{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T18:59:53Z","timestamp":1722970793481},"reference-count":27,"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>Many protein structures determined in high-throughput structural genomics centers, despite their significant novelty and importance, are available only as PDB depositions and are not accompanied by a peer-reviewed manuscript. Because of this they are not accessible by the standard tools of literature searches, remaining underutilized by the broad biological community.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To address this issue we have developed TOPSAN, The Open Protein Structure Annotation Network, a web-based platform that combines the openness of the wiki model with the quality control of scientific communication. TOPSAN enables research collaborations and scientific dialogue among globally distributed participants, the results of which are reviewed by experts and eventually validated by peer review. The immediate goal of TOPSAN is to harness the combined experience, knowledge, and data from such collaborations in order to enhance the impact of the astonishing number and diversity of structures being determined by structural genomics centers and high-throughput structural biology.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>TOPSAN combines features of automated annotation databases and formal, peer-reviewed scientific research literature, providing an ideal vehicle to bridge a gap between rapidly accumulating data from high-throughput technologies and a much slower pace for its analysis and integration with other, relevant research.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-426","type":"journal-article","created":{"date-parts":[[2010,8,17]],"date-time":"2010-08-17T19:17:27Z","timestamp":1282072647000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["TOPSAN: a collaborative annotation environment for structural genomics"],"prefix":"10.1186","volume":"11","author":[{"given":"Dana","family":"Weekes","sequence":"first","affiliation":[]},{"given":"S Sri","family":"Krishna","sequence":"additional","affiliation":[]},{"given":"Constantina","family":"Bakolitsa","sequence":"additional","affiliation":[]},{"given":"Ian A","family":"Wilson","sequence":"additional","affiliation":[]},{"given":"Adam","family":"Godzik","sequence":"additional","affiliation":[]},{"given":"John","family":"Wooley","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,8,17]]},"reference":[{"key":"3883_CR1","doi-asserted-by":"publisher","first-page":"1519","DOI":"10.1016\/j.str.2007.11.004","volume":"15","author":"JC Norvell","year":"2007","unstructured":"Norvell JC, Berg JM: Update on the protein structure initiative. Structure 2007, 15: 1519\u20131522. 10.1016\/j.str.2007.11.004","journal-title":"Structure"},{"key":"3883_CR2","unstructured":"Stanford Microarray Database[http:\/\/smd.stanford.edu\/statistics.html#general]"},{"key":"3883_CR3","unstructured":"Entrez Completed genomes[http:\/\/www.ncbi.nlm.nih.gov\/genomes\/lproks.cgi?view=1]"},{"key":"3883_CR4","unstructured":"History of the World Wide Web[http:\/\/en.wikipedia.org\/wiki\/History_of_the_World_Wide_Web]"},{"key":"3883_CR5","doi-asserted-by":"publisher","first-page":"RESEARCH0083","DOI":"10.1186\/gb-2002-3-12-research0083","volume":"3","author":"S Misra","year":"2002","unstructured":"Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, et al.: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol 2002, 3: RESEARCH0083. 10.1186\/gb-2002-3-12-research0083","journal-title":"Genome Biol"},{"key":"3883_CR6","unstructured":"\"Wikipedia, The Free Encyclopedia,\"[http:\/\/www.wikipedia.org]"},{"key":"3883_CR7","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/455022a","volume":"455","author":"M Waldrop","year":"2008","unstructured":"Waldrop M: Big data: Wikiomics. Nature 2008, 455: 22\u201325. 10.1038\/455022a","journal-title":"Nature"},{"key":"3883_CR8","doi-asserted-by":"publisher","first-page":"e184","DOI":"10.1371\/journal.pbio.0060184","volume":"6","author":"AR Pico","year":"2008","unstructured":"Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C: WikiPathways: pathway editing for the people. PLoS Biol 2008, 6: e184. 10.1371\/journal.pbio.0060184","journal-title":"PLoS Biol"},{"key":"3883_CR9","doi-asserted-by":"publisher","first-page":"R121","DOI":"10.1186\/gb-2008-9-8-r121","volume":"9","author":"E Hodis","year":"2008","unstructured":"Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL: Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol 2008, 9: R121. 10.1186\/gb-2008-9-8-r121","journal-title":"Genome Biol"},{"key":"3883_CR10","doi-asserted-by":"publisher","first-page":"R89","DOI":"10.1186\/gb-2008-9-5-r89","volume":"9","author":"B Mons","year":"2008","unstructured":"Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, et al.: Calling on a million minds for community annotation in WikiProteins. Genome Biol 2008, 9: R89. 10.1186\/gb-2008-9-5-r89","journal-title":"Genome Biol"},{"key":"3883_CR11","doi-asserted-by":"publisher","first-page":"baq009","DOI":"10.1093\/database\/baq009","volume":"1","author":"H Stehr","year":"2010","unstructured":"Stehr H, Duarte J, Lappe M, Bhak J, Bolser D: PDBWiki: added value through community annotation of the Protein Data Bank. Database 2010, 1: baq009. 10.1093\/database\/baq009","journal-title":"Database"},{"key":"3883_CR12","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1038\/ng.f.217","volume":"40","author":"R Hoffmann","year":"2008","unstructured":"Hoffmann R: A wiki for the life sciences where authorship matters. Nat Genet 2008, 40: 1047\u20131051. 10.1038\/ng.f.217","journal-title":"Nat Genet"},{"key":"3883_CR13","doi-asserted-by":"publisher","first-page":"e175","DOI":"10.1371\/journal.pbio.0060175","volume":"6","author":"JW Huss","year":"2008","unstructured":"Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI: A gene wiki for community annotation of gene function. PLoS Biol 2008, 6: e175. 