Integrating Data & the Online Article on SciVerse ScienceDirect

Integrating Data & the Online Article on SciVerseScienceDirect Hylke Koers, Content Innovation Manager DataCite Summer Meeting, Berkeley, August 25, 2011

Overview • Data & the Scientific Article • Supplementary Material • Connecting with Data Repositories • Online Linking Schemes • Entity-level & Article-level Linking • Examples • Applications • SciVerse Applications • Applications and Data • The Article of the Future

Supplementary Material • Authors can upload Supplementary Material with their paper • Pro’s • Coupling of data and article • Peer review • Citation mechanism • Preservation (byte-wise) • Con’s • Limited data type support • Compatibility (format support) • Limited capacity • Data not centrally stored

Connecting with Data Repositories • Supplementary material is not a perfect solution • Many poor solutions in use: data on PCs, university websites, personal homepages, ... • Data repositories: the community’s answer? • Scientists prefer independent data repositories above publishers • Domain-specific coordination • Centralized information “hubs” • “Raw data should be freelyaccessible to researchers” “... believe that, as a general principle, data sets, raw data outputs of research, and sets or subsets of that data should wherever possible be made freely accessible to other scholars ...”(Statement from STM & ALPSP, June 2006)

Connecting with Data Repositories • There is value in connecting Data and Articles: • Increase visibility, discoverability, and usage • Provide context, avoid misinterpretation and incorrect usage • 85% of researchers believe it is useful to link underlying digital research data to the formal literature (PARSE.Insight) • Collaboration between Publishers and Data Repositories: • Ensure long-term availability of useful content and context • Coordinate submission process / deposit mechanism

Overview • Data & the Scientific Article • Supplementary Material • Connecting with Data Repositories • Online Linking Schemes • Article-level & Entity-level Linking • Examples • Applications • SciVerse Applications • Applications and Data • The Article of the Future

Online Linking Schemes • SciVerseScienceDirect supports different linking arrangements: • Article-level: associate an article with a data set • Example: a data set that underlies the analysis in an article • Could be author-deposited or curated • Entity-level: link entities in articles to relevant data • Examples: taxons, chemicals, proteins, ... • Could be manual tagging: accurate, non-ambiguous, but additional work for the author • Could be text mining: retrospective, automatic, but less accurate (ambiguities)

Online Linking Schemes: Examples • Article Linking example: CCDC Link to CCDC database(indicates that information for thisarticle is available) Screenshot of journal article on ScienceDirect (http://dx.doi.org/10.1016/j.jfluchem.2009.07.015)

Online Linking Schemes: Examples • 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)

Online Linking Schemes: Examples • Entity Linking example: Genbank Accession Number Tagged Genbank entry(genetic sequence) Screenshot of journal article on ScienceDirect (http://dx.doi.org/10.1016/j.biortech.2010.03.063 )

Online Linking Schemes: Examples • 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)

Online Linking Schemes: Examples *: with Application

SciVerse Applications • Scientific literature: a node that could more efficientlyconnect resources • Mass of data available to researchers outside the formalliterature is huge and growing • Many disconnected nodes - minimal interoperability, even when connections exist • This is inefficient - task switching between multiple interfaces, hard to find resources... • An open platform for publishing can “un-silo” data and literature • Smart apps can facilitate interoperability, bring relevant data into context with papers • Integrated user experience, save researchers from searching in multiple data sources while reading the literature • Introduces researchers to new tools and resources they may never have found otherwise

SciVerse Applications Features & Benefits • Use information from SciVerse and the web • Support for rich user interfaces • Integrated directly into the online article • Simple to build using Content and Framework APIs • Open standards (Apache Shindig, Open Social)

SciVerse Applications & Data • SciVerse Applications enable the community to create the publishing platform they need by building their own applications. • Benefits for data repositories • Increase visibility, discoverability, and usage(ScienceDirect: ~600M page views/year) • Provide context: connect data with the formal literature, avoid misinterpretations and incorrect usage • Enable researchers to interactive explore data Sounds interesting? Come talk to us! (or email me after the conference at h.koers@elsevier.com)

Applications example: NCBI Genome Viewer • Scans the article and builds list of sequences based on NCBI accession numbers tagged in the article • View/analyze sequence data from genes in the article using NCBI Sequence Viewer • See specific information about each strand; zoom in/out; export data Screenshots of journal article on ScienceDirect (http://dx.doi.org/10.1016/j.ygeno.2007.07.010)

Applications example: PANGAEA • Document identifier sent to PANGAEA data repository for earth sciences • PANGAEA returns map plotted with locations where cited data was collected • Push-pins open with details of dataset and direct link to data on PANGAEA.de Screenshots of journal article on ScienceDirect (http://dx.doi.org/10.1016/S0377-8398(01)00044-5)

The Article of the Future • Presentation: structurally improve readability of the online article • Basis to deliver advanced functionality and content • Content: support rich research output(KML files, MOL files, ..) • Domain-specific approach, one size does not fit all • Connect with existing author workflow • Context: establish links with data repositories and other information resources

The Article of the Future www.articleofthefuture.com Prototypes in 7 domains with specific content enhancements and database links

Take-aways • Integration of Data and Articles brings value to researchers • Elsevier working together with data repositories to establish reciprocal linking • SciVerse Applications provides the tools to further integrate data and articles – please talk to us to explore the possibilities for your database! • The Article of the Future provides a new platform for improved online presentation, rich content, and valuable context from data repositories (and other resources) Thank you!

Backup: Data and the Scientific Article Researchers perceive data sets as “important, but hard to access” Publishing Research Consortium, 2010Researchers, N = 3824 • Important, but hard to access

Backup: SV Apps under the hood • JustGadgets • Simple HTML and JavaScript applications • Embedded in webpages and other apps. • Gadgets API is a part of the OpenSocial specification • iGoogle, LinkedIn, MySpace • Apache Shindig • Reference implementation of OpenSocial API v0.9 • “Contains” the gadgets on a page • Provides basic services like rendering, proxying requests • Provides plumbing for developing a framework and framework API’s for gadgets

Integrating Data & the Online Article on SciVerse ScienceDirect