{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:52:07Z","timestamp":1740135127728,"version":"3.37.3"},"reference-count":8,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,12,2]],"date-time":"2020-12-02T00:00:00Z","timestamp":1606867200000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["MR\/N005880\/1"],"award-info":[{"award-number":["MR\/N005880\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/N005880\/1"],"award-info":[{"award-number":["MR\/N005880\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Midlands Asthma and Allergy Research Association"},{"DOI":"10.13039\/501100000351","name":"British Lung Foundation","doi-asserted-by":"publisher","award":["BLFPHD17-1"],"award-info":[{"award-number":["BLFPHD17-1"]}],"id":[{"id":"10.13039\/501100000351","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Data handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, flexible metadata collection and linkage of related experimental data generated locally by vendor software.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>To address this problem, we created LabPipe, a flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>LabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-020-03908-5","type":"journal-article","created":{"date-parts":[[2020,12,2]],"date-time":"2020-12-02T12:03:16Z","timestamp":1606910596000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata"],"prefix":"10.1186","volume":"21","author":[{"given":"Bo","family":"Zhao","sequence":"first","affiliation":[]},{"given":"Luke","family":"Bryant","sequence":"additional","affiliation":[]},{"given":"Rebecca","family":"Cordell","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Wilde","sequence":"additional","affiliation":[]},{"given":"Dahlia","family":"Salman","sequence":"additional","affiliation":[]},{"given":"Dorota","family":"Ruszkiewicz","sequence":"additional","affiliation":[]},{"given":"Wadah","family":"Ibrahim","sequence":"additional","affiliation":[]},{"given":"Amisha","family":"Singapuri","sequence":"additional","affiliation":[]},{"given":"Tim","family":"Coats","sequence":"additional","affiliation":[]},{"given":"Erol","family":"Gaillard","sequence":"additional","affiliation":[]},{"given":"Caroline","family":"Beardsmore","sequence":"additional","affiliation":[]},{"given":"Toru","family":"Suzuki","sequence":"additional","affiliation":[]},{"given":"Leong","family":"Ng","sequence":"additional","affiliation":[]},{"given":"Neil","family":"Greening","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Thomas","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Monks","sequence":"additional","affiliation":[]},{"given":"Christopher","family":"Brightling","sequence":"additional","affiliation":[]},{"given":"Salman","family":"Siddiqui","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8053-435X","authenticated-orcid":false,"given":"Robert C.","family":"Free","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,12,2]]},"reference":[{"key":"3908_CR1","doi-asserted-by":"publisher","DOI":"10.2450\/2012.005S","author":"A D\u2019Alessandro","year":"2012","unstructured":"D\u2019Alessandro A, Giardina B, Federica G, Timperio AM, Zolla L. Clinical metabolomics: the next stage of clinical biochemistry. Blood Transfus. 2012;. https:\/\/doi.org\/10.2450\/2012.005S.","journal-title":"Blood Transfus"},{"issue":"1","key":"3908_CR2","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/s12553-016-0175-x","volume":"7","author":"H M\u00fcller","year":"2017","unstructured":"M\u00fcller H, Malservet N, Quinlan P, Reihs R, Penicaud M, Chami A, Zatloukal K, Dagher G. From the evaluation of existing solutions to an all-inclusive package for biobanks. Health Technol. 2017;7(1):89\u201395. https:\/\/doi.org\/10.1007\/s12553-016-0175-x.","journal-title":"Health Technol"},{"key":"3908_CR3","unstructured":"LIMSWiki. https:\/\/www.limswiki.org. Accessed 27 Oct 2020."},{"key":"3908_CR4","unstructured":"Kohnfelder L, Praerit G. The threats to our products. https:\/\/adam.shostack.org\/microsoft\/The-Threats-To-Our-Products.docx (1999). Accessed 27 Oct 2020."},{"issue":"suppl\u20132","key":"3908_CR5","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1093\/nar\/gkr469","volume":"39","author":"PL Whetzel","year":"2011","unstructured":"Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011;39(suppl\u20132):541\u20135. https:\/\/doi.org\/10.1093\/nar\/gkr469.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"3908_CR6","doi-asserted-by":"publisher","first-page":"025486","DOI":"10.1136\/bmjopen-2018-025486","volume":"9","author":"W Ibrahim","year":"2019","unstructured":"Ibrahim W, Wilde M, Cordell R, Salman D, Ruszkiewicz D, Bryant L, Richardson M, Free RC, Zhao B, Yousuf A, White C, Russell R, Jones S, Patel B, Awal A, Phillips R, Fowkes G, McNally T, Foxon C, Bhatt H, Peltrini R, Singapuri A, Hargadon B, Suzuki T, Ng LL, Gaillard E, Beardsmore C, Ryanna K, Pandya H, Coates T, Monks PS, Greening N, Brightling CE, Thomas P, Siddiqui S. Assessment of breath volatile organic compounds in acute cardiorespiratory breathlessness: a protocol describing a prospective real-world observational study. BMJ Open. 2019;9(3):025486. https:\/\/doi.org\/10.1136\/bmjopen-2018-025486.","journal-title":"BMJ Open"},{"issue":"18","key":"3908_CR7","doi-asserted-by":"publisher","first-page":"2354","DOI":"10.1093\/bioinformatics\/btq415","volume":"26","author":"P Rocca-Serra","year":"2010","unstructured":"Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010;26(18):2354\u20136. https:\/\/doi.org\/10.1093\/bioinformatics\/btq415.","journal-title":"Bioinformatics"},{"issue":"10","key":"3908_CR8","doi-asserted-by":"publisher","first-page":"2765","DOI":"10.1074\/mcp.O113.036681","volume":"13","author":"J Griss","year":"2014","unstructured":"Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu Q-W, del Toro N, P\u00e9rez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizca\u00edno JA, Hermjakob H. The mztab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. 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