{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:34:36Z","timestamp":1761237276024},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"S4","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2005,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Backgorund<\/jats:title>\n            <jats:p>The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to automate accesses to remote sites and to \"understand\" the information that it is managing in order to link data properly. Workflow management systems combined with Web Services are promising Information and Communication Technologies (ICT) tools. Some have already been proposed and are being increasingly applied to the biomedical domain, especially as many biology-related Web Services are now becoming available. Information on biological resources and on genomic sequences mutations are two examples of very specialized datasets that are useful for specific research domains.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The architecture of a system that is able to access and execute predefined workflows is presented in this paper. Web Services allowing access to the IARC TP53 Mutation Database and CABRI catalogues of biological resources have been implemented and are available on-line. Example workflows which retrieve data from these Web Services have also been created and are available on-line.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We present a general architecture and some building blocks for the implementation of a system that is able to remotely execute workflows of biomedical interest and show how this approach can effectively produce useful outputs. The further development and implementation of Web Services allowing access to an exhaustive set of biomedical databases and the creation of effective and useful workflows will improve the automation of <jats:italic>in-silico<\/jats:italic> analysis.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-6-s4-s24","type":"journal-article","created":{"date-parts":[[2005,12,3]],"date-time":"2005-12-03T07:14:06Z","timestamp":1133594046000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Web services and workflow management for biological resources"],"prefix":"10.1186","volume":"6","author":[{"given":"Paolo","family":"Romano","sequence":"first","affiliation":[]},{"given":"Domenico","family":"Marra","sequence":"additional","affiliation":[]},{"given":"Luciano","family":"Milanesi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,12,1]]},"reference":[{"key":"739_CR1","unstructured":"Workflow Management Coalition (WfMC)[http:\/\/www.wfmc.org\/]"},{"key":"739_CR2","first-page":"1904","volume":"13","author":"S Hoon","year":"2003","unstructured":"Hoon S, Kumar Ratnapu J, Chia J, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E: Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis. Genome Research 2003, 13: 1904\u20131915. doi:10.1101\/gr.1363103","journal-title":"Genome Research"},{"issue":"1","key":"739_CR3","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/bioinformatics\/17.1.73","volume":"17","author":"C Letondal","year":"2001","unstructured":"Letondal C: A Web interface generator for molecular biology programs in Unix. Bioinformatics 2001, 17(1):73\u201382. 10.1093\/bioinformatics\/17.1.73","journal-title":"Bioinformatics"},{"key":"739_CR4","volume-title":"BioWBI and WEE: Tools for Bioinformatics Analysis Workflows","author":"Life Sciences Practice Team","year":"2004","unstructured":"Life Sciences Practice Team: BioWBI and WEE: Tools for Bioinformatics Analysis Workflows. IBM Business Consulting Services-AIS; 2004."},{"issue":"17","key":"739_CR5","doi-asserted-by":"publisher","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","volume":"20","author":"T Oinn","year":"2004","unstructured":"Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004, 20(17):3045\u20133054. 10.1093\/bioinformatics\/bth361","journal-title":"Bioinformatics"},{"key":"739_CR6","unstructured":"Web Services activities at the World-Wide Web Consortium (W3C)[http:\/\/w3.org\/2002\/ws\/]"},{"key":"739_CR7","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/417119a","volume":"417","author":"L Stein","year":"2002","unstructured":"Stein L: Creating a bioinformatics nation. Nature 2002, 417: 119\u2013120. 10.1038\/417119a","journal-title":"Nature"},{"issue":"6","key":"739_CR8","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1093\/bioinformatics\/btg214","volume":"19","author":"DC Jamison","year":"2003","unstructured":"Jamison DC: Open Bioinformatics. (editorial). Bioinformatics 2003, 19(6):679\u2013680. 10.1093\/bioinformatics\/btg214","journal-title":"(editorial). Bioinformatics"},{"key":"739_CR9","unstructured":"Entrez Utilities Web Service at NCBI[http:\/\/eutils.ncbi.nlm.nih.gov\/entrez\/query\/static\/esoap_help.html]"},{"key":"739_CR10","unstructured":"Web Services at NCICB[http:\/\/ncicb.nci.nih.gov\/]"},{"key":"739_CR11","unstructured":"KEGG Web Services[http:\/\/www.genome.jp\/kegg\/soap\/]"},{"key":"739_CR12","unstructured":"MySQL data management system[http:\/\/www.mysql.com\/]"},{"key":"739_CR13","unstructured":"Common Access to Biological Resources and Information (CABRI) network service[http:\/\/www.cabri.org\/]"},{"key":"739_CR14","unstructured":"European Biological Resource Centres Network (EBRCN)[http:\/\/www.ebrcn.org\/]"},{"key":"739_CR15","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/S0076-6879(96)66010-8","volume":"266","author":"T Etzold","year":"1996","unstructured":"Etzold T, Ulyanov A, Argos P: SRS: information retrieval system for molecular biology data banks. Meth Enzymol 1996, 266: 114\u2013128.","journal-title":"Meth Enzymol"},{"key":"739_CR16","unstructured":"CABRI Guidelines for Catalogue Production: data input and authentication[http:\/\/www.cabri.org\/guidelines\/catalogue\/CPdata.html]"},{"issue":"6","key":"739_CR17","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1002\/humu.10081","volume":"19","author":"M Olivier","year":"2002","unstructured":"Olivier M, et al.: The IARC TP53 Database: new online mutation analysis and recommendations to users. Hum Mutat 2002, 19(6):607\u201314. 10.1002\/humu.10081","journal-title":"Hum Mutat"},{"key":"739_CR18","unstructured":"TP53 Mutation Database at IARC[http:\/\/www-p53.iarc.fr\/]"},{"key":"739_CR19","unstructured":"SRS implementation of IARC TP53 Mutation Database[http:\/\/srs.o2i.it\/]"},{"key":"739_CR20","unstructured":"Soaplab[http:\/\/www.ebi.ac.uk\/soaplab\/]"},{"key":"739_CR21","first-page":"509","volume-title":"Proceedings, UK e-Science, All Hands Meeting Editors \u2013 Simon J Cox","author":"M Senger","year":"2003","unstructured":"Senger M, Rice P, Oinn T: Soaplab \u2013 a unified Sesame door to analysis tools. Proceedings, UK e-Science, All Hands Meeting Editors \u2013 Simon J Cox 2003, 509\u2013513. ISBN-1\u2013904425\u201311\u20139"},{"key":"739_CR22","unstructured":"Demo Workflows[http:\/\/www.o2i.it\/workflows\/]"},{"issue":"1","key":"739_CR23","doi-asserted-by":"publisher","first-page":"i302","DOI":"10.1093\/bioinformatics\/btg1041","volume":"19","author":"R Stevens","year":"2003","unstructured":"Stevens R, Robinson A, Goble C: \n                    my\n                  Grid: personalised bioinformatics on the information grid. Bioinformatics 2003, 19(1):i302-i304. doi:10.1093\/bioinformatics\/btg1041 10.1093\/bioinformatics\/btg1041","journal-title":"Bioinformatics"},{"key":"739_CR24","unstructured":"Oncology over Internet Soaplab server[http:\/\/www.o2i.it:8080\/axis\/services]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-S4-S24.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T08:23:06Z","timestamp":1630484586000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-S4-S24"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,12]]},"references-count":24,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2005,12]]}},"alternative-id":["739"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-s4-s24","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,12]]},"assertion":[{"value":"1 December 2005","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S24"}}