Data management issues and how Societies can contribute · data . Processed Data and . Data...

Data management issues

and how Societies can contribute

David Martinsen Senior Scientist Digital Strategy and Platform Development, Publications Division American Chemical Society [email protected] AIP Assembly of Society Officers March 27, 2014 College Park, MD

27 March 2014

Outline 1. Background/Publisher Perspective 2. NISO/NFAIS Recommendation 3. Publisher Initiatives 4. Data Citation 5. Government Initiatives 6. Institutional Initiatives 7. Data Repositories 8. Research Data Advocacy 9. What can Societies Do?

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Resources for Data Management

Part 1: Background/Publisher Perspective

Avoiding a Digital Dark Age for Data: why data and publications belong together

Integration of Research Data and Publications Eefke Smit International Association of STM Publishers Director, Standards and Technology ICSTI workshop Delivering Data in Science PARIS, 5 March 2012

A famous paper in Nature: DNA structure - 1953

• 1 page • 2 authors • 1 figure • no data

Source: V. Kiermer, Nature Publishing Group, 2011

Nature in 2001: The human genome issue • 62 pages, 49 figures, 27 tables

Source: V. Kiermer, Nature Publishing Group, 2011

Publications with data

Processed Data and Data

Representations

Data Collections and Structured Databases

Raw Data and Data Sets

(1) Data contained and

explained within the article

(2) Further data explanations in

any kind of supplementary files to articles

(3) Data referenced from the article and

held in data centers and repositories (4) Data

publications, describing available datasets (5) Data in

drawers and on disks at the

institute

The Data Publication Pyramid

8

The Pyramid’s likely short term reality:

Pubs

Supps

Data Archives

Data on Disks and in Drawers

(1) Top of the pyramid is stable

but small (2) Risk that supplements to articles turn into Data Dumping

places (3) Too many

disciplines lack a community

endorsed data archive

(4) Estimates are that at least

75 % of research data is

never made openly avaiable

9

The Ideal Pyramid

Data In

Publications Article Supps

Data Archives

Data on Disks and in Drawers

(1) More integration of text and data, viewers

and seamless links to interactive

datasets (2) Only if data

cannot be integrated in

article, and only relevant extra explanations

(3) Seamless links (bi-directional)

between publications and data, interactive

viewers within the articles

(4) More Data Journals that

describe datasets, data mgt plans and data methods

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Part 2: NISO/NFAIS Recommendations on

Supplemental Journal Article Material

The NISO/NFAIS Working Group

Business Working Group Co-chairs: Linda Beebe (APA), Marie McVeigh (Thomson-Reuters ISI)

• Recommended Practices: scope and general principles • Definitions: supplemental material, article, data,

metadata • Roles and responsibilities of publishers, authors, editors,

peer reviewers, libraries, A&I services, repositories • Curation and life cycle: selection, peer review, editing,

presentation, providing context, referencing, citing, managing/hosting, discovery, preservation

• Discoverability & Linking • Intellectual property rights management

Technical Working Group Co-chairs: Dave Martinsen (ACS), Sasha Schwarzman (OSA)

• Metadata • Persistent identifiers • Preservation • Packaging and exchange • Supporting documentation

non-normative DTD Tag Library tagged samples

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Part 3: Publisher Initiatives

Moving forward our shared data agenda: a view from the publishing industry

Connecting with Data Repositories, 1

Link to CCDC database (indicates that information for this article is available)

Screenshot of journal article on ScienceDirect (http://dx.doi.org/10.1016/j.jfluchem.2009.07.015)

Article Linking example: CCDC


... clicking on the CCDC logo takes the reader to a page at the CCDC repository with data related to the article

Screenshot of information page at CCDC (Cambridge Crystallographic Data Centre)

Article Linking example: CCDC


Tagged Genbank entry (genetic sequence)

Screenshot of journal article on ScienceDirect (http://dx.doi.org/10.1016/j.biortech.2010.03.063 )

Entity Linking example: Genbank Accession Number


... clicking on the linked Genbank accession code takes the reader to an information page on the NCBI data repository about that specific genetic sequence

Screenshot of information page at NCBI (National Center for Biotechnology Information)

Entity Linking example: Genbank Accession Number


Database Subject Type of Linking CCDC Crystallography Article-level PANGAEA Earth Sciences Article-level* EMBL Molecular Interactions Chemistry Entity, tagging Molecular INTeraction DB Chemistry Entity, tagging Genbank Nucleotides Entity, tagging UniProt Proteins Entity, tagging Protein Data Bank Proteins Entity, tagging ClinicalTrials Medicine Entity, tagging TAIR (Arabidopsis) Model organism Entity, tagging Mendelian Inheritance in Men Genetics, inheritance Entity, tagging

*: with Application

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Data accessibility: Why?

