Data Curation Education - University Of Illinois

Data Curation Education - University Of Illinois

Research Practice and Research Libraries: Working toward High-Impact Information Services Carole L. Palmer Center for Informatics Research in Science & Scholarship (CIRSS) Graduate School of Library and Information Science University of Illinois at Urbana-Champaign OCLC Programs and Research 19 June 2008 The problem in a nutshell Utopian e-research scenarios promoted decades ago may now be obtainable goals. They will be enabled by the interplay of technology and user behavior. We have a reasonable understanding of changing technology but a limited understanding of changing user behavior and therefore a poor understanding of the interplay in the actual activities of reading, experimenting, analyzing, interpreting and problem solving. One problem is that much of our research doesnt identify the features most

likely to be explanatory and predictive, or indicate what interventions can make a real difference. In what follows, I draw on our studies of scholarly information work over the past decade to discuss how information use is changing in the practice of science and scholarship and reflect on where research libraries can direct their efforts to make a significant contribution. Higher stakes in getting information services right In the contemporary context of e-science, aiming directly to re-shape scientific endeavours and provide new infrastructures to support them, [the] goal of studying the detail of actual practice takes on a new significance. (Hine, 2005) The body of research on general trends in digital information use provides and important base, but often only a silhouette of the interplay between researchers and information. Studies need to be refined to investigate the role and value of information and how to improve research. how information fits in, interacts, fuels new discoveries what differences make a difference: disciplines and domains,

methodological strategies, project stages, etc. The story line We need to know more about scholarly research practiceshow scholars are working & wish to work with information, - the case of reading and determine what kinds of information support can really make a difference in how scholars work. - insights from a study of scientific discovery Management and reuse of data sets is one such area that depends on deep understanding of research practice, - insights from research on federating cultural heritage collections and on readying research librarianship for data curation responsibilities - the need to step up, but with skepticism. Reading is

complex Flickr user: sanofi2498 creative commons General trends in e-journal use well documented Nearly all STM journals are now available electronically access in the sciences is predominantly to these electronic versions 98% of medical researchers prefer e-journals (Hemminger, 2007) Web bouncing common, especially in medicine, life sciences (CIBER group - Nicholas, et al., 2006) Number of articles read is rising over 30% higher in 2006 than in the mid-90s Reading time per article is falling medical researchers about 24 minutes per article (Tenopir, 2006) But are these really indicators of reading? Our studies suggest researchers are not reading more, but rather scanning, exploring, and getting exposure to more sources. (Palmer, 2001, 2002)

Consistent with the recent reports by Tenopir and CIBER In fact, researchers may be practicing active reading avoidance. (Palmer, 2007; Renear, 2006, 2007) Researchers are rapidly navigating through more material, spending less and less time with each item, and attempting to assess and exploit content with as little actual reading as possible. Intensification of longstanding practices Indexing and citations help us decide whether or not articles are relevant without reading them. Abstracts and literature reviews help us take advantage of articles without reading them. The articles we do read provide summaries and discussions that help us take advantage of other articles without reading them. Colleagues, and graduate students, help us learn about and understand articles without reading them. And the apparatus (tables of contents, references, figures, etc.), distinctive formatting of text components (such as lists, equations, scientific names, etc.), help us exploit articles without reading

them. But researchers do read, in many different ways probing in new areas conference lurking to web exploration learning textbook-like explanations positioning directed searching of topic competing directed searching of people scanning, stay aware

reviews to alerting services & blogs rereading personal collections reading around following leads to thematic collections Other uses of the literature are equally important consulting - experimental resource to identify protocols instrumentation comparative results compiling customized personal collections laptops full of PDFs extracting core knowledge base facts for ontology development

building - source for database enrichment annotation, evidence Supporting creative and indirect uses of the literature Finding articles to read left-to-right, top-to-bottom is even less of an accurate representation of literature use than it ever was. We read less and less every year, yet are even more analytically engaged with the literature But the value of functions are far from uniform across fields: In the humanities, reading around, collecting, and rereading In the sciences, researchers likely to benefit from fast-paced, indirect, horizontal use of the literature. Advances dependent on encoding and associated metadata and ontologies greater application of analytical text mining and literature-based discovery Scientific discovery is work

