Defining Image Access
Defining Image Access: Requirements for interoperable discovery and delivery of image data stored in DSpace, EPrints and Fedora-based institutional repositories using a data web approach.
- October 2007
- The JISC has announced funding for a new project to construct a demonstrator data web, entitled FlyWeb: A Data Web between Repositories and other Data Sources, linking Drosophila Research Image Data with Publications. A link to the new wiki page for this FlyWeb Project, is FlyWeb_project.
The JISC Defining Image Access Project was a short requirements analysis project (January - July 2007), undertaken by Graham Klyne (Project Manager), Jun Zhao and David Shotton (PI) of the Image Bioinformatics Research Group of the University of Oxford, to investigate what is required to develop and provide discovery and delivery interoperability for research image data held in DSpace, EPrints and Fedora-based institutional repositories, the three main open-source software systems used within the UK HE/FE sector, using a data web approach.
The scope of this project was explicitly limited to images stored in the DSpace, EPrints and Fedora-based institutional repository systems at Cambridge, Imperial College London, Oxford and Southampton Universities. We focused on available image collections within these repositories, with the intent of identifying common metadata themes, and of articulate initial software designs for accessing and using that metadata to create a data web, with a view that these designs might later be enlarged to take account of wider requirements in future projects. This limited and focused approach was inspired by agile software development methodologies, that involve tackling a large problem area as a series of smaller, testable steps, each of which delivers some identifiable benefit. For this Defining Image Access Project, we were targeting the identification of similar or related concepts across uncoordinated repositories, that could provide a basis for meaningful cross-referencing of content.
The FINAL REPORT of the Defining Image Access Project, detailing our findings, conclusions, design concepts and recommendations for future developments, is to be found here. (The main report is here (pdf; 339 Kb), and the executive summary section is available separately here (pdf; 36.5 Kb).
Other related activities of the Image Bioinformatics Research Group are exploring access to images made available by journal publishers (see BioImageWeb Consortium), acquisition of laboratory image data with metadata appropriate for data web publication (see FlyData project), and development of more specific applications using image data web facilities to serve specific research user requirements.
Funded from the Discovery to Delivery strand of the JISC Repositories and Preservation Programme.
See also the JISC web page for this project: http://www.jisc.ac.uk/whatwedo/programmes/programme_rep_pres/defining_image_access.aspx
Planning and project resources
- DefiningImageAccess/ProjectPlan - project plan
- DefiningImageAccess/TechnicalPlan - key points of technical approach
- http://imageweb.zoo.ox.ac.uk/drupal/node/17 - project resources, files, presentations, blogs, etc.
- DefiningImageAccess/RepositorySurvey - notes for repository survey work
- DefiningImageAccess/PostProjectReview - notes for post-project review
- http://bioimage.ontonet.org/moin/IbrgPlanning - notes for future IBRG activity planning
Key dates as of June 2007
- JISC Digital Repositories Conference - Dealing with the Digital Deluge: 5/6 June
- Visit to Imperial: Friday 15th June
- Defining Image Access Project final meeting, Wolfson College Oxford: Friday 22nd June
- Project end date: 30th June 2007
- Completion Report submission: 30th June 2007
- Draft Final Report submission: 30th June 2007
- Final Report submission: 31st July 2007
Project meeting planning pages
- 5th January 2007, Project Kick-off Meeting. ( Event planning details.) Notes from the meeting are here.
- 9th February 2007, Workshop on Tools and Technologies for Semantic Interoperability Across Scholarly Repositories. (Event planning details.) Notes from the meeting are here.
- 9th March 2007, Project meeting to consider interaction of data webs with Intute Repository Search and other JISC initiatives. (Event planning details.) Notes from the meeting are here.
- 22nd June 2007, Final project meeting, presenting our findings and soliciting feedback. (Event planning details.) Notes from the meeting posted here.