• Researchers should get credit – data should be citable

• Help authors comply with funding agency accessibility requirements

• Data should be not only accessible, but usable – need industry standards and guidelines that suit community dependent needs

• Reduce barriers to furthering research

US National Science Board’s (NSB) Task Force on Data Policies issued its report on Digital Research Data Sharing and Management (NSB 2011) recommending “require grantees to make both the data and the methods and techniques used in the creation and analysis of the data accessible for the purposes of building upon or verifying figures, tables, findings, and conclusions in peer reviewed publications.”

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Data accessibility: How? • NSF funded project with AAS and AIP • Survey and Researcher workshops to gather community

requirements • Establish community specific metadata requirements

and format best practices • Pilot project to link to data sets from published articles

• OSTI will register the datasets for such Physics of Plasmas articles involved in the project.

• Allow researchers to use recommended repositories that fit with archiving and metadata standards

• DOIs for datasets will allow data to be cited as its own entity

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AAS/AIP data access project

Project goals: 1. Extend methods for providing access to data objects 2. Survey community attitudes about data sharing and re-use 3. Engage community in discussions about formats / metadata

Responds to calls for digital data curation and sharing • EC: Riding the Wave (2010) • UK/RIN: Collaborative Yet Independent (2011) • US NSB: Digital Research Data Sharing and Management (2011)

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0

10

20

30

40

50

60

70

80

90

100

%

AAS/AIP data sharing survey

1. 62% answered yes to the question – “In the past 2 years, have you shared the dataset(s) used to generate data

elements (tables, figures, etc.) of an article that you had published?”

2. How data was provided

Highlights regarding sharing data

3. 58% definitely / probably 28% possibly − “Within the next few years,

I will provide the dataset(s) that generated the data elements (tables, figures, etc.) as a supplement to an article submission.”

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0

10

20

30

40

50

60

70

80

90

Explore newquestions

Integratesources

Replicate work Other

%

0

10

20

30

40

50

60

70

Directly fromauthor

Large datarepository

PublishingJournal

Affiliatedinstitution

Other

%

AAS/AIP data sharing survey

1. 60% answered yes to the question – “In the past two years, have you requested, acquired, or worked with

datasets that were made available by other researchers as a supplement to a published article?”

2. How data was obtained

Highlights regarding using data

3. How data was used

Copyright © 2011 American Chemical Society Copyright © 2011 American Chemical Society

why is ACS concerned with data?

From The Journal of Organic Chemistry For Notes, Brief Communications, and Articles, all

experimental procedures and listings of compound characterization data must be included in the manuscript file’s experimental section, and not in the supporting information. The supporting information should contain only copies of spectra, chromatograms, graphs, tables, crystallographic data, and computational data.


why is ACS concerned with data?bbb integrity of published research

and reproducibilty The Journal upholds a high standard for compound

characterization to ensure that compounds being added to the chemical literature have been correctly identified and can be synthesized in known yield and purity by the reported preparation, isolation, and purification methods. For all new compounds, evidence adequate to establish both identity and degree of purity (homogeneity) must be provided. Purity documentation must be provided for known compounds whose preparation by a new or improved method is reported. For combinatorial libraries containing more than 20 compounds, complete characterization data must be provided for at least 20 diverse members. Authors may be asked to provide copies of original spectra or analytical reports if an editor or reviewer raises a question about any of the reported results.



and reproducibilty

Crystal structures: Regardless of the level of detail of the discussion of the structure, a Crystallographic Information File (CIF) containing complete details of data collection, crystal and unit-cell parameters, structure solution and refinement, and tables of atomic coordinates and thermal parameters, bond lengths, bond angles, and torsion angles should be furnished as supporting information.



and reproducibilty

Purity: Evidence for documenting compound purity should include one or more of the following:

• A standard 1D proton NMR spectrum or proton-decoupled

carbon NMR spectrum showing at most trace peaks not attributable to the assigned structure. A copy of a spectrum with a signal-to-noise ratio sufficient to permit seeing peaks with 5% of the intensity of the strongest peak should be included in the supporting information. The normal full range of chemical shifts should be displayed (usually 0–10 ppm for proton; 0–220 ppm for carbon). For new compounds, copies of both proton and carbon spectra are required (see ‘Identity’ above).



and reproducibilty

Spectral Data: Reproductions of spectra will be published in the results and discussion section only when concise numerical summaries are inadequate for the discussion. Papers dealing primarily with interpretation of spectra, and those in which band shape or fine structure needs to be illustrated, may qualify for this exception. When presentation of spectra is essential, only the pertinent sections, prepared as figures, should be included. Spectra used as adjuncts to the characterization of compounds should be included in the supporting information.


