{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:19:35Z","timestamp":1761862775726},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3015,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: We present a method for inferring and constructing transport reactions for transporter proteins based primarily on the analysis of the names of individual proteins in the genome annotation of an organism. Transport reactions are declarative descriptions of transporter activities, and thus can be manipulated computationally, unlike free-text protein names. Once transporter activities are encoded as transport reactions, a number of computational analyses are possible including database queries by transporter activity; inclusion of transporters into an automatically generated metabolic-map diagram that can be painted with omics data to aid in their interpretation; detection of anomalies in the metabolic and transport networks, such as substrates that are transported into the cell but are not inputs to any metabolic reaction or pathway; and comparative analyses of the transport capabilities of different organisms.<\/jats:p>\n               <jats:p>Results: On randomly selected organisms, the method achieves precision and recall rates of 0.93 and 0.90, respectively in identifying transporter proteins by name within the complete genome. The method obtains 67.5% accuracy in predicting complete transport reactions; if allowance is made for predictions that are overly general yet not incorrect, reaction prediction accuracy is 82.5%.<\/jats:p>\n               <jats:p>Availability: The method is implemented as part of PathoLogic, the inference component of the Pathway Tools software. Pathway Tools is freely available to researchers at non-commercial institutions, including source code; a fee applies to commercial institutions.<\/jats:p>\n               <jats:p>Contact: \u00a0tomlee@ai.sri.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn180","type":"journal-article","created":{"date-parts":[[2008,6,27]],"date-time":"2008-06-27T07:43:13Z","timestamp":1214552593000},"page":"i259-i267","source":"Crossref","is-referenced-by-count":34,"title":["Annotation-based inference of transporter function"],"prefix":"10.1093","volume":"24","author":[{"given":"Thomas J.","family":"Lee","sequence":"first","affiliation":[{"name":"1 Artificial Intelligence Center, SRI International, Menlo Park, CA, USA and 2Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW, Australia"}]},{"given":"Ian","family":"Paulsen","sequence":"additional","affiliation":[{"name":"1 Artificial Intelligence Center, SRI International, Menlo Park, CA, USA and 2Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW, Australia"}]},{"given":"Peter","family":"Karp","sequence":"additional","affiliation":[{"name":"1 Artificial Intelligence Center, SRI International, Menlo Park, CA, USA and 2Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW, Australia"}]}],"member":"286","published-online":{"date-parts":[[2008,7,1]]},"reference":[{"key":"2023020210392222200_B1","doi-asserted-by":"crossref","first-page":"D724","DOI":"10.1093\/nar\/gkm961","article-title":"The mouse genome database (MGD): mouse biology and model systems","volume":"36","author":"Bult","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020210392222200_B2","doi-asserted-by":"crossref","first-page":"D511","DOI":"10.1093\/nar\/gkj128","article-title":"MetaCyc: a multiorganism database of metabolic pathways and enzymes","volume":"34","author":"Caspi","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023020210392222200_B3","doi-asserted-by":"crossref","first-page":"D623","DOI":"10.1093\/nar\/gkm900","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases","volume":"36","author":"Caspi","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020210392222200_B4","doi-asserted-by":"crossref","first-page":"D423","DOI":"10.1093\/nar\/gkj090","article-title":"Dictybase, the model organism database for dictyostelium discoideum","volume":"34","author":"Chisholm","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023020210392222200_B5","doi-asserted-by":"crossref","first-page":"D440","DOI":"10.1093\/nar\/gkm883","article-title":"The gene ontology project in 2008","volume":"36","author":"Consortium","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020210392222200_B6","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100155","article-title":"A genome-scale metabolic reconstruction for Escherichia coli k-12 mg1655 that accounts for 1260 ORFs and thermodynamic information","volume":"3","author":"Feist","year":"2007","journal-title":"Mol. 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