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D8.2 Launch of the GEN2PHEN Knowledge Centre
Posted Wed, 19/08/2009 - 12:13 by
Acacia Reiche
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HEALTH-F4-2007-200754
www.gen2phen.org
D8.2 Launch of the GEN2PHEN Knowledge Centre
WP8 – GEN2PHEN Knowledge Centre
V3.0 Final
Lead beneficiary: ULEIC Date: 11/08/2009 Nature: Report Dissemination level: PU
(Public)
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 2 of 17
TABLE OF CONTENTS DOCUMENT INFORMATION .................................................................................................. 3 DOCUMENT HISTORY ............................................................................................................. 3 DEFINITIONS .............................................................................................................................. 4 1. INTRODUCTION.................................................................................................................. 5 2. OVERVIEW OF FEATURES .............................................................................................. 5 2.1. GENERAL SITE DESIGN ...................................................................................................... 5 2.2. HOME PAGE ....................................................................................................................... 6 2.3. NEWS ................................................................................................................................. 8 2.4. EVENTS ............................................................................................................................ 11 2.5. COMMUNITY .................................................................................................................... 12 2.5.1. Blogs ........................................................................................................................ 12 2.5.2. Interest Groups ........................................................................................................ 12 2.6. ABOUT GEN2PHEN........................................................................................................ 14 2.7. PARTNERS’ ZONE ............................................................................................................. 14 2.8. SECURED ACCESS TO CONTENT ........................................................................................ 16 3. INITIAL UPTAKE AND USAGE...................................................................................... 17 4. SUMMARY .......................................................................................................................... 17
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 3 of 17
Document Information
Grant Agreement HEALTH-F4-2007-200754 Number Full title Project URL Acronym GEN2PHEN
Genotype-To-Phenotype Databases: A Holistic Solution http://www.gen2phen.org
EU Project officer Frederick Marcus (Frederick.Marcus@ec.europa.eu) Deliverable Work package Delivery date Status Nature Dissemination Level Report Public Number 8.2 Number 8 Contractual Title Title Month 18 Launch of GEN2PHEN Knowledge Centre GEN2PHEN Knowledge Centre Actual final Other August 2009
Version 1.0 Prototype Confidential
Authors (Partner) Adam J. Webb (ULEIC) Responsible Author Adam J. Webb Partner (ULEIC) Email ajw51@leicester.ac.uk Phone +44 (0)116 229 7273
Document History
Name Date Version Description
A. Webb A. Reiche, D. van Gent A. Webb
06/08/09 10/08/09 11/08/09
1.0 2.0 3.0
Initial draft Review Second draft
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 4 of 17
Definitions
Partners of the GEN2PHEN Consortium are referred to herein according to the following codes: ULEIC – University of Leicester (UK) – Coordinator EMBL – European Molecular Biology Laboratory (Germany) – Beneficiary FIMIM – Fundació IMIM (Spain) – Beneficiary LUMC – Leiden University Medical Center (Netherlands) – Beneficiary INSERM – Institut National de la Santé et de la Recherche Médicale (France) – Beneficiary KI – Karolinska Institutet (Sweden) – Beneficiary FORTH – Foundation for Research and Tecnology Hellas (Greece) – Beneficiary CEA – Comissariat à l’Energie Atomique (France) – Beneficiary EMC – Erasmus Universitair Medisch Centrum Rotterdam (Netherlands) – Beneficiary UH.FGC – Helsingin Yliopisto (Finland) – Beneficiary UAVR – Universidade de Aveiro (Portugal) – Beneficiary UWC – University of the Western Cape (South Africa) – Beneficiary CSIR – Council of Scientific and Industrial Research (India) – Beneficiary SIB – Swiss Institute of Bioinformatics (Switzerland) – Beneficiary UNIMAN – The University of Manchester (UK) – Beneficiary BIOBASE – BioBase GmbH. (Germany) – Beneficiary deCODE – Islensk Erfoagreining EH (Iceland) – Beneficiary PHENO – Phenosystems S.A. (Belgium) – Beneficiary BCP – Biocomputing Platforms Ltd. Oy (Finland) – Beneficiary
Grant Agreement: The agreement signed between the beneficiaries and the European Commission for the undertaking of the GEN2PHEN project (HEALTH-200754). Project: The sum of all activities carried out in the framework of the Grant Agreement by the Consortium. Work plan: Schedule of tasks, deliverables, efforts, dates and responsibilities corresponding to the work to be carried out for the GEN2PHEN project, as specified in Annex I to the Grant Agreement. Consortium: The GEN2PHEN Consortium, conformed by the above-mentioned legal entities. Consortium agreement: The agreement concluded amongst GEN2PHEN participants for the implementation of the Grant Agreement. Such an agreement shall not affect the parties’ obligations to the Community and/or to one another arising from the Grant Agreement.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 5 of 17
1. INTRODUCTION
WP8 is concerned with the gathering and dissemination of knowledge to the genotype-tophenotype (G2P) community. This includes internal and external training activities for the project, and the general supply of GEN2PHEN developments to the public. Towards achieving this goal, we launched the initial version of the GEN2PHEN Knowledge Centre (deliverable 8.2) on May 22nd 2009 (http://www.gen2phen.org). The GEN2PHEN Knowledge Centre aims to be a major G2P internet portal and will help enable knowledge management throughout the GEN2PHEN project. The site also endows the GEN2PHEN project with maximal visibility, and thereby promotes good community interactions. The GEN2PHEN Knowledge Centre will be a ‘virtual centre of excellence’ for G2P field, designed to provide general information on field developments, specific information on the GEN2PHEN project, and full and immediate access to all the project deliverables/outputs that the G2P community might wish to access. This will eventually include search capabilities, both for individual databases and for holistic searching of the G2P database domain. The site also supports community discussions on topics of interest, and carries lists of upcoming G2P meetings.