data submission for characterizing compounds

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Some Data Journals

NEW TRADITIONAL

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Recent Development at PLOS • http://www.plos.org/plos-data-policy-faq/ • http://dx.doi.org/10.1371/journal.pbio.1001797 Data are any and all of the digital materials that are collected and analyzed in the pursuit of scientific advances. In line with its stance on providing Open Access to research articles themselves, PLOS strongly believes that, to best foster scientific progress, the underlying data should be made freely available for researchers to use, wherever this is legal and ethical. Data availability allows validation, replication, reanalysis, new analysis, reinterpretation, or inclusion into meta-analyses, and facilitates reproducibility of research [1]. Making data available for all these uses provides a better “bang for the buck” out of scientific research, much of which is funded from public or nonprofit sources. Ultimately, our viewpoint is quite simple: Ensuring access to the underlying data should be an intrinsic part of the scientific publishing process.

http://www.plos.org/plos-data-policy-faq/

http://dx.doi.org/10.1371/journal.pbio.1001797

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Part 4: Data Citation

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DataCite Facts

• DataCite is a not-for-profit organization whose aim is to: • establish easier access to research data on the Internet • increase acceptance of research data as legitimate,

citable contributions to the scholarly record • support data archiving that will permit results to be

verified and re-purposed for future study.

• DataCite US: California Digital Library, OSTI, Purdue University Libraries

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DataCite DOI Services • DataCite serves as a DOI registration agency, like CrossRef • Acts as resolving “agent” for dataset DOIs. “All DataCite DOIs

resolve to a public landing page that contains information about the associated dataset and a direct link to the dataset itself. Maintains information in the DataCite Metadata Store.

• DataCite allows DOI resolution to multiple formats of the same data. Suppliers can specify multiple resource URLs

• CrossRef and DataCite collect bibliographic metadata about the works they link to and collaborate. Therefore, this metadata can be retrieved from the dx.doi.org DOI resolver too, using content negotiation to request a particular representation of the metadata.

http://dx.doi.org/

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Part 5: Government Initiatives

(a few examples)

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Part 6: Institutional Initiatives

(a few examples)

A Few Examples of Library Initiatives

• Johns Hopkins University (http://dmp.data.jhu.edu/)

• California Digital Library (https://dmp.cdlib.org)

• Purdue University (https://purr.purdue.edu/dmp/)

• University of North Carolina (http://guides.lib.unc.edu/researchdatatoolkit)

• Stanford University (http://dataplan.stanford.edu)

• DPN – Digital Preservation Network (http://www.dpn.org)

DPN Members

Data Curation Programs

• U. of Illinois: Digital Curation Education Program (DCEP):

– http://cirss.lis.illinois.edu/CollMeta/dcep.html

• U. of North Carolina: Post-Masters Certificate: Data Curation:

– http://sils.unc.edu/programs/graduate/post-masters-certificates/data-curation

• U. of Tennessee: Data Curation Education in Research Centers (DCERC):

– http://www.sis.utk.edu/dcerc

• April 30, 2013: Introduction to Data Science MOOC

– http://escience.washington.edu/blog/data-science-mooc-engages-students-solving-problems-real-organizations

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Part 7: Data Repositories

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Part 8: Research Data Advocacy

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Caution: Editorial Nature 464, 649-650 (1 April 2010) |

doi:10.1038/464649a; Published online 31 March 2010

The human genome at ten

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Nature 464, 649-650 (1 April 2010) | doi:10.1038/464649a; Published online 31 March

2010 Editorial: The Human Genome at Ten

“But for all the intellectual ferment of the past decade, has human health truly benefited from

the sequencing of the human genome? A startlingly honest response can be found on pages 674 and 676, where the leaders of the public and private efforts, Francis Collins and Craig Venter,

both say ‘not much’.”

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Part 9: What is the role for Societies?

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What is the role for Societies? • Ensure that supplemental materials are published with

an emphasis on preservation and reusability • Foster best practices to help address concerns over

reproducibility (note: launch of Meta-Research Innovation Center at Stanford http://med.stanford.edu/metrics/)

• Keep track of the evolving environment • Listen to your members concerns and help frame the

discussion • Help your members comply with data management plans • Work with institutions, vendors, and researchers to gain

experience in handling and publishing data

http://med.stanford.edu/metrics/

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Conclusion: There is a lot happening in a diversity of environments. Societies

and Publishers have something to offer, but this is going to be a collaborative

effort.

Data management issues

and how Societies can contribute

David Martinsen Senior Scientist Digital Strategy and Platform Development, Publications Division American Chemical Society AIP Assembly of Society Officers March 27, 2014 College Park, MD

Data management issues and how Societies can contribute · data . Processed Data and . Data...

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