Flickr user: stancia creative commons How do we improve conditions for discovery? Information and Discovery in Neuroscience (IDN Project) NSF/CISE/Digital Technologies and Society, #0222848 What information conditions are associated with advancements and problems during the course of research? What role can literature based discovery (LBD) play in daily scientific practice? Partnership with Arrowsmith Project Based on Swansons (1986) notion of undiscovered public knowledge Smalheiser & Swansons system adapted for PubMed end users Conceived of as tool for hypothesis testing implicit relationships among literature A and literature C. Study of information practices and informatics efforts 12 project-based cases at 4 labs, 11 key informants, 25 total participants 1/3 of participants field testers for Arrowsmith

Qualitative Interviewing project-based critical incidents (44 sessions) Information Diary Arrowsmith search logs Information activity logs (137 records) Field Observation information activities research processes work environment (19 hours)

(progress, problems, shifts) Key aspects of research design Partnering with neuroscientists who are actively investing in and customizing digital resources and tools for themselves and their communities best indicators of how researchers wish to engage with information technology in their work. Longitudinal case study chronicling of projects and relationship to larger programs of research extended use of personal diaries in conjunction with critical incident interview data verification of reported information activities and importance over time refinement and validation of our information categorization scheme Rich cases representing range of neurosciences LAB 1 Research types / techniques

clinical studies and computational neuroscience fMRI LAB 2 neuronal substrate of learning and memory electrophysiology neuroinformatics - computing tools for neuroscience application Project Characterizations clinical neuroscience investigating reward systems using brain area activation basic neuroscience affect of lesions on acquisition

and extinction of discriminative behavior computer science computational neuroscience - modeling - imaging - fMRI (functional, structural) - psychology - psychiatry - electrophysiology - behavioral neuroscience - anatomy - cell biology - biochemistry - neuropsychology - neurophysiology

LAB 3 microscopy, telescience, and anatomy microscopy and tomography basic neuroscience characterizing mouse models of disease (using microscopy and imaging techniques) ontology development for shared databases - Primary Domains (as represented in collaborations and use of literature) - anatomy - microscopy

- computer science - biology - neuroinformatics - biochemistry - neurophysiology Progress and problems related to information work Greatest advancements associated with visualization of data Knowledge of brain anatomy (people, information resources and tools) playing pivotal role in moving research forward Difficulty locating specifics on protocols, instrumentation, measurements, experimental context, etc. Retrospective, non-digital literature often ignored Review articles essential for keeping up with information and for learning in new areas Unexpected LBD applications Surprisingly, hypothesis assessment rare with Arrowsmith Information Activity Totals

Assessing finding Searching deeply in own domain Exploring outside domain Exploring in own domain Known-item searching Problem-solving Searching specifically outside domain Arrowsmith Diary Information Diary Assessing hypothesis 0 5 10 15

20 25 Number of Activities 30 35 Most frequent activities Assessing finding against the literature How important is this result? increased in frequency over time Exploring outside own domain What am I missing? 54% focused on clinical concepts or diseases difficulty evaluating importance of information found

Searching deeply in own domain Is this project worth investing in? analyzing risk or verifying viability of a research project But, low frequency more important for discovery Importance of Information Resulting from Activities 120 Categories Importance Ranking (%) 100

Percent ranked Potentially or Definitely Important n = 123 80 60 40 29 23 25 19 20 11

11 3 2 0 Searching specifically outside domain Problemsolving Assessing Known-item Searching finding search deeply own domain

Exploring outside domain Assessing Exploring hypothesis own domain Categories with Importance Rankings Information work as weak or strong Extending Herbert Simons conceptualization of weak / strong methods (Simon, Langley, and Bradshaw, 1981) Weak (novice, trial & error) Ill-structured problem space Unsystematic steps

Low domain knowledge Data driven Seek and search Strong (expert, tried-and-true) Structured problem space Systematic steps High domain knowledge Theory driven Recognize and calculate Importance of weak approaches . . . fundamentality of a piece of scientific work is almost inversely proportional to the clarity of vision with which it can be planned. (Simon, Langley, & Bradshaw, 1981, p. 5). may be all that is available on the frontiers of knowledge

(Simon et al., 1987) required for revolutionary science (Kuhn, 1962) And, our previous studies of interdisciplinary scientists and scholars show weak conditions common in their research. (Palmer 1996, 1999, 2001; Palmer & Neumann, 2002) How does the weak/strong framework help us? Strong information work is most routine and codified Weak information work is the most arduous and most speculative Weak work highest in preparation stages of research Assessing preliminary hypotheses Feasibility assessment Building new interdisciplinary collaborations High in all cases where new learning involved Developing a new research technique The most productive points for information support are likely to be at ends of the weak / strong continuum.

