Science Library Pad

ECDL 2006 and DLSci06 proceedings

The proceedings (PDF) from the workshop Digital Library Goes e-Science (DLSci06) are now freely available online.

As well, the proceedings from the European Conference on Research and Advanced Technology for Digital Libraries, 2006 (ECDL 2006) are available in paper or digital format, but not for free.  You will need a Springer subscription.

Julio Gonzalo, Costantino Thanos, M. Felisa Verdejo, Rafael C. Carrasco (Eds.): Research and Advanced Technology for Digital Libraries, 10th European Conference, ECDL 2006, Alicante, Spain, September 17-22, 2006, Proceedings. Lecture Notes in Computer Science 4172 Springer 2006, ISBN 3-540-44636-2

The Digital Bibliography & Library Project (DBLP) provides handy links to the individual articles, which are available (if you have licensed access) through SpringerLink. See their page on ECDL 2006 proceedings, or their links for all previous ECDL conference proceedings.

The presentations (i.e. the PowerPoint files) are not online yet; I don't know when they will be.

ECDL 2006 - DLSci06 - DILIGENT grid-based DL

Leonardo Candela, Donatella Castelli, Christoph Langguth, Pasquale Pagano, Heiko Schuldt, Manuele Simi and Laura Voicu
On-Demand Service Deployment and Process Support in e-Science DLs: the DILIGENT Experience

http://www.diligentproject.org/

(Also see notes from tutorial Distributed Infrastructures for Digital Libraries.)

Motivation

* research is multidisciplinary and co-operative effort
* may use a virtual resource organization that doesn't last a long time or have DL expertise
* but the DL is an important tool

DELOS view: from DL to Knowledge Commons
* from content-centric to person-centric
* from info storage to communication and collaboration support
* from centrally-located text to distributed and heterogenous data sources

New DL development model
* DL built by dynamically aggregating the needed resources
* new functionality combined in user-defined workflows

Service-Oriented Architecture over Grid Framework

[complex diagram]

* New functionality delivered by workflows of services

Services Overview

* Mediation
* Information Space Management
* Access
* User and Resource Management
* Presentation
  - user-oriented access point to the DL
  - plug and play community-specific tools
  - [something about JSR168 portlets and other stuff]
* Enabling
  - monitoring, other operations domain functions

Service Detail

* the Keeper Service
  - deploy and monitor user-defined virtual DLs

* the Information Service
  - gathers, stores and supplies information about the resources constituting DILIGENT
    and needed to the other services
  - XML-based resource profiles
  - push and pull modalities i.e. query and subscribe/notify

Process Design and Validation

Implement complex services by combining existing ones, a.k.a. "programming in the large"
* control flow
* data flow
* transaction behavior and execution guartees for concurrency and failure handling
* XML, SOAP and WSDL as technologies
* BPEL as a foundation for process specification

[diagram of tool]

Process Execution

* built on top of OSIRIS
* runs BPEL tasks?

ECDL 2006 - DLSci06 - TextGrid

Andreas Aschenbrenner, Peter Gietz, Marc Wilhelm Küster, Christoph Ludwig and Heike Neuroth
TextGrid - a modular platform for collaborative textual editing

http://www.textgrid.de/

BMBF e-Science Programme

http://www.bmbf.de/de/298.php

* 2005-2009
* 100 institutions
* 100 million Euros

* focuses
  - elearning
  - d-grid
  - knowledge networking

TextGrid - a community grid for the humanities

combined metadata, annotations, etc. on German documents

Workflow

[diagram]

Planning - Digitisation - Annotation - Publication

demo of Anjo Anjewierden's work

TextGrid goal is to build

* an open adaptable extensible infrastructure

4 layers of TextGrid

* tools
* services
* middleware
* Resources (texts)

Tools

both a grid-connected portal, and a portable rich client

Text Archives

Services

* standard-based, modular, open
* Web Services: registration, workflow, exposure

Middleware

* Data grid
* Service grid
* Information Services
* AAI - GridShib

His question:
* where can we find common components?

