a centre of expertise in data curation and preservation Reflections on open scholarship: process, product and people Dr Liz Lyon, DCC Associate Director Outreach Director,
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a centre of expertise in data curation and preservation Reflections on open scholarship: process, product and people Dr Liz Lyon, DCC Associate Director Outreach Director, UKOLN, University of Bath, UK This work is licensed under a Creative Commons Licence Attribution-ShareAlike 2.0 Funded by: 2nd International Digital Curation Conference, November 2006 a centre of expertise in data curation and preservation Three themes • How? – Unpacking the title: open scholarship • What? – Creating and using science-ready archives • Who? – “Digital natives” as data scientists 2nd International Digital Curation Conference, November 2006 •Publicly available? •Shared? •Inclusive? •Collaborative? What do we mean by “open”? •Participative? •Non-proprietary? Scholarship today? “Open Access” Data-driven science Datacentric 2020 vision Reference datasets as infrastructure “Open source science” Research into neglected tropical diseases http://www.thesynapticleap.org/ http://openwetware.org/wiki/Main_Page Synthetic biology: materials for (bio) mash-ups? Interesting IPR issues….. Bioblog Blogs, blogs and metablogs…. http://www.flickr.com/photos/64696485@N00/13146762/ The Tool Box? The Peer Review Process? http://www.ch.ic.ac.uk/wiki2/index.php/Mauveine The Scientific Paper? Crystal Structure reports data-rich scientific articles Original slide: • Brian McMahon, • IUCr • • • • • • 3-d positional coordinates Atomic motions Molecular geometry Chemical bonding Crystal packing Chemical behaviour arising from structure Two dedicated IUCr journals: Acta Cryst. C, E Important part of scientific discussion in many other titles: Acta Cryst. B, D, F Validation of data through publication • Data-centric scholarly “publications” • Raw, primary, derived data integrated with interpretations • Mandatory submission of data with text a centre of expertise in data curation and preservation 2nd The database publication? International Digital Curation Conference, November 2006 http://declanbutler.info/blog/?p=58#more-58 The “mash-up” Data from FAO, WHO + Google Earth Pause for thought….. • Big science communities – Grid-enabled applications – Large managed open data archives – Funder policy driver • Small(er) science communities – Collaborative and social software – Evolving open wikis and blogs – Grassroots driver • Curation and preservation issues – Burgeoning wiki and blog content – Web archiving • Positioning of repositories??? Big science Funder-mandated sharing? Top down “science-ready archives” Small science Community culture Discipline? Institution? Bottom up • Laboratory protocols: common practice • Instrumentation: proprietary software • Standard specifications and formats Data capture • Working towards standard specifications in the lab – – – – Open Microscopy Environment OME Medical imaging DICOM Flow cytometry standard FCS Mass Spectrometry Standards Working Group mzData vs mzXML • Laboratory management data systems in development RepoMMan: Repository Metadata and Management (Univ Hull) using WS-BPEL Airport Maintenance Engineer Workflow: m2m? Visual Inspection DS&S Maintenance Analyst (Fleet Manager) Aircraft Lands Quote Diagnosis Rolls Royce Domain Expert DAME signal processing workflows using Grid Services Brief Diagnosis / Prognosis Check Diagnoses [ unknown ] Diagnosis Result Detailed Diagnosis / Prognosis [ fault unresolved ] [ Clear ] [ known ] [ information required ] Provide Information Maintenance Procedure Release Engine e-Scientist desktop? Slide: Carole Goble complete [ diagnosis Maintenance Result [ fault resolved ] Request Information Analyst [ unknown ] Decision Detailed Analysis [ diagnosis ] Expert Decision [ information required ] Sign-off Diagnosis Provide Further Details Request Further Details Silchester: A VRE for Archaeology Harmonisation and normalisation • Standard Deposit API (GNU eprints, Dspace, Fedora) • Dublin Core Application Profile for ePrints (+ Eduserv) • Requirements: richer metadata set, support for value-added services, version identification, appropriate copy (OA), citations • Based on FRBR • Data model for scholarly works • Application profile includes simple and qualified DC properties The ePrints application profile • simple DC properties (the usual suspects … ) – identifier, title, abstract, subject, creator, publisher, type, language, format • qualified DC properties – access rights, licence, date available, bibliographic citation, references, date modified • new properties – grant number, affiliation