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caNanoLab Data Curation Overview

caNanoLab Data Curation Overview. NCI Nano WG June 6, 2013. Data Curation Procedures. Publication Identification. Data Extraction. caNanoLab Submission. ISA-TAB-Nano Creation. Author Notification. Data Publication. Publication Identification.

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caNanoLab Data Curation Overview

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  1. caNanoLab Data Curation Overview NCI Nano WG June 6, 2013

  2. Data Curation Procedures Publication Identification Data Extraction caNanoLab Submission ISA-TAB-Nano Creation Author Notification Data Publication

  3. Publication Identification • NCI Nanotechnology Alliance representatives identify publications based on criteria for curation: • Publication is meaningful to the cancer nanotechnology field (cutting-edge science) • Associated meaningful data is available in the publication –or- from the investigator • Data is complete (e.g. contains material composition details and linkage information) • NCI Nanotechnology Alliance representatives prioritize list of identified publications

  4. Data Extraction • The curator reviews the prioritized publication and establishes the number of samples, characterizations, and available data and figures • Sample names are created following the established sample naming convention: • Abbreviation(s) of: institution names - name of the first author (without middle name), journal title, year of publication - and sample sequence number (e.g. SNL_UNM-CAshleyACSNano2012-01). • Information on the association of samples and characterizations is maintained in a text file • Definitions are established for new terms and recorded, if applicable • Questions and any issues (e.g. discrepancies) are identified for future correspondence with the publication author

  5. Example Data Extraction

  6. caNanoLab Submission caNanoLab Submission Workflow

  7. Sample Submission General Sample Information

  8. Sample Composition Submission Functionalizing Entities Chemical Associations Sample Constituents

  9. Characterization Submission Characterization Information and Findings

  10. Publication Submission Publication Information with PubMed I/F

  11. ISA-TAB-Nano Creation • The curator creates the Investigation File and identifies applicable ontologies, and associated studies, protocols, and assays • The curator creates a Material File for each sample in the investigation • The Material File represents the composition of the sample • The curator creates Study Files for each identified study • The Study File associates samples with the study • Details of biospecimens are included in the Study File • References to nanomaterials are included in the Study File • For studies involving physico-Chemical characterizations, the sample is the nanoparticle • For studies involving in vitro or in vivo characterizations, the sample is the biospecimen (e.g. cell line, animal) and the nanoparticle is the study factor (e.g. treatment) • The curator creates Assay Files for each identified assay

  12. Author Notification • The publication author is contacted, when possible, to obtain additional data and/or clarification on questions or discrepancies • The caNanoLab data is updated based on author feedback or additional information • The ISA-TAB-Nano files are updated based on author feedback or additional information

  13. Data Publication • Once the sample submission into caNanoLab has been finalized, the curator generates the data availability matrix and makes the data available for public viewing in caNanoLab • The curator posts the completed ISA-TAB-Nano Files to the ISA-TAB-Nano Wiki Data Availability Matrix Sample Access

  14. Data Curation Statistics caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine Nanotechnology Informatics Special Edition 2013 (Submitted)

  15. Data Curation Challenges and Opportunities • Challenges • Making primary data supporting publications available to and re-usable by the research community • Inefficiencies associated with manual data curation from publications • Opportunities • Emphasize policies and resources that promote and incentivize standards-based data capture directly by the data producers • Participate in efforts that encourage primary data sharing in the scientific community (e.g., http://www.fged.org, http://www.force11.org/, http://biosharing.org/) and adopt and support the best practices of these communities • Work together with the ISA community (http://isacommons.org/) to extend the ISA Tools software suite to support the nanotechnology data extensions to ISA-TAB (ISA-TAB-Nano) and make it easier to share nanotechnology data among different data resources in a standards based manner caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine Nanotechnology Informatics Special Edition 2013 (Submitted)

  16. References • caNanoLab References • Application: https://cananolab.nci.nih.gov • Wiki: https://wiki.nci.nih.gov/display/caNanoLab/caNanoLab+Wiki+Home+Page • ISA-TAB-Nano References • Wiki: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano • Publication (Submitted) • Gaheen S, Hinkal GW, Morris SA, Lijowski M, Heiskanen, M, Klemm J. caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine Nanotechnology Informatics Special Edition 2013

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