- DefiningImageAccess/Progress/20070126 - 26 Jan 2007
- DefiningImageAccess/Progress/20070222 - 22 Feb 2007
- DefiningImageAccess/Progress/20070315 - 15 Mar 2007
- DefiningImageAccess/Progress/20070404 - 4 Apr 2007
- DefiningImageAccess/Progress/20070427 - 27 Apr 2007
- DefiningImageAccess/Progress/20070511 - 11 May 2007
- DefiningImageAccess/Progress/20070607 - 7 June 2007
- DefiningImageAccess/Progress/20070716 - 16 July 2007
- DefiningImageAccess/Progress/20070801 - 1 August 2007
- DefiningImageAccess/Progress/Next - Notes for next progress review meeting
A one-page progress report sent to Balviar Notay on 17 April 2007 for presentation to the JISC Integrated Information Environment (JIEE) Committee is to be found here
- Diagram of data webs for the project wiki (see: software overview diagram, needs including in wiki). See also presentation linked from http://imageweb.zoo.ox.ac.uk/drupal/node/31.
- add a definition of an image to the wiki pages; clarify that we deal with image as (mostly) opaque entities, and depend on available information/metadata.
- Jun is undertaking a more detailed trial of image annotations in ePrints; when this is done, we should jointly review the wiki and tidy its content.
- http://imageweb.zoo.ox.ac.uk/pub/2007/DefiningImageAccess/FinalReport/ - Final report
- http://imageweb.zoo.ox.ac.uk/drupal/files/DIA_FinalReport_2007-08-17.pdf - final report as submitted to JISC
- http://imageweb.zoo.ox.ac.uk/drupal/files/DIA_FR_Executive%20Summary_2007-08-17.pdf - executive summary of final report
- DefiningImageAccess/Report - outline and early material for final report
- DefiningImageAccess/Presentation - outline and material for project presentation
- Defining Image Access - project web site (this page)
- Meetings/20060915/DefiningImageAccess-Planning - Early thoughts with Dan Brickley for shaping the project.
Kickoff meeting and other project plenary meetings:
- 5th January 2007, The Defining Image Access kickoff meeting
- The minutes can also be found in Minutes of the Project Kickoff Meeting on January 5th, 2007 (Word file).
- 9th February 2007, Workshop on Tools and Technologies for Semantic Interoperability Across Scholarly Repositories.
- 9th March 2007, Project meeting to consider interaction of data webs with Intute Repository Search and other JISC initiatives.
- 22nd June 2007, Final project meeting, presenting our findings and soliciting feedback.
- Meetings/20070122/Dspace@Cambridge - meeting with Patricia Killiard and Tom De Mulder at Cambridge University Library, to discuss Dspace@Cambridge repository.
- Meetings/20070416/DefiningImageAccess-ECS-Southampton - various meetings at ECS, Southampton University.
- Meetings/20070503/DefiningImageAccess-SERS-Oxford - meeting with OULS/SERS to discuss Oxford repository projects.
- Meetings/20070615/DefiningImageAccess-ImperialCollege - meeting to discuss Imperial College repository related projects.
Other related meetings
- Meetings/20070115/CEH-Explorations - exploratory meeting with Dawn Field and Bela Tiwari at NERC / CEH, Oxford.
- Meetings/20070220/NEBC-Workshop - workshop held at CEH in Oxford about bionformatics software tools, especially related to microarray experiments
- Meetings/20070124/SurveySchemas - meeting with Jun Zhao to discusss schemas for survey data.
- Meetings/20070131/SemanticPortals_etc - meeting with Nikki Rogers and Damian Steer at ILRT.
- Meetings/20070131/DefiningImageAccess-TASI - meeting with Carla Youngs, Grant Young and Damian Steer concerning TASI.
- JISC Repository Programme "Digital Deluge" meeting, Manchester:
- Meetings/20060618-TonyHey-eScience-Oxford - Tony Hey talks at Oxford on e-Science and scholarly communication. I was struck that so much of what he said is reflected in our current and envisaged work.
- See also: Miscellaneous for related projects and meeting information.
- The Digital Image, 16th March 2007: a multidisciplinary symposium that explores the role of images in various fields of research. (http://www.oerc.ox.ac.uk/oerc/events/digital-image.xml). Notes from the meeting are here.
- Data Webs: New Visions for Research Data on the Web Presentations from the June 2006 Research Information Network Workshop of this title, providing background to the project.
- Defining Image Access project kick-off meeting - David Shotton, introductory presentation (PowerPoint).
- University of Southampton Repositories - Diversity and media types 5 Jan 2007 - Jessie Hey, presentation at the project kick-off meeting (PowerPoint).
- Ontologies, Images and Databases - a presentation by David Shotton (PDF).
