Adrian Burton & Kate Le May

Data sharing and biomedical journals

Australian National Data Service

6 June 2016

The Australian National Data Service (ANDS) makes Australia’s research data assets more valuable for researchers, research institutions and the nation.

Data is no longer a waste product of research

by carterzufeltdesign

Directions in Public Policy

“To the greatest extent and with the fewest

constraints possible publicly funded

scientific research data should be open,

while at the same time respecting concerns

in relation to privacy, safety, security and

commercial interests, whilst acknowledging

the legitimate concerns of private partners.

G8 Science Ministers’ Statement 13 June 2013

“Australia’s capacity to remain competitive in the

digital economy is contingent upon its ability to

harness the value of data.”

“The Australian Government will…where possible,

ensure non-sensitive publicly funded research data is

made open for use and reuse”

Australian Government Public Data Policy Statement 7-Dec-2015

Directions in Funders Policy

“3.2.2 To promote access to the benefits of research, such data should be

collected, stored and accessible in such a way that they can be used in future

research projects.” National Statement on Ethical Conduct in Human Research

A11.5.2 “The ARC considers data management planning an important part of

the responsible conduct of research and strongly encourages the depositing

of data arising from a Project in an appropriate publically accessible subject

and/or institutional repository” ARC Discovery Program

Directions in Journal Policy

“PLOS journals require authors to make all data

underlying the findings described in their

manuscript fully available without restriction,

with rare exception.”

Data Availability Policy

“A condition of

publication in a Nature

journal is that authors

are required to make

materials, data, code,

and associated

protocols promptly

available to readers

without undue

qualifications….”

http://www.nature.com/authors/policies/availability.html

“there is an ethical obligation to responsibly share

data generated by interventional clinical trials

because participants have put themselves at

risk…”

“….proposes to require authors to share with

others the deidentified individual-patient data

underlying the results presented in the article…”

Proposed changes to Recommendations for the Conduct, Reporting, Editing,

and Publication of Scholarly work in Medical Journals - January 2016

Directions in Journal Practice

Acceptable Data-Sharing Methods

A compulsory data availability statement must specify how data will be shared:

• Data deposition in a repository (strongly recommended)

• Data in supporting information files

• Data made available to all interested researchers upon request (only by exception)

• Data available from a third party (only by exception)

http://journals.plos.org/plosone/s/data-availability

Joint Data Archiving Policy (JDAP)

“[Journal] requires, as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive, such as [list of approved archives here]. Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future.

http://datadryad.org/pages/jdap

Joint Data Archiving Policy (JDAP)

“Authors may elect to have the data publicly available at time of publication, or, if the technology of the archive allows, may opt to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information such as human subject data or the location of endangered species.”

http://datadryad.org/pages/jdap

Directions in Data Infrastructure

Directions in national data infrastructure

• NCRIS

• ANDS, RDS

• Institutional capacity

• EU Science Cloud

• MRFF?

http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories

Unstructured and/or Large Data

Dryad Digital Repository

figshare

GigaDB

Harvard Dataverse Network

Open Science Framework

Zenodo

Sequencing

dbSNP

dbVar

Database of Genomic Variants Archive (DGVa)

DNA DataBank of Japan (DDBJ)

EBI Metagenomics

EMBL Nucleotide Sequence Database (ENA)

European Variation Archive (EVA)

GenBank

miRBase

NCBI Sequence Read Archive (SRA)

NCBI Trace Archive

Uniprot

Omics

ArrayExpress

Biological General Repository for Interaction Datasets (BioGRID)

Database of Interacting Proteins (DIP)

dbGAP

The European Genome-phenome Archive (EGA)

IntAct Molecular Interaction Database

Gene Expression Omnibus (GEO)

GenomeRNAi

GPM DB

MetaboLights

PeptideAtlas

Proteomics Identifications (PRIDE)

ProteomeXchange

Structural Databases

Biological Magnetic Resonance Data Bank (BMRB)

Crystallography Open Database (COD)

Coherent X-ray Imaging Data Bank (CXIDB)

Electron Microscopy Data Bank (EMDB)

FlowRepository

Protein Circular Dichroism Data Bank (PCDDB)

Worldwide Protein Data Bank (wwPDB)

Neuroscience

Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI)

Citation metrics for research data

http://wokinfo.com/products_tools/multidisciplinary/dci/

Citation metrics for data

As for journal articles, data citation metrics are:●a measure of impact and reuse●based on citations in reference lists●facilitated by consistent citation format

eg. Stueckle, TA; Lu, Y; Davis, ME (2012): Whole genome expression profile of lung epithelial cells following chronic

arsenic exposure. ArrayExpress Archive. http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-33520

ANDS is collaborating with Thomson Reuters to grow Australian content in the Data Citation Index.http://www.ands.org.au/online-services/research-data-australia/data-citation-index

Gaps, opportunities, common interests for AHMEN and ANDS

ANDS materialsGuides

• Publishing and sharing sensitive data

• Ethics, consent and data sharing

• De-identification

• Data citation

• Copyright, data and licensing

Medical and Health data page

http://www.ands.org.au/working-with-

data/enabling-data-reuse/medical-

and-health

ANDS Guide to publishing sensitive data

How to confidentialise data?

Conditional accessEthics and consent

LicensingRespositories

Ownership

http://ands.org.au/guides/sensitivedata

Symposium

• Editors

• Publishers

• Infrastructure providers

• Funders

• Research leaders

Policy development

Dryad recommended elements and examples of journal data policies

http://wiki.datadryad.org/Journal_instructions

adrian.burton@ands.org.aukate.lemay@ands.org.au

With the exception of logos, third party images or where otherwise indicated, this

work is licensed under the Creative Commons Australia Attribution 3.0 Licence.

ANDS is supported by the Australian

Government through the National Collaborative

Research Infrastructure Strategy Program.

Monash University leads the partnership with

the Australian National University and CSIRO.