2. OVERVIEW OF FEATURES
2.1. General Site Design The design of the site aims to expand the appearance and colour scheme of the GEN2PHEN logo to the entire website. This has been accomplished by using the logo’s colours and shapes throughout the site’s design. The Knowledge Centre logo (Figure 1) extends the GEN2PHEN logo, adding an icon representing a central hub for access and data exchange with multiple resources. The icon scales well, and is used as the ‘bookmark’ icon that appears in the address bar and ‘bookmarks/favourites’ list in many internet browsers. The icon aims to establish a strong visual identity for the website as a distinct entity to the project itself, while still retaining a clear relationship to the project’s own logo. The icon appears throughout the site and across the site’s dissemination materials.
Figure 1: GEN2PHEN Knowledge Centre logo
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 6 of 17
2.2. Home Page The home page of the site (Figure 2) allows quick and simple access to the site’s core features and most recently posted content. The top of the page provides a login/registration link (with the option of using an OpenID 1 ). While registration is not necessary to view the majority of content on the Knowledge Centre, it does afford certain benefits. Users must be registered to contribute to the site (this measure reduces unwanted ‘spam’ submissions). In addition, registered users can be alerted to new content, join ‘Interest Groups’ and may be granted access to restricted areas at an administrator’s discretion. Registration itself is unrestricted and available to all members of the public. Logged-in users see a ‘Profile’ link, allowing them to update details such as email address, password, institution, research interests etc. A search box, which is supported by a categorised list of search terms found in the ‘more options’ link, is available to both unregistered and registered users. A row of tabbed dropdown menus provides access to the various sections of the site. A banner provides a welcome message, which can be made to alternate through numerous images promoting various aspects of the site. A list of ‘alerts’ is given a prominent position to inform visitors of recent GEN2PHEN activities, with links either to pages in the Knowledge Centre or to external resources.
OpenID is a universal internet ID system which can be used across many websites. Rather than requiring a user to authenticate themselves using a username/password combination held at the Knowledge Centre, users can choose to be authenticated by their chosen OpenID provider. For example, a user wishes to sign-in using their Google™ account. They select “Sign in with Google™” on the Knowledge Centre, and are passed to Google’s own login page. Once they have logged in here, they are passed back to the Knowledge Centre and automatically signed in (or registered if they are a new user). With this system, the Knowledge Centre does not handle sensitive username/password data, and the user can choose who should handle their internet ID. Furthermore, they can use their same OpenID across many websites.
1
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 7 of 17
Figure 2: Homepage of the GEN2PHEN Knowledge Centre.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 8 of 17
The home page features a large tabbed area designed to highlight the most recent and unread content of the site. Logged in users are initially presented with a list of new unread content, but may switch to lists of all recent content, the most recent news articles, or a listing of events. This provides returning users with a very quick overview of what has changed since their last visit and rapid access to the most recent content. Logged in users will also be presented with a list of links by which they may contribute to the site. The links are dependent on their own particular privileges. Users are encouraged to make regular posts, start or edit wiki pages (pages which can be edited by other users), advertise events, write or link to interesting news articles, or post documents. Documents posted in common formats (such as Microsoft Office, PDFs etc) can be displayed on Knowledge Centre pages directly, saving users the need to download files and install specialist software to view documents. Every page on the site has a ‘Contact Us’ link on the bottom allowing visitors to contact the project. An RSS feed provides automated updates of comments made to uploaded items. Users can subscribe to the RSS feed through clicking on the RSS icon in the right column of the home page. 2.3. News A central feature of the GEN2PHEN Knowledge Centre is the aggregation of news articles and abstracts pertinent to the G2P community. Abstracts and short summaries are gathered from relevant journals and other online resources. These are selected for relevance by an editor and include links to full articles, wherever they may be hosted. Users may read these abstracts and short summaries and leave comments within the Knowledge Centre. Listings of the latest news articles are available from the homepage, and on the main news page. The main news page (Figure 3) highlights a top story, a short list of other featured articles, and a full listing of news articles added to the site. All news articles can be searched for through the site-wide search facility. Each news article page (Figure 4) features links back to the main news page and a listing of most recent news articles added to the main site. Users are encouraged to contribute news articles to the site through prominent links on the main news page and on each news article page. Users may submit full stories or provide links to stories. Stories are published to the Knowledge Centre at an editor’s discretion. The news pages provide a regularly updated service to the G2P community, and provide a regular supply of new content to the Knowledge Centre. Such rapid accumulation of new content is hoped to encourage visitors to return to the site on a regular basis.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 9 of 17
Figure 3: The main news page of the site. A 'top story' and a number of headlines are highlighted.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 10 of 17
Figure 4: An example of a single news item page. Recent articles are listed in the left-hand panel, along with prominent links encouraging users to contribute news items of their own or provide links to existing stories.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 11 of 17
2.4. Events The GEN2PHEN Knowledge Centre provides listings of conferences, courses and other events that may be of interest to the G2P community. A basic event listing is available on the homepage as well as in the ‘Events’ section. Events may also be viewed on an interactive calendar (Figure 5) or a clickable interactive map. Each event has its own page with a brief description, dates and times, and location (a small map is also displayed, with a link to a larger interactive map). Users are encouraged to advertise their own events, with prominent links leading to a simple ‘Add Event’ form. Submitted events are added to the site subject to an editor’s approval.
