first-page":"D480","DOI":"10.1093\/nar\/gkm882","volume":"36","author":"M Kanehisa","year":"2008","unstructured":"Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al.: KEGG for linking genomes to life and the environment. Nucl Acids Res 2008, 36: D480-D484. 10.1093\/nar\/gkm882","journal-title":"Nucl Acids Res"},{"key":"3548_CR10","doi-asserted-by":"publisher","first-page":"R39","DOI":"10.1186\/gb-2007-8-3-r39","volume":"8","author":"I Vastrik","year":"2007","unstructured":"Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, et al.: Reactome: a knowledge base of biologic pathways and processes. Genome Biol 2007, 8: R39. 10.1186\/gb-2007-8-3-r39","journal-title":"Genome Biol"},{"key":"3548_CR11","doi-asserted-by":"publisher","first-page":"D623","DOI":"10.1093\/nar\/gkm900","volume":"36","author":"R Caspi","year":"2008","unstructured":"Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, et al.: The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases. Nucl Acids Res 2008, 36: D623-D631. 10.1093\/nar\/gkm900","journal-title":"Nucl Acids Res"},{"key":"3548_CR12","doi-asserted-by":"publisher","first-page":"D674","DOI":"10.1093\/nar\/gkn653","volume":"37","author":"CF Schaefer","year":"2009","unstructured":"Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, et al.: PID: the Pathway Interaction Database. Nucl Acids Res 2009, 37: D674-D679. 10.1093\/nar\/gkn653","journal-title":"Nucl Acids Res"},{"key":"3548_CR13","doi-asserted-by":"publisher","first-page":"e1000385","DOI":"10.1371\/journal.pcbi.1000385","volume":"5","author":"S Klamts","year":"2009","unstructured":"Klamts S, Haus UU, Theis F: Hypergraphs and Cellular Networks. Plos Computational Biology 2009, 5: e1000385. 10.1371\/journal.pcbi.1000385","journal-title":"Plos Computational Biology"},{"key":"3548_CR14","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13: 2498\u20132504. 10.1101\/gr.1239303","journal-title":"Genome Res"},{"key":"3548_CR15","doi-asserted-by":"publisher","first-page":"D623","DOI":"10.1093\/nar\/gkm900","volume":"36","author":"R Caspi","year":"2008","unstructured":"Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, et al.: The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases. Nucl Acids Res 2008, 36: D623-D631. 10.1093\/nar\/gkm900","journal-title":"Nucl Acids Res"},{"key":"3548_CR16","doi-asserted-by":"publisher","first-page":"W352","DOI":"10.1093\/nar\/gki431","volume":"33","author":"Z Hu","year":"2005","unstructured":"Hu Z, Mellor J, Wu J, DeLisi C: VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res 2005, 33: W352-W357. 10.1093\/nar\/gki431","journal-title":"Nucleic Acids Res"},{"key":"3548_CR17","doi-asserted-by":"publisher","first-page":"R22","DOI":"10.1186\/gb-2003-4-3-r22","volume":"4","author":"BJ Breitkreutz","year":"2003","unstructured":"Breitkreutz BJ, Stark C, Tyers M: Osprey: a network visualization system. Genome Biol 2003, 4: R22. 10.1186\/gb-2003-4-3-r22","journal-title":"Genome Biol"},{"key":"3548_CR18","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: BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res 2006, 34: W466-W471. 10.1093\/nar\/gkl308","journal-title":"Nucleic Acids Res"},{"key":"3548_CR19","volume-title":"BioData Min","author":"GA Pavlopoulos","year":"2009","unstructured":"Pavlopoulos GA, Wegener AL, Schneider R: A survey of visualization tools for biological network analysis. BioData Min 2009., 1:"},{"key":"3548_CR20","doi-asserted-by":"publisher","first-page":"2651","DOI":"10.1093\/bioinformatics\/btm401","volume":"23","author":"M Suderman","year":"2007","unstructured":"Suderman M, Hallett M: Tools for visually exploring biological networks. Bioinformatics 2007, 23: 2651\u20132659. 10.1093\/bioinformatics\/btm401","journal-title":"Bioinformatics"},{"key":"3548_CR21","unstructured":"Cytoscape plugins[http:\/\/www.cytoscape.org\/plugins\/index.php]"},{"key":"3548_CR22","unstructured":"Pathway Commons[http:\/\/www.pathwaycommons.org\/]"},{"key":"3548_CR23","unstructured":"Intact[http:\/\/www.ebi.ac.uk\/intact\/]"},{"key":"3548_CR24","unstructured":"Cytoscape Plugin for MiMI[http:\/\/mimiplugin.ncibi.org\/index.html]"},{"key":"3548_CR25","doi-asserted-by":"publisher","first-page":"2495","DOI":"10.1093\/bioinformatics\/btm373","volume":"23","author":"J Hernandez-Toro","year":"2007","unstructured":"Hernandez-Toro J, Prieto C, De Las Rivas J: APID2NET: unified interactome graphic analyzer. Bioinformatics 2007, 23: 2495\u20132497. 