Can predict the kinds of activities and stages of research where weak and strong information work will be centralized. (Palmer, Cragin, & Hogan, 2007) Strengthening weak work Some, but not all, weak work should be stronger, more routine, codified, especially in informatics and data intensive research literature based discovery for hypothesis testing instrumentation and methods fact-finding ontology and standards development for data repositories management and reuse of data Data sets as special Collections Flickr `: r h creative commons

Curation Profiles Project (IMLS NLG 2007-2009) CIRSS with Purdue University Libraries (D. Scott Brandt, PI) Investigating curation requirements across sciences in collaboration with librarians working closely with researchers on issues of scientific research data management and curation researcher data / metadata workflow policies for archiving and access system requirements for managing data in a repository identify roles of librarians and skill sets they need to support archiving and sharing Complexities of data collections Primary and secondary data, mobilized to produce new primary research, and their various transformations Data Characteristics Crystallography Type 1. Raw data binary image frames

2. Phased file electron density 3. Integrated data amplitudes of molecules 4. Corrected data according to theory Format 1. Binary diffraction images based on the software 2. Different electron density image 3. Multiple formats 4. CIF file Size 1. About 2,400 frames -1Mb each about/over 1Gb 2. > 100Mb 3. 5-6 Mb 4. < 1 Mb

Workflow well-defined stages, for measurement or analytical purposes, in sequence; output of one stage constitutes the input to the next; for publication CIF considered final result of experiment Generated by instruments, people, in the lab, in the field, etc. data characteristics storage & security standards / metadata / interoperability preservation access sharing

intellectual property quality control services linking & citation visualization Research libraries role most evident in small science Data from Big Science is easier to handle, understand and archive. Small Science is horribly heterogeneous and far more vast. In time Small Science will generate 2-3 times more data than Big Science. (Lost in a Sea of Science Data S.Carlson, The Chronicle of Higher Education, 23/06/2006.) big science data small science data Challenges of small, cross-disciplinary science Data needs assessment of UIUC Faculty of the Environment; daunting to define, reach, respond to the user community. Faculty Population for Initial Needs Assessment by Department

6 6 5 Illinois State Surveys No. Dept/s with <4 faculty 5 4 5 5 Natural Res & Env Sci 43 Civil & Environmental Eng VeterinarySciences Crop Sciences

7 Plant Biology 7 Architecture and Landscape Architecture Agricultural Engineering 7 Geography 7 37 Geology Agr & Cons Econ

7 Animal Sciences 8 Atmospheric Sciences Food Science & Human Nutrition 10 Mechanical & Industrial Eng 24 10 Animal Biology Waste Management Research Ctr Anthropology

Electrical & Computer Eng 12 13 17 14 16 Materials Science & Engineering Urban & Reg Planning Chemistry How do we identify and represent analytical potential Researchers have clear ideas about what data sets do not need to be saved or preserved, but may not be able to predict potential of long-term use by others, especially for applications in other fields collective value or applications of the many, often specialized, distributed collections in large-scale aggregations

theoretical modelers earliest adopters With cultural heritage collections, decades of opportunity-driven digital projects have resulted in overall lack of cohesion of digital content. Need to aim for contextual mass, not just critical mass (Palmer, 2004) through more systematic collection of complementary content What are the meaningful organizing units for data sets? Fundamental problems of scale & granularity Flat representation of digital collections; small window into large, diverse accumulation of content - all items appear equal - strengths, special features not evident Diminished intentionality - purpose of and relationships among collections not evident Collection level metadata solutions not straightforward - what constitutes a set - how to handle transformations and new composites, and relationships to original sets

