Main Page

From ImageWeb

This web site contains information about the activities and projects of the Image Bioinformatics Research Group, accessible from the menu in the left margin.

News

December 2009: The JISC has funded a small rapid innovation project entitled MILARQ - Multiple Indexes Across LARQ, the object of which is to improve the performance of data webs accessing RDF triplestores using SPARQL queries, by providing indexing of their content, thereby mimicking some of the benefits of a relational database. MILARQ will run from April 2010, and will be undertaken in partnership with the company Epimorphics, which has prime responsibility for the codebase of the Jena platform and the JenaTDB triple store that we are using in the CLAROS Project.

November 2009: A paper describing the OpenFlyData data web services for integrating Drosophila gene expression images and other genomic data (http://www.openflydata.org) has recently been submitted to J. Biomedical Informatics. A preprint of this paper and its supplementary files are available from http://imageweb.zoo.ox.ac.uk/pub/2010/Publications/.

October 2009: The JISC has funded a major project entitled ADMIRAL - A Data Management Infrastructure for Research across the Life Sciences. ADMIRAL will run from October 2009 to March 2011 inclusive, and is being undertaken in collaboration with the Oxford University Library Service that runs the Oxford DataBank, with the British Library, and with Science Commons. A link to the project page is given on the left.

July 2008: Engagement in semantic publishing activities - see The SPIDER Project (Semantic Publishing for Infectious Disease Epidemiology Research) and Meetings/20080627/SpiderMeeting

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.

Projects and activities

The ADMIRAL Project - A Data Management Infrastructure for Research Across the Life Sciences
CLAROS project - CLassical Art Research Online Services
Spider Project - Semantic publishing
Datastage file annotation
Identifier/vocabulary pages

Previous projects

Shuffl project - Supporting curation of small-scale research data for web publication
FlyWeb - A Data Web for Linking Laboratory Image Data with Public Databases and Publication Repositories. A proof-of-concept data web to integrate research image data from the FlyTED database with related data from the Berkeley Drosophila Genome Project, FlyBase, FlyAtlas and other sources. This project builds on the findings of the data web requirements analysis project Defining Image Access.
BioImageWeb Consortium - notes about BioImageWeb Consortium goals, meetings and other activities.
Research Information Network (RIN) meetings - information and notes from meetings hosted by RIN.
- http://www.rin.ac.uk/data-webs - Data webs: new visions for research data on the Web
- http://www.rin.ac.uk/digital-data-workshop - Getting the most out of data, Making the most of research
The ImageStore Project - a series of case studies into requirements, feasibility and cost for long-term digital preservation of images and video - part of the DCC SCARP project.
Collaborative Ontology Normalization - notes of an experiment in collaborative normalization of the Cell Type Ontology.
Defining Image Access - defining requirements and exploring techniques for accessing images in institutional repositories.
- Project resources - presentations, plans, administrative files, etc.
FlyData project - acquisition and local web publication of research images and metadata to provide decision support to the immediate research project, and to facilitate republication of research data and results for use by data webs.
- Fly-TED web site: http://www.fly-ted.org/
Fly-TED project - web publication of Drosophila testis gene expression images and associated metadata, using EPrints software.

About Image Web: Creating a web of research image data

An Image Data Web is a new concept for publication of and access to research image data, using Web2.0 and Semantic Web tools to combine centrally and privately published research data, creating a resource that can support new lines of research not necessarily envisaged when the original data was created, including in silico research activities that discover new knowledge through analysis of available published data. David Shotton's introduction and presentation to the original Research Information network (RIN) meeting about Data Webs give more background.

We have been pursuing this vision through the following interlinked activities:

The JISC-funded Defining Image Access Project, a requirements gathering exercise based on existing institutional repositories
The BioImageWeb Consortium, an informal grouping of academic researchers and publishers, exploring possibilities to enhance the value of journal publications by linking them with web publication of research image data
The ImageStore Project, a series of case studies into requirements, feasibility and cost for long-term digital preservation of images and video, funded by the Digital Curation Centre.
The FlyData Project, which aims to create a web-based laboratory data management system for gathering research images and related metadata, providing decision support directly to the research project, and facilitating the publication of research results and images as part of an image data web.
The FlyWeb Project, a JISC-funded project to create the OpenFlyData data web.
The CLAROS Project, which is taking these same ideas and applying them to the integration of classical art data.