Q: Can we see the rich client?
A: Not yet, we plan to build it on Eclipse

ECDL 2006 - DLSci06 - Provenance Explorer

Kwok Cheung and Jane Hunter
Provenance Explorer - A Tool for Viewing Provenance Trails and Constructing Scientific Publication Packages

* Modelling scientific discovery process
* Tools for constructing and publishing scientific models

Scientific Publishing - increasing demands to
* publish raw and derivative data
* document precise provencance
* share data models
* enble duplication and validation
* protect IP
* facilitate training / learning objects

Huge number of elements you should capture to enable reproduction of experiments

Huge Knowledge Management Challenges
* very large data set
* distributed data sets
* etc.

Need to capture the the provenance

* may display/share various levels of detail
* selective archiving

Lineage data/metadata

* workflow is prospective
* provenance is retrospective

Capture the Semantic Descriptions of components

FUSION project

http://metadata.net/sunago/fusion.htm

ontologies: ABC, MPEG-7, FUSION, OME

Image labelling

* Rules-by-example
  - then you can automatically generate semantics

Based on built-up semantics, you can generate automatic displays.

Hypothesis testing interface

Also, can specify new areas of interest e.g. by identifying sparse areas in the 3D display of results.
This can automatically generate parameters for new experiments.

Extended Harmony ABC model for experiments.

http://jodi.ecs.soton.ac.uk/Articles/v02/i02/Lagoze/

Result - extended ABC

Then: Modelling eScience Provenance

[various screenshots of the application]

Architecture

* JGraph
* Algernon inference engine
* Protege OWL
* Jena semantic web framework

Working on

* Scientific Model/Publication construction tools
* Search, Browse and Retrieval

[diagram of architecture]

Preservation of Composite Objects
* Use RDF/XML to package metadata
* Maintain preservation for both
  - composite objects
  - atomic objects

PANIC Architecture

PANIC (Preservation webservices Architecture for Newmedia and Interactive Collections)

http://metadata.net/panic/

AONS

* Automated Obsolescence Notification Service

* Collaboration between
  - UQ
  - NLA
  - ANU?

ECDL 2006 - DLSci06 - eSciDoc

eSciDoc - a Scholarly Information and Communication Platform in the Age of eScience
Matthias Razum

This was a very good presentation.  I particularly appreciated the silo diagram.

http://www.escidoc-project.de/homepage.html

Scholarly Communication - Rip, Mix, Burn

* Scholarship inherently recursive
* Therefore scholars are both information consumers and information producers at the same time
* Referencing or reusing material of all times enables scholars o weave a knowledge network of related information objects
* Good scientific practice requires provenance data for objects and versioning

Example: Knowledge Network around cuneiform tablet

* Metadata
* Transcription - Metadata
  - Translation - Metadata
  - Annotation

[wonderful silo diagram]

What should an institutional repository be?

* institutional memory
* allow for reuse - allow for associating information objects in novel contexts
* support interdisciplinary work
* open, application-independent and flexible,
  thus laying the ground today for repurposing the information in future applications

Turning Static Objects into Living Knowledge

* e-Scholarship ( = e-science = e-research ) allows to publish all intermeidate results of knowledge
  generation from first ideas, theories, discussions with peers to final results
* need to support users early in their work process, so they can share immediately with peers
* leads to interactive authoring environments with support for collaboration and annotations
* objects lose their static nature and become 'active nodes' in a network of knowledge

Q (Rachel): How to connect from a wiki to an institutional repository?
A: Maybe it is possible.  There was a project - NSDL - wiki based on Fedora.

eSciDoc
* 6 million euro five-year grant (2004-2009)
* aim to build an integrated information, communication and publishing platform for web-based
  scientific work
* NOT a research project, aims at stablishing an innovative production system

[diagram]

