caNanoLab Data Curation Overview NCI Nano WG June 6, 2013

Data Curation Procedures 2 NCI Nano Alliance identifies publica- tions based on curation criteria Curator extracts data from publica- tion Curator submits data into caNano- Lab Curator creates ISA-TAB- Nano files NCI Nano Alliance requests additional informa- tion from author Curator enables public view of data Publication Identification Data Extraction caNanoLab Submission ISA-TAB-Nano Creation Author Notification Data Publication

Publication Identification NCI Nanotechnology Alliance representatives identify publications based on criteria for curation: 1.Publication is meaningful to the cancer nanotechnology field (cutting-edge science) 2.Associated meaningful data is available in the publication –or- from the investigator 3.Data is complete (e.g. contains material composition details and linkage information) NCI Nanotechnology Alliance representatives prioritize list of identified publications 3

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- CAshleyACSNano ). 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 4

Example Data Extraction 1 Plain mesoporous silica nanoparticle TEM, SEM, DLS, nitrogen sorption, zeta potential 2 AEPTMS modified silica nanoparticle zeta potential 3 AEPTMS modified silica nanoparticle loaded with Silencer Select negative control siRNA, cytotoxicity 4 DOPC protocells (AEPTMS modified) loaded with Silencer Select negative control siRNA cytotoxicity 5 DOTAP lipid nanoparticle loaded with Silencer Select negative control siRNA cytotoxicity 6 DOPC protocell (unmodified core no AEPTMS) siRNA concentration 7 DOTAP protocell (unmodified core no AEPTMS) siRNA concentration 8 DOPC protocell (AETMS modified core) siRNA concentration, siRNA release, size, zeta potential 9 DOPC lipid nanoparticle siRNA concentration, siRNA release, size, zeta potential 10 DOTAP lipid nanoparticle siRNA concentration, zeta potential, siRNA release, size 5

caNanoLab Submission 6 caNanoLab Submission Workflow

Sample Submission 7 General Sample Information

Sample Composition Submission 8 Sample Constituents Chemical Associations Functionalizing Entities

Characterization Submission 9 Characterization Information and Findings

Publication Submission 10 Publication Information with PubMed I/F

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 11

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 12

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 WikiISA-TAB-Nano Wiki 13 Data Availability Matrix Sample Access

Data Curation Statistics Nanomaterial Type#Description biopolymer43a polymer formed by a living organism carbon black2a material produced by the incomplete combustion of carbon-rich organic fuels in low oxygen conditions carbon nanotube50 a nanotube comprised of one or more graphite sheets (graphene) of hexagonal arrays of carbon rolled into seamless cylinders with capped ends carbon particle1an amorphous nanopowder formed by laser techniques dendrimer74 a polymeric molecule that has a highly-branched, three-dimensional tree-like architecture, synthesized with monomers where shells of branched molecules are added in discrete steps to a central core emulsion88a colloid in which both phases are liquids that are immiscible with each other fullerene16any cagelike, hollow molecule composed of hexagonal and/or pentagonal groups of carbon atoms liposome34 a supramolecular structure, which is a closed vesicle that forms on hydration of dry phospholipids above its transition temperature metal oxide186a nanomaterial composed of a metal oxide metal132a nanomaterial composed of a metal metalloid36a nanomaterial with properties between a metal or non-metal nanohorn7a single-walled carbon nanostructure with an irregular horn-like shape nanorod33a nanoscale rod composed of either metallic or semiconductor material or a mixture of both nanoshell1 a three-dimensional nanostructure that is composed of a spherical core surrounded by a few nanometers in thickness. If the shell is made of metal, then it is called a metallic nanoshell. polymer188a nanomaterial composed of single or multiple monomers quantum dot73 a nanometer size fragment of semiconductor material, whose excitons (electron-hole pairs) are confined in three spatial dimensions silica43a nanomaterial composed of a silicon oxide 14 caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine Nanotechnology Informatics Special Edition 2013 (Submitted)

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., and adopt and support the best practices of these communitieshttp:// –Work together with the ISA community ( 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 mannerhttp://isacommons.org/ 15 caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine Nanotechnology Informatics Special Edition 2013 (Submitted)

References caNanoLab References –Application: –Wiki: ki+Home+Page ki+Home+Page ISA-TAB-Nano References –Wiki: 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