10.1371\/journal.pbio.0060175","journal-title":"PLoS Biol"},{"key":"3883_CR14","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1002\/prot.10202","volume":"49","author":"P Kuhn","year":"2002","unstructured":"Kuhn P, Lesley SA, Mathews II, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, et al.: Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution. Proteins 2002, 49: 142\u2013145. 10.1002\/prot.10202","journal-title":"Proteins"},{"key":"3883_CR15","doi-asserted-by":"publisher","first-page":"7966","DOI":"10.1073\/pnas.86.20.7966","volume":"86","author":"J Dynes","year":"1980","unstructured":"Dynes J, Firtel R: Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library. Proc Natl Acad Sci USA 1980, 86: 7966\u20137970. 10.1073\/pnas.86.20.7966","journal-title":"Proc Natl Acad Sci USA"},{"key":"3883_CR16","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1016\/S0969-2126(03)00097-2","volume":"11","author":"II Mathews","year":"2003","unstructured":"Mathews II, Deacon AM, Canaves JM, McMullan D, Lesley SA, Agarwalla S, Kuhn P: Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein. Structure 2003, 11: 677\u2013690. 10.1016\/S0969-2126(03)00097-2","journal-title":"Structure"},{"key":"3883_CR17","doi-asserted-by":"publisher","first-page":"10295","DOI":"10.1021\/bi0490439","volume":"43","author":"N Agrawal","year":"2004","unstructured":"Agrawal N, Lesley SA, Kuhn P, Kohen A: Mechanistic studies of a flavin-dependent thymidylate synthase. Biochemistry 2004, 43: 10295\u201310301. 10.1021\/bi0490439","journal-title":"Biochemistry"},{"key":"3883_CR18","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1038\/nature07973","volume":"458","author":"EM Koehn","year":"2009","unstructured":"Koehn EM, Fleischmann T, Conrad JA, Palfey BA, Lesley SA, Mathews II, Kohen A: An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene. Nature 2009, 458: 919\u2013923. 10.1038\/nature07973","journal-title":"Nature"},{"key":"3883_CR19","first-page":"89","volume-title":"Poster presented at The Second Automated Function Prediction Meeting: 30 August - 1 September 2006; San Diego, CA","author":"S Sri Krishna","year":"2006","unstructured":"Sri Krishna S, Weekes D, Edwards CX, McMullan D, Jambon M, Li W, Kozbial P, Zubieta C, Doctor KS, Jaroszewski L, et al.: The Open Protein Structure Annotation Network [abstract].In Poster presented at The Second Automated Function Prediction Meeting: 30 August - 1 September 2006; San Diego, CA Edited by: Ana PC Rodrigues, Barry J Grant, Adam Godzik, Iddo Friedberg. 2006, 89\u201390. [http:\/\/biofunctionprediction.org\/files\/afp2006-print-program.pdf]"},{"key":"3883_CR20","doi-asserted-by":"publisher","first-page":"1544","DOI":"10.1126\/science.1174671","volume":"325","author":"Y Zhang","year":"2009","unstructured":"Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A: Three-dimensional structural view of the central metabolic network of Thermotoga maritima . Science 2009, 325: 1544\u20131549. 10.1126\/science.1174671","journal-title":"Science"},{"key":"3883_CR21","doi-asserted-by":"publisher","first-page":"2860","DOI":"10.1093\/bioinformatics\/bth300","volume":"20","author":"L Chen","year":"2004","unstructured":"Chen L, Oughtred R, Berman HM, Westbrook J: TargetDB: a target registration database for structural genomics projects. Bioinformatics 2004, 20: 2860\u20132862. 10.1093\/bioinformatics\/bth300","journal-title":"Bioinformatics"},{"key":"3883_CR22","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1016\/S0968-0004(97)01140-7","volume":"22","author":"RA Laskowski","year":"1997","unstructured":"Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM: PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci 1997, 22: 488\u2013490. 10.1016\/S0968-0004(97)01140-7","journal-title":"Trends Biochem Sci"},{"key":"3883_CR23","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1145\/514183.514185","volume":"2","author":"RT Fielding","year":"2002","unstructured":"Fielding RT, Taylor RN: Principled design of the modern web architecture. ACM Transactions on Internet Technology (TOIT) (New York: Association for Computing Machinery) 2002, 2: 115\u2013150.","journal-title":"ACM Transactions on Internet Technology (TOIT) (New York: Association for Computing Machinery)"},{"key":"3883_CR24","doi-asserted-by":"publisher","first-page":"D281","DOI":"10.1093\/nar\/gkm960","volume":"36","author":"RD Finn","year":"2008","unstructured":"Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A: The Pfam protein families database. Nucleic Acids Res 2008, 36: D281\u2013288. 10.1093\/nar\/gkm960","journal-title":"Nucleic Acids Res"},{"key":"3883_CR25","first-page":"536","volume":"247","author":"AG Murzin","year":"1995","unstructured":"Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247: 536\u2013540.","journal-title":"J Mol Biol"},{"key":"3883_CR26","doi-asserted-by":"publisher","first-page":"W284","DOI":"10.1093\/nar\/gki418","volume":"33","author":"L Jaroszewski","year":"2005","unstructured":"Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A: FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res 2005, 33: W284\u2013288. 10.1093\/nar\/gki418","journal-title":"Nucleic Acids Res"},{"key":"3883_CR27","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1093\/nar\/gkg062","volume":"31","author":"FM Pearl","year":"2003","unstructured":"Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA: The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res 2003, 31: 452\u2013455. 10.1093\/nar\/gkg062","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-426.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T05:29:01Z","timestamp":1630474141000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-426"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,17]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3883"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-426","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,8,17]]},"assertion":[{"value":"19 May 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 August 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 August 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"426"}}