Data curation is contentious K. Sawyer creative commons What does LIS have to offer data curation? In the tradition of research librarianship, professionals must understand the landscape of research resources and how resources work together: Collect and manage data in ways that add value and promote sharing and integration across laboratories, institutions, and fields of research. Build and maintain data systems that work in concert with digital libraries, archives, and repositories, and

the indexing systems, metadata standards, ontologies, etc. associated with digital data and products. Extending library functions to new content The active and on-going management of data through its lifecycle of interest and usefulness to scholarship, science, and education. Activities enable data discovery and retrieval maintain data quality add value provide for re-use over time archiving preservation Tasks appraisal and selection representation authentication

data integrity maintaining links format conversions Whats new for libraries and librarians? Closer engagement with scientists during research production, more sophisticated understanding of the differences in research cultures across domains potential for more direct contributions to the scientific enterprise Facilitation of data deposition to local, disciplinary, larger federations New collaborations and constituencies campus IT, research officers Development of data curation principles and systematic practices Professionalizing curation of research data CIRSS initiatives with research / data centers in the sciences and humanities to develop Data curation concentration in MSLIS 2 IMLS Laura Bush 21st Century Librarian Program Grants

Science, Heidorn, PI / Humanities, Renear, PI Focus on digital data collection and management, representation, preservation, archiving, standards, and policy. Develop curriculum, internships, promote & share DC expertise. 1st summer institute for academic librarians, June 2008 Digital Curation Centres 6th International Conference in 2010 Curators inside research libraries & research centers Science Partners Biomedical Informatics Research Network (BIRN), UCSD Missouri Botanical Garden Smithsonian Institution Field Museum of Natural History U.S. Geological Survey Marine Biological Laboratory US Army ERDC-CERL Humanities Partners Institute for Technology in the Arts and Humanities (IATH), Committee on Documentation (CIDOC) of the International Council of Museums (ICOM)

Center for Computing in the Humanities, Kings College London OCLC Women Writers Project Perseus References Hemminger, B. M., Lu, D., Vaughan, K.T.L., Adams, S. J. (in press). Information seeking behavior of academic scientists. Journal of the American Society for Information Science & Technology. Hine, C. (2005). Material culture and the shaping of e-science. First International Conference on E-Social Science . Manchester, UK. Nicholas, D., Huntington, P., Jamali, H. R., & Dobrowolski, T. (2006). Characterising and evaluating information seeking behaviour in a digital environment: Spotlight on the bouncer. Information Processing and Management 43, 1085-1102. Palmer, C. L. (1996). Information work at the boundaries of science: Linking information services to research practices. Library Trends 45(2), 165-191. Palmer, C. L. (1999). Structures and strategies of interdisciplinary science. Journal of the American Society for Information Science 50(3), 242-253. Palmer, C. L. (2001). Work at the Boundaries of Science: Information and the Interdisciplinary Research Process. Dordrecht: Kluwer. Palmer, C. L. & Neumann, L. (2002). The information work of interdisciplinary humanities scholars: Exploration and

translation. Library Quarterly 72 (January), 85-117. Palmer, C. L., Cragin, M. H., and Hogan, T.P. (2007). Weak information work in scientific discovery. Information Processing and Mangement 43 no. 3: 808-820. Renear, A. H. (2006). Ontologies and STM publishing. STM Innovations, London, UK, 1 December, 2006. Renear, A. H. (2007). Standard domain ontologies: The rate limiting step for the "Next Big Change" in scientific communication. The 233rd American Chemical Society National Meeting, Chicago, IL, 25-29 March, 2007. Simon, H. A., Langley, P. W., & Bradshaw, G. L. (1981). Scientific discovery as problem solving. Synthese, 47(1), 127. Swanson, D.R. (1986). Undiscovered public knowledge. Library Quarterly, 56(2), 103-18. Tenopir, C. (2006). How electronic journals are changing scholarly reading patterns. CONCERT Annual Meeting, Taipei, Taiwan, 2006. Questions & comments, please [email protected] Center for Informatics Research in Science and Scholarship (CIRSS)

Arrowsmith LBD: the ABC Model Articles about an AB relationship A Raynauds syndrome AB B blood viscosity etc. C BC dietary fish oil Articles about a BC relationship

AB and BC are complementary but disjoint : They can reveal an implicit relationship between A and C in the absence of any explicit relation. The researcher assesses titles in the B literature identified by the system for fit or contribution to problem.

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