{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T18:19:57Z","timestamp":1761675597905},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Mass spectrometry experiments in the field of proteomics produce lists containing tens to thousands of identified proteins. With the protein information and property explorer (PIPE), the biologist can acquire functional annotations for these proteins and explore the enrichment of the list, or fraction thereof, with respect to functional classes. These protein lists may be saved for access at a later time or different location. The PIPE is interoperable with the Firegoose and the Gaggle, permitting wide-ranging data exploration and analysis. The PIPE is a rich-client web application which uses AJAX capabilities provided by the Google Web Toolkit, and server-side data storage using Hibernate.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/pipe.systemsbiology.net<\/jats:p>\n               <jats:p>Contact: \u00a0pshannon@systemsbiology.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn363","type":"journal-article","created":{"date-parts":[[2008,7,18]],"date-time":"2008-07-18T00:25:07Z","timestamp":1216340707000},"page":"2110-2111","source":"Crossref","is-referenced-by-count":29,"title":["The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data"],"prefix":"10.1093","volume":"24","author":[{"given":"H.","family":"Ramos","sequence":"first","affiliation":[{"name":"1 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA, 2Institute of Molecular Systems Biology and Competence Center for Systems Physiology and Metabolic Disease, ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]},{"given":"P.","family":"Shannon","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA, 2Institute of Molecular Systems Biology and Competence Center for Systems Physiology and Metabolic Disease, ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]},{"given":"R.","family":"Aebersold","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA, 2Institute of Molecular Systems Biology and Competence Center for Systems Physiology and Metabolic Disease, ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"},{"name":"1 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA, 2Institute of Molecular Systems Biology and Competence Center for Systems Physiology and Metabolic Disease, ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"},{"name":"1 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA, 2Institute of Molecular Systems Biology and Competence Center for Systems Physiology and Metabolic Disease, ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2008,7,16]]},"reference":[{"key":"2023020211094325600_B1","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1186\/1471-2105-8-456","article-title":"The Firegoose: a two-way integration of diverse data from different bioinformatics web resources with desktop applications","volume":"8","author":"Bare","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020211094325600_B2","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/bioinformatics\/btl567","article-title":"Using GOstats to test gene lists for GO term association","volume":"23","author":"Falcon","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020211094325600_B3","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/msb4100024","article-title":"A uniform proteomics MS\/MS analysis platform utilizing open XML file formats","volume":"1","author":"Keller","year":"2005","journal-title":"Mol. Syst. Biol."},{"key":"2023020211094325600_B4","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023020211094325600_B5","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/1471-2105-7-176","article-title":"The Gaggle: an open-source software system for integrating bioinformatics software and data sources","volume":"7","author":"Shannon","year":"2006","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/18\/2110\/49049591\/bioinformatics_24_18_2110.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/18\/2110\/49049591\/bioinformatics_24_18_2110.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:10:14Z","timestamp":1675336214000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/18\/2110\/191097"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,7,16]]},"references-count":5,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2008,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn363","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,9,15]]},"published":{"date-parts":[[2008,7,16]]}}}