* Repository at the core
* layer of services
* layer of security
* build apps on top of these
  - publication management
  - scholarly workbench
  - eLib
  - eLab Journal

  helper apps: user management

ideally, the scientists should be able to build apps on this platform

Publication Management

* Workflows
  - very complex - every institution different
* Metadata
  - everyone has their own idea what the correct scheme is

Scholarly Workbench

* collaboration, for humanities

eLib

* dark archive of all commercially-licensed content
(postponed)

eLabJournal

(postponed)

Services
* Object Manager
* Content Type Modeler
* Metadata Modeler
* Formats Manager
* Workflow Manager
* Data Interopability
* Search & Browse
* License Management
* Personalization
* Basket Manager

Q (me): To what extent does it depend on Fedora?
A: In theory the services deal with the repository as an abstract layer, but in practice currently
   you must have Fedora

Framework Services

* The framework is an enabling technology
  - scholars can focus on domain-specific application logic
  - enable scholars to focus on their "business logic" / "scholarly logic"

Content Model

Q (Rachel): Are you using RDF containers?
A: Conceptually we are using METS containers.
Comment (Jane): Fedora uses RDF internally.

* some generic object patterns

* ability to attach licenses to content items

* ability to manage content item versions

ECDL 2006 - DLSci06 - UQueensland eResearch projects

Jane Hunter
Next Generation Digital Library Services for eScience - Delivering on the Hype
U Queensland

http://www.itee.uq.edu.au/~jane/
http://www.itee.uq.edu.au/~eresearch/

Big List of eScience Middleware

DART project

http://www.itee.uq.edu.au/~eresearch/projects/dart/

[list of work packages]

* Secure annotation e.g. with Shibboleth?
* Integration of Fedora and Storage Research Broker (SRB)

* Improving search interfaces

Case Studies

* microscopists
* protein crystallographers
* environmental/ecosystem scientists
* VIRGIL project

GRANI project for Nanostructural Analysis Network Organization

http://www.itee.uq.edu.au/~eresearch/projects/grani/

Challenges

[huge list]

eScience Workflow

http://kepler-project.org/

Kepler
BPEL4WS

Modelling eScience Provenance

Tools for scientific provenance, with different levels of views.

Scientific Model Package - everything wrapped up into data + publication ***

Stuff about teleobservation of experiments

DART - Annotation of Crystallographic Structures

You could almost automate the creation of a paper about a new structure - by integration with data.

[demo of advanced annotation of 3D crystallographic data structure]

Semantic WildNet

* integrate bird/snake sightings with climate sensor data with topographic data
* SPARQL query interface + Google Earth

Collaborative Tools

* Chat
* Videoconf
  - Access Grid Sessions
* Wikis, Blogs
* Shared Applications

Vannotea

http://www.itee.uq.edu.au/~eresearch/projects/vannotea/

Collaborative Multimedia Annotation
3D Object Annotation

Secure Annotation e.g. on eprints server

The annotation server is a sidebar for a browser

Q (me): What about preservation
A: We have a project that is addressing that

PANIC (Preservation webservices Architecture for Newmedia and Interactive Collections)

http://metadata.net/panic/

Q: Will this content be reusable?  The tools are very domain-specific.
A: Very aware of this issue.  Have already demonstrated reuse of content.  Developing core services.

Q: What are some shared pieces of infrastructure?

A: Workflow
Realtime Shared App
Data integration
E-lab notebooks

ECDL 2006 - DLSci06 - eScience Knowledge-based vision

Claudia Niederee, Thomas Risse
e-Science: A knowledge based vision

http://www.ipsi.fraunhofer.de/

e-Science in Transition

* a broader look now beyond just grid and storage

Digitial Libraries

* have meanwhile reached a certain maturity

Possibly synergies

* E-science funcitonality as a natural extension of the scientific digital library
* learn from DL experiences and best practices
* reduce the risk of "re-inventing the wheel"

Comments: Grid not a good match for libraries - collaboration is key, where we can participate.

