{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,23]],"date-time":"2024-08-23T18:28:03Z","timestamp":1724437683387},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"S3","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>One of the primary challenges in translational research data management is breaking down the barriers between the multiple data silos and the integration of 'omics data with clinical information to complete the cycle from the bench to the bedside. The role of contextual metadata, also called provenance information, is a key factor ineffective data integration, reproducibility of results, correct attribution of original source, and answering research queries involving \"<jats:bold>W<\/jats:bold> hat\", \"<jats:bold>W<\/jats:bold> here\", \"<jats:bold>W<\/jats:bold> hen\", \"<jats:bold>W<\/jats:bold> hich\", \"<jats:bold>W<\/jats:bold> ho\", \"Ho<jats:bold>w<\/jats:bold>\", and \"<jats:bold>W<\/jats:bold> hy\" (also known as the <jats:bold>W7<\/jats:bold> model). But, at present there is limited or no effective approach to managing and leveraging provenance information for integrating data across studies or projects. Hence, there is an urgent need for a paradigm shift in creating a \"provenance-aware\" informatics platform to address this challenge. We introduce an ontology-driven, intuitive <jats:underline>Sem<\/jats:underline> antic <jats:underline>P<\/jats:underline> r<jats:underline>o<\/jats:underline> teomics <jats:underline>D<\/jats:underline> ashboard (<jats:bold>SemPoD<\/jats:bold>) that uses provenance together with domain information (semantic provenance) to enable researchers to query, compare, and correlate different types of data across multiple projects, and allow integration with legacy data to support their ongoing research.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The SemPoD platform, currently in use at the Case Center for Proteomics and Bioinformatics (CPB), consists of three components: (a) Ontology-driven Visual Query Composer, (b) Result Explorer, and (c) Query Manager. Currently, SemPoD allows provenance-aware querying of 1153 mass-spectrometry experiments from 20 different projects. SemPod uses the systems molecular biology provenance ontology (SysPro) to support a dynamic query composition interface, which automatically updates the components of the query interface based on previous user selections and efficientlyprunes the result set usinga \"smart filtering\" approach. The SysPro ontology re-uses terms from the PROV-ontology (PROV-O) being developed by the World Wide Web Consortium (W3C) provenance working group, the minimum information required for reporting a molecular interaction experiment (MIMIx), and the minimum information about a proteomics experiment (MIAPE) guidelines. The SemPoD was evaluated both in terms of user feedback and as scalability of the system.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>SemPoD is an intuitive and powerful provenance ontology-driven data access and query platform that uses the MIAPE and MIMIx metadata guideline to create an integrated view over large-scale systems molecular biology datasets. SemPoD leverages the SysPro ontology to create an intuitive dashboard for biologists to compose queries, explore the results, and use a query manager for storing queries for later use. SemPoD can be deployed over many existing database applications storing 'omics data, including, as illustrated here, the LabKey data-management system. The initial user feedback evaluating the usability and functionality of SemPoD has been very positive and it is being considered for wider deployment beyond the proteomics domain, and in other 'omics' centers.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-6-s3-s20","type":"journal-article","created":{"date-parts":[[2012,12,17]],"date-time":"2012-12-17T13:15:10Z","timestamp":1355750110000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["A semantic proteomics dashboard (SemPoD) for data management in translational research"],"prefix":"10.1186","volume":"6","author":[{"given":"Catherine P","family":"Jayapandian","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meng","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rob M","family":"Ewing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guo-Qiang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Satya S","family":"Sahoo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,12,17]]},"reference":[{"key":"1005_CR1","doi-asserted-by":"crossref","unstructured":"Editorial-Introduction: Challenges and Opportunities. Science. 2011, 331 (6018): 692-692.","DOI":"10.1126\/science.331.6018.692"},{"key":"1005_CR2","doi-asserted-by":"crossref","unstructured":"Editorial: Integrating with integrity. Nat Genet. 2010, 42 (1): 1-","DOI":"10.1038\/ng0110-1"},{"key":"1005_CR3","volume-title":"Workshop on Data Derivation and Provenance: 2002; Chicago","author":"C Goble","year":"2002","unstructured":"Goble C: Position Statement: Musings on Provenance, Workflow and (Semantic Web) Annotations for Bioinformatics. Workshop on Data Derivation and Provenance: 2002; Chicago. 