Scientific Data overview of Data Descriptors - WT Data-Literature integration, Dec 2013

Supported by:!

Now open for submissions Launching May 2014

Advisory Panel including senior researchers, funders, librarians and curators Michael Huerta ● National Institutes of Health, USA ● Mark Thorley ● Natural Environment Research Council, UK ● Patricia Cruse ● University of California, USA ● Susan Gregurick ● Office of Biological and Environmental Research, Department of Energy, USA ● Ioannis Xenarios ● Swiss Institute of Bioinformatics, Switzerland ● Chris Bowler ● IBENS, France ● Mark Forster ● Syngenta, UK ● Anthony Rowe ● Johnson & Johnson, USA ● Stephen Chanock ● National Cancer Institute, USA ● Weida Tong ● National Center for Toxicological Research, FDA, USA ● Albert J. R. Heck ● Utrecht University, The Netherlands ● Johanna McEntyre ● EMBL-EBI, European Bioinformatics Institute, UK ● Simon Hodson ● CODATA, France ● Joseph R. Ecker ● Howard Hughes Medical Institute & Salk Institute, USA ● Stephen Friend ● Sage Bionetworks, USA ● Jessica Tenenbaum ● Duke Translational Medicine Institute, USA ● Anne-Claude Gavin ● EMBL, Germany ● David Carr ● Wellcome Trust, UK ● Wolfram Horstmann ● University of Oxford, UK ● Piero Carninci ● RIKEN Omics Science Center, Japan ● Pascale Gaudet ● Swiss Institute of Bioinformatics, Switzerland ● Judith A. Blake ● The Jackson Laboratory, USA ● Richard H. Scheuermann ● J. Craig Venter Institute, USA ● Caroline Shamu ● Harvard Medical School, USA

Susanna-Assunta Sansone Honorary Academic Editor (University of Oxford, UK)

Andrew L Hufton Managing Editor

Victoria Newman Editorial Curator

Ruth Wilson Publisher

www.nature.com/scientificdata [email protected] @ScientificData

Introducing a new content type:!

Data Descriptor!

Credit for Sharing Your Data Open-access Focused on Data Reuse Peer-reviewed, curated Promoting Community Data Repositories

Introducing a new content type:!

Data Descriptor!

Session 2: Publishing Data Aims of this session: to explore how data is being represented and cited in research articles; to showcase new data publishing products, and consider how the edges between articles and data are joined or defined. How can we maximize integrated utility across the different data resources used by scientists?

Session 3: Credit, Attribution, Reproducibility and Provenance Aims of this session: in an integrated information space, it is essential to have transparency on the sources and methods of scientific outputs. How do scientific articles contribute to this goal? Are they sufficiently addressing requirements, what are the most useful approaches and how might they be actioned?

Credit for Sharing Your Data Open-access Focused on Data Reuse Peer-reviewed, curated Promoting Community Data Repositories

Data Descriptor

Synthesis

Analysis

Conclusions

Interpretation

What is the sample?

What did I do to generate the data?

Where is the data?

How was the data processed?

Who did what when?

Summary of Data Descriptor

Facts

Data Descriptor

Journal article

Data Descriptor vs. traditional article!

NARRATIVE

•  The data descriptor is only concerned with the facts behind the methodology of data generation/collection and processing!

•  A data descriptor can be:!–  submitted prior to journal article !–  submitted at the same time as the journal article!–  submitted after journal article!

Two sample Data Descriptors now online!

Data Descriptor has 2 components!

Article or

narrative component (PDF and HTML)

Experimental metadata or

structured component (in-house curated, machine-readable formats)

Supported by

Data Descriptor - article !

Sections:!•  Title!•  Abstract!•  Background & Summary!•  Methods!•  Technical Validation!•  Data Records!•  Usage Notes !•  Figures & Tables !•  References!•  Data Citations!!

In traditional publications this information is not provided in a sufficiently detailed manner

However this information is essential for understanding, reusing, and reproducing datasets









Data Descriptor – experimental metadata (CC0)!

funded by:


funded by:

General-purpose, configurable format, designed to support: •  description of the experimental workflow, making the

annotation explicit and discoverable •  provenance tracking •  use community standards, such as minimal reporting

guidelines and terminologies o  over 300 ‘ontologies’ and over 60 guidelines

•  conversions to - a growing number of - other metadata formats

o  e.g. used by EBI repositories o  and as linked data

Data Descriptor – experimental metadata (CC0)!General-purpose, configurable format, designed to support: •  description of the experimental workflow, making the

annotation explicit and discoverable •  provenance tracking •  use community standards, such as minimal reporting

guidelines and terminologies o  over 300 ‘ontologies’ and over 60 guidelines

•  conversions to - a growing number of - other metadata formats

o  e.g. used by EBI repositories o  and as linked data

ISA is implemented by several service providers running systems that are •  local, institute-based

o  e.g. Harvard Stem Cell Institute •  project, consortium-based

o  e.g. ToxBank serving a research cluster of seven EU FP7 Health projects

•  global, international repositories •  e.g. EBI’s MetaboLights

•  and another ‘data journal, GigaScience in GigaDB


Includes fields describing: •  each study, linking to relevant sections of the

Data Descriptor article •  authors’ details, including ORCID •  publications •  funding sources and funders’ name, via FundRef •  experimental factors •  study design •  assays •  protocols




In-house curation team: •  assists users to submit the structured content

via simple templates and an internal authoring tool

•  performs value-added semantic annotation of the experimental metadata

For advanced users/service providers willing to export ISA-Tab for direct submission, we will release a technical specification:

analysis !method! script!

Data file or !record in a database!

Discover similar datasets!

SciData DD

Structured content

Structured content allows users to link, with one click, to other datasets studying the same tissue, disease, organism, or using the same experimental platform!

SciData DD

Structured content

SciData DD

Structured content

SciData DD

Structured content

SciData DD

Structured content

SciData DD

Structured content

SciData DD

Structured content

SciData DD

Structured content

SciData DD

Structured content

SciData DD

Structured content

Same tissue

Same organism

Same assay

Community Data

Repositories

Complementing both journal articles and data repositories ! Export to various formats

(ISA_tab, RDF, etc)

Other data-related activities at NPG!•  Figure source data

-  putting data behind figures/graphs -  implemented at Molecular System Biology, rolled out at Nature and

progressively across all other Nature branded titles

Wang et al, Nature, 2013 doi:10.1038/nature12730

Other data-related activities at NPG!•  Figure source data

-  putting data behind figures/graphs -  implemented at Molecular System Biology, rolled out at Nature and

progressively across all other Nature branded titles

•  Extended data -  expandable text and extra figures; rolled out at Nature

•  Data citation -  tackling both styling and format; monitoring community developments,

such the Data Citation Synthesis Group -  to be rolled out across all Nature branded titles and Scientific Data

•  Code reproducibility -  peer review, availability and reuse

•  Supported community databases -  criteria for selection, common list across all NPG titles

•  NPG’s Linked Data release – CC0

Scientific Data overview of Data Descriptors - WT Data-Literature integration, Dec 2013

Technology

data descriptor article

data records

data citations

publishing data

data reusepeer

data reusesession

sample data descriptors

different data resources