10.1093\/bioinformatics\/btm373","journal-title":"Bioinformatics"},{"key":"3548_CR26","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1093\/bioinformatics\/btm553","volume":"24","author":"A Zinovyev","year":"2008","unstructured":"Zinovyev A, Viara E, Calzone L, Barillot E: BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 2008, 24: 876\u2013877. 10.1093\/bioinformatics\/btm553","journal-title":"Bioinformatics"},{"key":"3548_CR27","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","volume":"1","author":"A Funahashi","year":"2003","unstructured":"Funahashi A, Tanimura N, Morohashi M, Kitano H: CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 2003, 1: 159\u2013162. 10.1016\/S1478-5382(03)02370-9","journal-title":"BIOSILICO"},{"key":"3548_CR28","doi-asserted-by":"publisher","first-page":"3754","DOI":"10.1093\/nar\/gkf492","volume":"30","author":"Q Xu","year":"2009","unstructured":"Xu Q, Modrek B, Lee C: Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res 2009, 30: 3754\u20133766. 10.1093\/nar\/gkf492","journal-title":"Nucleic Acids Res"},{"key":"3548_CR29","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1038\/nrg2164","volume":"8","author":"GS Wang","year":"2007","unstructured":"Wang GS, Cooper TA: Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007, 8: 749\u2013761. 10.1038\/nrg2164","journal-title":"Nat Rev Genet"},{"key":"3548_CR30","unstructured":"NCBI Mapview[http:\/\/www.ncbi.nlm.nih.gov\/mapview]"},{"key":"3548_CR31","doi-asserted-by":"crossref","unstructured":"Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, et al.: The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 2006, (34 Database):D187-D191. 10.1093\/nar\/gkj161","DOI":"10.1093\/nar\/gkj161"},{"key":"3548_CR32","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25\u201329. 10.1038\/75556","journal-title":"Nat Genet"},{"key":"3548_CR33","doi-asserted-by":"publisher","first-page":"D480","DOI":"10.1093\/nar\/gkm882","volume":"36","author":"M Kanehisa","year":"2008","unstructured":"Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al.: KEGG for linking genomes to life and the environment. Nucl Acids Res 2008, 36: D480-D484. 10.1093\/nar\/gkm882","journal-title":"Nucl Acids Res"},{"key":"3548_CR34","volume-title":"Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders","author":"VA McKusick","year":"2009","unstructured":"McKusick VA: Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders. Baltimore: Johns Hopkins University Press; 2009."},{"key":"3548_CR35","first-page":"1","volume-title":"The NCBI Handbook","author":"JU Pontius","year":"2009","unstructured":"Pontius JU, Wagner L, Schuler GD: UniGene: a unified view of the transcriptome. In The NCBI Handbook. Bethesda (MD): National Center for Biotechnology Information; 2009:1\u201312."},{"key":"3548_CR36","doi-asserted-by":"publisher","first-page":"D61","DOI":"10.1093\/nar\/gkl842","volume":"35","author":"KD Pruitt","year":"2007","unstructured":"Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35: D61-D65. 10.1093\/nar\/gkl842","journal-title":"Nucleic Acids Res"},{"key":"3548_CR37","doi-asserted-by":"publisher","first-page":"D138","DOI":"10.1093\/nar\/gkh121","volume":"32","author":"A Bateman","year":"2004","unstructured":"Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths JS, et al.: The Pfam protein families database. Nucleic Acids Res 2004, 32: D138-D141. 10.1093\/nar\/gkh121","journal-title":"Nucleic Acids Res"},{"key":"3548_CR38","unstructured":"PubMed[http:\/\/www.ncbi.nlm.nih.gov\/Pubmed\/]"},{"key":"3548_CR39","unstructured":"JUNG: Java Universal Network\/Graph Framework[http:\/\/jung.sourceforge.net\/]"},{"key":"3548_CR40","unstructured":"JFreeChart[http:\/\/www.jfree.org\/jfreechart\/]"},{"key":"3548_CR41","unstructured":"CERN colt project[http:\/\/acs.lbl.gov\/~hoschek\/colt\/]"},{"key":"3548_CR42","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1038\/nrg2164","volume":"8","author":"GS Wang","year":"2007","unstructured":"Wang GS, Cooper TA: Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007, 8: 749\u2013761. 10.1038\/nrg2164","journal-title":"Nat Rev Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-91.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T12:15:47Z","timestamp":1630498547000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-91"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,2,17]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3548"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-91","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,2,17]]},"assertion":[{"value":"25 July 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"91"}}