2002"},{"key":"1005_CR4","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1186\/1471-2105-12-461","volume":"12","author":"SS Sahoo","year":"2011","unstructured":"Sahoo SS, Nguyen V, Bodenreider O, Parikh P, Minning T, Sheth AP: A unified framework for managing provenance information in translational research. BMC Bioinformatics. 2011, 12: 461-10.1186\/1471-2105-12-461.","journal-title":"BMC Bioinformatics"},{"key":"1005_CR5","volume-title":"Entity Relationship Workshop on Information Retrieval and Conceptual Modeling","author":"T Lee","year":"1997","unstructured":"Lee T, Bressan S: Multimodal Integration of Disparate Information Sources with Attribution. Entity Relationship Workshop on Information Retrieval and Conceptual Modeling. 1997"},{"key":"1005_CR6","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1007\/3-540-44450-5_6","volume":"1974","author":"P Buneman","year":"2000","unstructured":"Buneman P, Khanna S, Tan WC: Data Provenance: Some Basic Issues. Lecture Notes in Computer Science. 2000, 1974: 87-93. 10.1007\/3-540-44450-5_6.","journal-title":"Lecture Notes in Computer Science"},{"key":"1005_CR7","volume-title":"3rd International Semantic Web Conference ISWC2004: 2004; Hiroshima, Japan: Springer","author":"J Zhao","year":"2004","unstructured":"Zhao J, Wroe C, Goble C, Stevens R, Quan D, Greenwood M: Using Semantic Web Technologies for Representing e-Science Provenance. 3rd International Semantic Web Conference ISWC2004: 2004; Hiroshima, Japan: Springer. 2004"},{"key":"1005_CR8","first-page":"76","volume-title":"AMIA Clinical Research Informatics Summit. San Francisco","author":"GQ Zhang","year":"2010","unstructured":"Zhang GQ, Siegler T, Saxman P, Sandberg N, Mueller R, Johnson N, Hunscher D, Arabandi S: VISAGE: A Query Interface for Clinical Research. AMIA Clinical Research Informatics Summit. San Francisco. 2010, 76-80."},{"key":"1005_CR9","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1038\/nbt.1411","volume":"26","author":"CF Taylor","year":"2008","unstructured":"Taylor CF: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008, 26: 889-896. 10.1038\/nbt.1411.","journal-title":"Nat Biotechnol"},{"key":"1005_CR10","doi-asserted-by":"publisher","first-page":"894","DOI":"10.1038\/nbt1324","volume":"25","author":"S Orchard","year":"2007","unstructured":"Orchard S: The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotechnology. 2007, 25: 894-898. 10.1038\/nbt1324.","journal-title":"Nature Biotechnology"},{"key":"1005_CR11","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1038\/nbt1329","volume":"25","author":"CF Taylor","year":"2007","unstructured":"Taylor CF: The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007, 25: 887-893. 10.1038\/nbt1329.","journal-title":"Nat Biotechnol"},{"key":"1005_CR12","volume-title":"W3C Provenance Working Group","author":"T Lebo","year":"2012","unstructured":"Lebo T, Sahoo SS, McGuinness D: PROV-O: The PROV Ontology (Working Draft). W3C Provenance Working Group. 2012"},{"key":"1005_CR13","volume-title":"Technical report","author":"O Bodenreider","year":"2010","unstructured":"Bodenreider O: Quality assurance in biomedical terminologies and ontologies. Technical report. 2010, Bethesda: Lister Hill National Center for Biomedical Communications, National Library of Medicine"},{"issue":"1","key":"1005_CR14","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038\/75556.","journal-title":"Nat Genet"},{"issue":"Suppl 9","key":"1005_CR15","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-8-S9-S1","volume":"8","author":"DA Natale","year":"2007","unstructured":"Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH: Framework for a protein ontology. BMC Bioinformatics. 2007, 8 (Suppl 9): S1-10.1186\/1471-2105-8-S9-S1.","journal-title":"BMC Bioinformatics"},{"key":"1005_CR16","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1021\/pr0503533","volume":"5","author":"A Rauch","year":"2006","unstructured":"Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whitaker J, States D, Hanash S, Paulovich A, McIntosh MW: Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments. J Proteome Res. 2006, 5: 112-121. 10.1021\/pr0503533.","journal-title":"J Proteome Res"},{"key":"1005_CR17","unstructured":"The National Center for Biomedical Ontology. (retrieved on May 18, 2012), [http:\/\/bioontology.org]"},{"key":"1005_CR18","unstructured":"The Ontology for Biomedical Investigations. (retrieved on May 18, 2012), [http:\/\/obi-ontology.org\/]"},{"issue":"8","key":"1005_CR19","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1093\/bioinformatics\/btq099","volume":"26","author":"J Malone","year":"2010","unstructured":"Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010, 26 (8): 1112-1118. 10.1093\/bioinformatics\/btq099.","journal-title":"Bioinformatics"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-6-S3-S20.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T20:46:23Z","timestamp":1630529183000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-6-S3-S20"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12]]},"references-count":19,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["1005"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-6-s3-s20","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12]]},"assertion":[{"value":"17 December 2012","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S20"}}