- Slide 5, "How to describe and classify things" is taken from The Celestial Emporium of Benevolent Knowledge by Jorge Luis Borges, which was introduced to us by Alan Rector.
- Image semantics and image sharing - lecture by David Shotton, given at The Digital Image Symposium (PDF).
- Data webs for locating research images stored in heterogeneous distributed repositories - presentation by David Shotton, Southampton seminar, 16th April 2007 (Powerpoint).
Reviews of related work
- DefiningImageAccess/RelatedWork - project review of the related work
- DefiningImageAccess/Resources - other related resources
- DefiningImageAccess/Articles - related articles and commentary
- DefiningImageAccess/SoftwareEvaluation - notes for software evaluation
- DefiningImageAccess/ReviewSchema - the schema used to annotate or classify the related work survey
Reviews of partner image repositories
- DefiningImageAccess/RepositorySurvey - notes for repository survey work
- DefiningImageAccess/OtherRepositories - general information about repositories outside our project
- DefiningImageAccess/ScenarioNotes - notes for scenarios for image repository use
- DefiningImageAccess/RecommendationNotes - notes for recommendations relating to image repositories
- DefiningImageAccess/Components - outline of data web software structure and components
- DefiningImageAccess/SoftwareDesign - notes about the design of data web software components
- The following Data Web System Diagram is by Graham Klyne, 16-02-2007
- Data web components - updated diagram, 16-Apr-2007.
- Event information data web - alternative formulation of data web diagram, 02-May-2007.
- DefiningImageAccess/OAIMore - describes the brainstorming of enabling OAI-PMH to expose metadata beyond the mandatory Dublin Core metadata
- http://lists.w3.org/Archives/Public/semantic-web/2007Jun/0185.html - a message from Dan Brickley that references some Schematron work in conjunction with SPARQL, maybe useful for metadata validation?
- DefiningImageAccess/Glossary - list of terms and acronyms used with special meaning in topic areas related to this project
- DefiningImageAccess/TaggingExperiments - some experiments with tagging
- DefiningImageAccess/TagCloud -- experiments with creating tag clouds
- DefiningImageAccess/mSpace -- experiments with mSpace and 3Store
Image Bioinformatics Research Group pages
- Data Webs pages from the Image Bioinformatics Research Group wiki: our goal is to migrate relevant information from these pages to the ImageWeb wiki; until then, these links may serve:
- http://bioimage.ontonet.org/moin/DataWebs - general notes and links relating to our data webs ideas
- http://bioimage.ontonet.org/moin/DataWebsPlanning - rough planning notes for a range of activities related to data webs
- http://bioimage.ontonet.org/moin/DefiningImageAccessPlanning - early planning notes for the Defining Image Access project; these should now be subsumed by the project plan (DefiningImageAccess/ProjectPlan)
- http://bioimage.ontonet.org/moin/DatawebsMeetings - notes from early data webs meetings
- http://bioimage.ontonet.org/moin/DatawebsRecruitment - draft advert for staff recruitment for Defining Image Access, FlyData and beyond.
- http://imageweb.zoo.ox.ac.uk/drupal/node/21 - administrative resources are attached to this page
- Expenses Claim Form for Defining Image Access Project Kick-Off Meeting - claim form in Excel format
- Expenses Claim Form for Defining Image Access Project February Workshop - claim form in Excel format
- Events/yyyymmdd/DefiningImageAccess-Template - (Skeleton page for project meeting event entry - currently for cut-and-paste; later use MW templating capabilities?)
- DefiningImageAccess-WikiSnips - snips of wiki source code for creating repeated constructs
- DefiningImageAccess-Templates - list of interesting or useful templates in this wiki
- http://imageweb.zoo.ox.ac.uk/ - front page for ImageWeb server
Partners and Contacts:
How to upload files for shared access
Semantic Media Wiki
Special pages to be consulted for semantic annotation
Useful help pages
- http://ontoworld.org/wiki/Help:Inline_queries - Semantic Media Wiki inline queries
- http://www.mediawiki.org/wiki/Manual:Navigation_bar - Media Wiki navigation Bar manual
- http://www.mediawiki.org/wiki/Extension:Pdf_Export - PDF export facility
- http://wikipdf.sourceforge.net/, http://sourceforge.net/projects/wikipdf/ - Another wiki to PDF option
-- GrahamKlyne 17:25, 29 November 2006 (UTC)