institution, status, version, copyright holder • properties from other schemes – funder, supervisor, editor (MARC relators) – name, family name, given name, workplace homepage, mailbox, homepage (FOAF) • clearer use of existing relationships – has version, is part of • new relationship properties – has adaptation, has translation, is expressed as, is manifested as, is available as • vocabularies – access rights, entity type, resource type and status Slide: Julie Allinson, UKOLN, Andy Powell, Eduserv Use DC Application Profile for ePrints? Data description and discovery • Validation, publication & discovery of data models & schema • eBank Application Profile http://www.ukoln.ac.uk/projects/ebankuk/schemas/ • Harmonisation and normalisation of metadata and semantics • DOI http://dx.doi.org/10 • .1594/ecrystals.chem.soton.ac.uk/145 Rights & Citation policy http://ecrystals.chem.soton.ac.uk/rights.html • Crystallography: a community working together eCrystals ‘Global Federation’ Model Data creation & capture in “Smart lab” Data discovery, linking, citation Laboratory repository This work is licensed under a Creative Commons Licence Attribution-ShareAlike 2.0 Presentation services / portals Data discovery, linking, citation Publishers: peerreview journals, conference proceedings, etc Deposit 23/10/2006 Data analysis, Publication transformation, mining, Institutional modelling data repositories Deposit , Validation Search, harvest Aggregator services Search, harvest Validation Search, harvest Subject Repository Deposit Deposit Curation Preservation Deposit Institution Library & Information Services Data deposit & sharing: roles and responsibilities • • • • Funder Institution Faculty Individual Noor et al PLoS Biol 4(7) 2006 eBank Project exemplar Adding value: aggregating & linking data + interpretations “Repository wow-factor”… …or adding value through user interface tools… Facilitating use and re-use: text mining tools • Adding value Second pause for thought… • We need to work with instrument suppliers • We need to understand more about workflow • We need to develop new ways of adding value to datasets through innovative user tools and services • We need more evidence of how data is used and re-used (or not…) Getting the skills mix • Communities, teams, individuals • International Virtual Observatory Alliance – Global community – Virtual organisation • Multi-disciplinary team approach – eBank Project exemplar: computer scientists, domain scientists (chemists), digital library experts – Lessons learnt: e-Science Human Factors Audit Report 2006 Roy Kawalsky, Loughborough • NSF Report 2005 Long-lived digital data collections – “Data scientist” Wanted! data scientist ? Digital natives as data scientists? • eBank Project: assessing role of research data in u/g Chemical Informatics and MChem courses at Univ. of Southampton • Pedagogic evaluation by Grainne Conole • Report imminent…. “There were several parts to the course – We started off with how to get 2D and 3D representations of molecules onto a computer using a one-dimensional format, a SMILE string …so just ways of like getting data into a format so that it can be easily shared between different computers or different people without having to change lots of things” “Well basically I’ve done nothing like it before, so it’s the first time I’ve sort of delved into computing or computational chemistry … quite nice, quite enjoyed starting off with just like a string of data and pop it into say a database, just a flat string of numbers basically and then come out with a crystal structure, which is exactly what it should represent which is quite cool” Source: Grainne Conole New skills requirements: • interdisciplinary • quantitative • data curation Integrate within the curriculum Wingreen & Botstein Mol Cell Biol 7, 2006 Final pause for thought… • Various approaches to develop and obtain digital curation skills • Skills are there but often in discrete communities: we need to bring communities together (like at this conference…) • Integration within the curriculum: undergraduate students, library & information science, archival studies, computer science • Provide recognition and a career path for emerging data scientists a centre of expertise in data curation and preservation Take home messages • Scholarship is changing fast • Big science and open source science both create significant digital curation challenges • Science-ready archives are the goal • Native data scientists are coming • The culture will change too………. 2nd International Digital Curation Conference, November 2006 a centre of expertise in data curation and preservation Thank you…. 2nd International Digital Curation Conference, November 2006