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Source-to-Output Repositories Aspects of repositories use: employing an ecology-based approach to report on user requirements in chemistry and the biosciences.

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Presentation on theme: "Source-to-Output Repositories Aspects of repositories use: employing an ecology-based approach to report on user requirements in chemistry and the biosciences."— Presentation transcript:

1 Source-to-Output Repositories Aspects of repositories use: employing an ecology-based approach to report on user requirements in chemistry and the biosciences Panayiota Polydoratou Dagmar Biegon

2 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Outline StORe project The ecology approach - Concepts Example Observations

3 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest StORe project (http://jiscstore.jot.com/WikiHome)http://jiscstore.jot.com/WikiHome Funded: under the Joint Information Systems Committee (JISC – Digital Repositories Programme and by the Consortium of Research Libraries in the British Isles (curl – Duration: 2 years ( ) Partners: University of Edinburgh (lead) University of York, representing White Rose Partnership University of Birmingham London School of Economics University of Manchester Imperial College London University College London UK Data Archive (UKDA) Johns Hopkins University Seven disciplines Archaeology, Astronomy, Biochemistry, Biosciences, Chemistry, Physics, Social Policy

4 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest StORe project (http://jiscstore.jot.com/WikiHome)http://jiscstore.jot.com/WikiHome Aimed to: Address the area of interactions between output repositories of research publications and source repositories of primary research data. Determine the functionality that is required by researchers in both types of repository. Identify options for increasing the value of using primary data in source repositories at the point where researchers submit to or download papers from output repositories.

5 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest StORe project (http://jiscstore.jot.com/WikiHome)http://jiscstore.jot.com/WikiHome Method: Surveys of researchers that identify workflows and norms in the use of source and output repositories Deliverable: a generic technical specification of the functional enhancements to source and output repositories that were identified by researchers participating in the survey; pilot middleware built using this generic technical specification and demonstrated through the linking of holdings in the UK Data Archive to research papers stored in output repositories

6 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Characteristics of research in chemistry and the biosciences 1 Interdisciplinary research Strong bonds with biological, engineering, environmental, material, physics and computing sciences Diverse sets of research data, e.g. can be experimental, observational, computational Publication to print journals usually requires the deposition of data to support the paper

7 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Characteristics of research in chemistry and the biosciences 2 Bioscientists, especially those involved in research at gene and protein level usually generate large data sets which have to be organised and stored in specific repositories. Example: Human Genome Project Humans have approximately 21,000 genes the number of possible sequences of DNA pairs (about 3 billion) translates into a huge number of possible combinations in DNA and proteins. The majority of todays gene and protein researchers will rely on information searching in publicly accessible, Internet-enabled databases, where the data generated by other research groups is stored

8 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Ecology-based approach – Concepts 1 Scale = levels in an ecological view Entities = tangible things in a repository ecosystem Species = particular type of entities Interactions = activities between different species Resources = content of the interactions

9 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Ecology-based approach – Concepts 2 SCALE Levels of granularity – could be from Organism to Population to Community to Ecosystem StORe perspective = The users of a system or service represent organisms or a population in an ecosystem.

10 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Ecology-based approach – Concepts 3 ENTITY Many things can be entities from humans to repositories to a service, etc. StORe perspective, humans = academic and research staff and PhD students, the business analysts, and the system developers. repositories = several domain-specific source and output repositories and the consequent service that they provide as facilitators to free and open access to information.

11 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Ecology-based approach – Concepts 4 Species = particular type of entities Researchers at different education levels, in different disciplines, with different roles Repositories of different types (e.g., source/output, institutional/commercial, general/subject specific, etc.) Service (provision of a support system for research, facilitation of open access to information, etc.)

12 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Ecology-based approach – Concepts 5 Interactions Between humans (amongst researchers – indicative of different patterns of research norms) Between humans and machines (differences at the point of submission to a source/output repository to the point of searching and retrieving information from a source/output repository) Between machines (by directional links between source and output repositories)

13 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Ecology-based approach – Concepts 6 Resource Content of interactions between humans, humans and machines and machines to machines. Primarily information (can take the form of processed or unprocessed data, exchange of data and conversations amongst researchers, etc.)

14 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Ecology-based approach – Concepts 7 Factors Users ability/experience with systems Availability of data (including both present and long term archiving) Systems functionality Clear demonstration of potential benefits and take on by the target community/population Requirements imposed by third parties (e.g., funding bodies, legal aspects of availability and access to information, etc.)

15 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Example* What sort of thing (repository or service) is this? What does it relate to (other repositories or services)? What does it depend on? How adaptable it is? What helps it to thrive? *Example questions used on the model that R. John Robertson presented at: R. John Robertson (2007). The repository ecology: an approach to understanding repository and service interactions. Presentation at OAI5. (http://indico.cern.ch/contributionDisplay.py?contribId=11&sessionId=10&confId=5710)http://indico.cern.ch/contributionDisplay.py?contribId=11&sessionId=10&confId=5710

16 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Depositing to a source repository based on a use case

17 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Observations Scale Organism level – a researcher submitting data to a source repository Species Researchers (a bioscientist interacting with other bioscientists, groups, institutions, system administrators) Repositories (GenBank, PubMed) Service (Making research available)

18 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Observations Interactions Humans (interactions to decide about which source repository to submit, obtain clearance from research groups and institutions, check legal aspects of deposition) Humans – machines (form for submission, filling in associated metadata, lab book data) Machines to machines (source to output repository, primary data to publication, assorted metadata, mapping and conversion of file formats) Resources Primary data, published data, files in various formats, metadata associated with the files

19 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Observations Factors Easy and quick to use system Sustainable system Perceived value/quality of the service and take on by the community it is intended (e.g., reliability and availability of data, etc.) Institutional/funding bodies requirement

20 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Observations Use case maybe relatively simple to represent but in practice several factors are affecting the use and evolution of a system/service Representation by an ecology-based approach may prove more beneficial to map but potentially more difficult to represent all species and possible interactions that could take place in one single deposition of data, for example. Maybe some aspects are easier to represent by an ecology-based approach, e.g. interactions

21 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest Thank you! Panayiota Polydoratou & Dagmar Biegon

22 ECDL2007 Workshop: Towards an European repository ecology, 21st September 2007, Budapest References Human Genome Project (http://www.ornl.gov/sci/techresources/Human_Genome/ home.shtml)http://www.ornl.gov/sci/techresources/Human_Genome/ home.shtml StORe project (http://jiscstore.jot.com/WikiHome)http://jiscstore.jot.com/WikiHome R. John Robertson (2007). The repository ecology: an approach to understanding repository and service interactions. Presentation at OAI5. (http://indico.cern.ch/contributionDisplay.py?contribId=11 &sessionId=10&confId=5710)http://indico.cern.ch/contributionDisplay.py?contribId=11 &sessionId=10&confId=5710 Data Archive (http://www.data-archive.ac.uk/)http://www.data-archive.ac.uk/


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