caNanoLab Data Curation Overview

NCI Nano WGJune 6, 2013

Data Curation Procedures

2

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)

1. 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-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

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 Wiki

13

Data Availability Matrix

Sample Access

Data Curation StatisticsNanomaterial Type # Description

biopolymer 43 a polymer formed by a living organism

carbon black 2 a material produced by the incomplete combustion of carbon-rich organic fuels in low oxygen conditions

carbon nanotube 50 a nanotube comprised of one or more graphite sheets (graphene) of hexagonal arrays of carbon rolled into seamless cylinders with capped ends

carbon particle 1 an amorphous nanopowder formed by laser techniques

dendrimer 74 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

emulsion 88 a colloid in which both phases are liquids that are immiscible with each other

fullerene 16 any cagelike, hollow molecule composed of hexagonal and/or pentagonal groups of carbon atoms

liposome 34 a supramolecular structure, which is a closed vesicle that forms on hydration of dry phospholipids above its transition temperature

metal oxide 186 a nanomaterial composed of a metal oxide

metal 132 a nanomaterial composed of a metal

metalloid 36 a nanomaterial with properties between a metal or non-metal

nanohorn 7 a single-walled carbon nanostructure with an irregular horn-like shape

nanorod 33 a nanoscale rod composed of either metallic or semiconductor material or a mixture of both

nanoshell 1 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.

polymer 188 a nanomaterial composed of single or multiple monomers

quantum dot 73 a nanometer size fragment of semiconductor material, whose excitons (electron-hole pairs) are confined in three spatial dimensions

silica 43 a 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., 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

15

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

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

16