Related work and resources

Resources/WebData - Web-accessible data resources.
Resources/ExternalWebSharing - External web facilities for collecting, organizing and sharing information

ImageWeb Drupal server - blogs and other ImageWeb related information
Image Bioinformatics Research Group wiki - Some material should be migrated to this wiki web site.

Events

IBRG internal activities

JournalClub

CitationNetworkVisualization

Technical notes

Javascript Development Tools

Links and references

Light-weight Semantic Web technologies

Architectural Styles and the Design of Network-based Software Architectures, Roy Fielding, PhD Thesis, http://www.ics.uci.edu/~fielding/pubs/dissertation/top.htm. (Chapter 5 describes REST.)

Collaborative knowledge gardening, Jon Udell, http://www.infoworld.com/article/04/08/20/34OPstrategic_1.html. An old but interesting piece on tagging compared with taxonomy.

Folksonomies - Cooperative Classification and Communication Through Shared Metadata, Adam Mathes, http://www.adammathes.com/academic/computer-mediated-communication/folksonomies.html.

A Semantic Portal for the International Affairs Sector, J. Contreras, V. R. Benjamins, M. Blázquez, S. Losada, R. Salla, J. Sevilla, D. Navarro, J. Casillas, A. Mompó, D. Patón, O. Corcho, P. Tena, I. Martos, http://www.cs.man.ac.uk/~ocorcho/documents/EKAW2004_ContrerasEtAl.pdf

Image Annotations

Standards for image annotation using Semantic Web, Latifur Khana, Department of Computer Science, University of Texas at Dallas, http://dx.doi.org/10.1016/j.csi.2006.03.006

Related work in Oxford

The Digital Image - symposium organized by David Shotton
- Meetings/20070316/TheDigitalImage
- http://www.oerc.ox.ac.uk/oerc/events/digital-image.xml
Animal behaviour - flight research and related
- http://users.ox.ac.uk/~zool0206/flow.html
- http://users.ox.ac.uk/~zool0261/
- http://users.ox.ac.uk/~zool0261/flightdynamics.htm
- http://users.ox.ac.uk/~abrg/OBI/ (Oxford Bionics Initiative)

This Media Wiki

Consult the User's Guide for information on using the wiki software.

NOTE: as of May 2011, the hosting environment has changed, due to corruption of the previous system disk. The new environment is based on Ubuntu 10.04, with mySql and MediaWiki installed from the Ubuntu repositories, with wiki and other data restored from HFS backups.

Database dump and backup scripts have been copied and adapted from the previous system.

Getting started

Configuration settings list
- The configuration file is /var/www/html/wiki/LocalSettings.php, with a backup copy at /var/www/html/wiki/config/.
MediaWiki FAQ
- See also http://www.mediawiki.org/wiki/Preventing_Access#1.5_upwards about account creation restrictions.
- See also http://www.mediawiki.org/wiki/Extension:ConfirmAccount about installing an account confirmation extension (the files have been downloaded to /var/www/html/wiki/extensions).
MediaWiki release mailing list.
See also the tips from the Defining Image Access wiki.

Administration links

Special:Userlogin - access to page to create new account
Special:Userrights - user rights management
Special:SMWAdmin - Semantic Media Wiki admin

Accessing the wiki MySql database

log in as root
Start the mysql client with the appropriate credentials (entering the password when prompted):

 /usr/bin/mysql -u root -p

Issue the following command:

 USE wikidb;

(See also: http://bioimage.ontonet.org/moin/ZakynthosSetup, section 3.3.1)

Resetting a MediaWiki user password

From http://people.planetpostgresql.org/greg/index.php?/archives/74-Reset-a-user-password-on-MediaWiki.html:

If you need to change/reset a user password on MediaWiki, this is how you do it for MySQL:

UPDATE user SET user_password =
  md5(CONCAT('123-',md5('newpassword'))) WHERE user_id=123;

If you are using Postgres to power your MediaWiki system, reset the password like this:

UPDATE mwuser SET user_password =
  md5('123-' || md5('newpassword')) WHERE user_id=123;

Bonus tip: to update the Navigation box on the left-hand of the screen, edit the page on your wiki called MediaWiki:Sidebar. This is probably the most asked question for people who successfully install MediaWiki.