Data management issues and how Societies can contribute
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1 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
2 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? 27 March 2014
3 Resources for Data Management Part 1: Background/Publisher Perspective 27 March 2014
4 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
5 A famous paper in Nature: DNA structure page 2 authors 1 figure no data Source: V. Kiermer, Nature Publishing Group, 2011
6 Nature in 2001: The human genome issue 62 pages, 49 figures, 27 tables Source: V. Kiermer, Nature Publishing Group, 2011
7 The Data Publication Pyramid (2) Further data explanations in any kind of supplementary files to articles (4) Data publications, describing available datasets 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 (3) Data referenced from the article and held in data centers and repositories (5) Data in drawers and on disks at the institute
8 The Pyramid s likely short term reality: (4) Estimates are that at least 75 % of research data is never made openly avaiable (2) Risk that supplements to articles turn into Data Dumping places Pubs Supps Data Archives Data on Disks and in Drawers (1) Top of the pyramid is stable but small (3) Too many disciplines lack a community endorsed data archive 8
9 The Ideal Pyramid (2) Only if data cannot be integrated in article, and only relevant extra explanations (4) More Data Journals that describe datasets, data mgt plans and data methods Data In Publications Article Supps Data Archives (1) More integration of text and data, viewers and seamless links to interactive datasets (3) Seamless links (bi-directional) between publications and data, interactive viewers within the articles Data on Disks and in Drawers 9
10 Resources for Data Management Part 2: NISO/NFAIS Recommendations on Supplemental Journal Article Material 27 March 2014
11 The NISO/NFAIS Working Group
12 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
13 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
14 Resources for Data Management Part 3: Publisher Initiatives 27 March 2014
15 Moving forward our shared data agenda: a view from the publishing industry
16 Connecting with Data Repositories, 1 Article Linking example: CCDC Link to CCDC database (indicates that information for this article is available) Screenshot of journal article on ScienceDirect (
17 Connecting with Data Repositories, 2 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)
18 Connecting with Data Repositories, 3 Entity Linking example: Genbank Accession Number Tagged Genbank entry (genetic sequence) Screenshot of journal article on ScienceDirect ( )
19 Connecting with Data Repositories, 4 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)
20 Connecting with Data Repositories, 5 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
21 27 March 2014
22 Data accessibility: Why? 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. 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 27 March 2014
23 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 27 March 2014
24 AAS/AIP data access project 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) 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 27 March 2014
25 AAS/AIP data sharing survey Highlights regarding sharing data 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 % % 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. 27 March 2014
26 AAS/AIP data sharing survey Highlights regarding using data 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 % % How data was used 0 Directly from author Large data repository Publishing Journal Affiliated institution Other 0 Explore new questions Integrate sources Replicate work Other 27 March 2014
27 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. Copyright 2011 American Chemical Society
28 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. Copyright 2011 American Chemical Society
29 why is ACS concerned with data?bbb integrity of published research 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. Copyright 2011 American Chemical Society
30 why is ACS concerned with data?bbb integrity of published research 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; ppm for carbon). For new compounds, copies of both proton and carbon spectra are required (see Identity above). Copyright 2011 American Chemical Society
31 why is ACS concerned with data?bbb integrity of published research 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. Copyright 2011 American Chemical Society
32 data submission for characterizing compounds Copyright 2011 American Chemical Society
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34 Some Data Journals NEW TRADITIONAL 27 March 2014
35 Recent Development at PLOS 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. 27 March 2014
36 Resources for Data Management Part 4: Data Citation 27 March 2014
37 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 27 March 2014
38 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. 27 March 2014
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41 Resources for Data Management Part 5: Government Initiatives (a few examples) 27 March 2014
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46 Resources for Data Management Part 6: Institutional Initiatives (a few examples) 27 March 2014
47 A Few Examples of Library Initiatives Johns Hopkins University ( California Digital Library ( Purdue University ( University of North Carolina ( Stanford University ( DPN Digital Preservation Network (
48 DPN Members
49 Data Curation Programs U. of Illinois: Digital Curation Education Program (DCEP): U. of North Carolina: Post-Masters Certificate: Data Curation: U. of Tennessee: Data Curation Education in Research Centers (DCERC): April 30, 2013: Introduction to Data Science MOOC
50 Resources for Data Management Part 7: Data Repositories 27 March 2014
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56 Resources for Data Management Part 8: Research Data Advocacy 27 March 2014
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58 Resources for Data Management Caution: Editorial Nature 464, (1 April 2010) doi: /464649a; Published online 31 March 2010 The human genome at ten 27 March 2014
59 Nature 464, (1 April 2010) doi: /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. 27 March 2014
60 Resources for Data Management Part 9: What is the role for Societies? 27 March 2014
61 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 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 27 March 2014
62 Resources for Data Management 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. 27 March 2014
63 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
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