Goal: scientific working place of the future that enables focusing on creative tasks -   
      knowledge-based e-Science infrastructure

Future Directions:
* From digital content to innovation resources (Resources)
* From document classification to domain and market understanding (Context)
* From collaboration tools to virtual teams (Collaboration)
* From digital libraries to virtual research environments (Interaction)
  - also intelligent services that take over routine tasks from the research
* From provision of documents to active support of creativity (Creativity)
  - extremely difficult to support with info. technology
* From information provision to support of the innovation process (Process)

Have to have lots of flexibility to support creativity.

Example: Systematic Re-use of Innovation Resources

Innovation Resources
* Tools and Services
* Expertise
* Scientific data
* Scientific documents
* Methods

Challenges
* Encourage the re-use of resources
* Discover adequate resources within the current working context
* Consideration of existing rights of use
* Automate the description of resources where possible

Rachel - citations and linking to data

* Establishment of an annotation pipeline for the (semi) automatic enrichment of resources
  (scientific data and services)

From data to enriched data (by describing the data with the programs, methods and parameters used to create it).

Needed: Pipeline for (semi) automatic enrichment - domain specific
        Ontologies and models for the description
        Extended editors for data integration

e-Science Architecture Blueprint

[diagram]

FRESCO = Fraunhofer e-Science Cockpit

http://www.ipsi.fraunhofer.de/i-info/en/content/view/97/0/

Fraunhofer is very large, distributed organization - 58 institutes, 12400 employees

Fraunhofer e-Science Vision

* Support of the scientific innovation process for applied research by providing
[long list of things]

* Seamless and traceable integration of scientific data into the publication process

* Development of the Fraunhofer e-Science Infrastructure

Idea of e-Science Cockpit: Navigation within the innovation space

Infrastructure
* Integration basis for tech with content
* Provide base services and standardized interfaces
* Scalable and extensible

Did a big study with a questionnaire, as part of strongly user-oriented technology design

Found a high readiness for sharing data

Approach:
- Adequate technology launch
  - Stepwise integration into the working process

ECDL 2006 - Digital Library eScience programme

The preliminary programme for the Digital Library eScience workshop is available,
which is good, since it is about to start in a few minutes.

I will be blogging the presentations as much as possible.
Category DLSci06.

Program (Preliminary)

    09:00 - 10:30

• Claudia Niederee, Thomas Risse
  e-Science: A knowledge based vision
• Jane Hunter
  Next Generation Digital Library Services for eScience - Delivering on the Hype

10:30 - 11:00

• Coffee break

11:00 - 13:00

• Matthias Razum
  eSciDoc - A Scholarly Information and Communication Platform in the Age of eScience
• Kwok Cheung and Jane Hunter
  Provenance Explorer - A Tool for Viewing Provenance Trails and Constructing Scientific Publication Packages
• Andreas Aschenbrenner, Peter Gietz, Marc Wilhelm Küster, Christoph Ludwig and Heike Neuroth
  TextGrid - a modular platform for collaborative textual editing

13:00 - 14:30

• Lunch break

14:30 - 16:30

• Leonardo Candela, Donatella Castelli, Christoph Langguth, Pasquale Pagano, Heiko Schuldt, Manuele Simi and Laura Voicu
  On-Demand Service Deployment and Process Support in e-Science DLs: the DILIGENT Experience
• Bhaskar Mehta and Peter Fankhauser
  To Grid or not to Grid: Digital libraries based on Grid infrastructure
• Rachel Heery
  Concluding Summary
• Discussions

upcoming Digital Library e-Science Workshop

UPDATE 2006-09-22: I attended this workshop and blogged it under category DLSci06.  ENDUPDATE

Workshop: Digital Library Goes e-Science
Thursday, Sep. 21, 2006

This workshop aims to discuss an e-Science service portfolio for the scientific communities (which really provides "enhanced science" support), the role of digital library functionality and digital library research in building such a next generation e-Science infrastructure, and the challenges for digital library and e-Science research that evolve from this perspective.

Workshop to be held in conjunction with ECDL 2006
September, 17-22, 2006. Alicante, Spain