Figure 5: An example of the GEN2PHEN Calendar. Clicking on an event brings up a short description, with links to longer descriptions.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 12 of 17
2.5. Community The ‘Community’ section of the website groups together contribution links, blogs and ‘Interest Groups’.
2.5.1. Blogs
The Knowledge Centre provides facilities for selected users to maintain regular blogs (web logs, or personal online diaries). Such blog entries can be used to stimulate and provoke debate on relevant issues, or simply to highlight interesting developments to the community. As with many areas of the site, users are encouraged to partake in discussions based on these entries by leaving comments fostering further debate and community interaction.
2.5.2. Interest Groups
In a manner similar to regular internet forums, ‘Interest Groups’ provide areas of the site dedicated to certain fields (for an example, see Figure 6). Unlike regular forums however, users may post documents, regular posts, wiki pages (which may be edited by other group members thus easing the production of collaborative documents), news articles or even events into these groups. Each group may also be maintained a dedicated group administrator, who can manage group posts and memberships. Posts within groups may be restricted to the group, or made available to all users of the site. For members of a group, any new posts made within that group will also be listed on the Knowledge Centre’s home page. This alerts members to new posts made in the groups they are members of.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 13 of 17
Figure 6: An Interest Group. Users may join and post to these specialist groups.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 14 of 17
2.6. About GEN2PHEN The ‘About GEN2PHEN’ section details the GEN2PHEN project across a number of pages, and will become an access point for GEN2PHEN-generated resources. Details on the project are divided into several sections: • General Information • Partners List of partners, with links to institution web pages • Project Summary and Objectives A brief outline of the project’s core aims and objectives • Background and Concept • Future Vision - Current Reality • The GEN2PHEN Strategy Details the core objectives of the project: o To analyse the G2P field and thus determine emerging needs and practices o To develop key standards for the G2P database field o To create generic database components, services and integration infrastructures for the G2P database domain o To create search modalities and data presentation solutions for G2P knowledge o To facilitate the process of populating G2P databases o To build a major G2P internet portal o To deploy GEN2PHEN solutions to the community o To address system durability and long-term financing o To undertake a whole-system utility and validation pilot study 2.7. Partners’ Zone The Partners’ Zone is a special ‘Interest Group’ restricted to GEN2PHEN partners. Items posted here are only available to partners, but may be made publically available if need be. Items are categorised by work package (WP) and resource type (e.g. meeting minutes, deliverable etc.) and may be easily located via a special menu. The partners’ zone also contains lists of completed and pending deliverables listed by work package (along with a work package description, see Figure 7) and as a complete list (all work packages). All resources in the Partners’ Zone may therefore be easily located and all are subject to strict access control. Users who are not GEN2PHEN partners do not see links to the Partners’ Zone, nor to any content posted therein (unless it has been made publically available). Such restrictions also apply to any files posted in the Partners’ Zone.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 15 of 17
Figure 7: The work package pages allow easy access to project documents organised by work package. Completed deliverables, a list of pending deliverables, any other relevant documents and a brief work package description are available here. As with all Interest Groups on the site, many different types of content can be posted to the Partners’ Zone: documents (with an in-browser viewer for convenience) (Figure 8), regular posts, news articles, wiki pages and events. In the case of events (such as General Assembly Meetings), these will also appear on the site’s main event calendar and event listing, but will only be visible to GEN2PHEN partners. GEN2PHEN partners may review successive changes made to a post via the ‘Revisions’ tab. The interactive features available on the Knowledge Centre facilitate consortium review procedures (e.g. comments can be made on project documents). This centralises resources and reduces the need to send multiple emails and files to partners.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 16 of 17
Any new posts made within the Partners’ Zone will be listed on the site’s homepage for GEN2PHEN partners only.
Figure 8: Viewing documents in the GEN2PHEN Knowledge Centre. Documents uploaded here can be previewed within the web browser. This particular document was posted into the partners' zone but has been made available to the general public. 2.8. Secured access to content All posts in are stored in a secure database and can only be accessed via the Knowledge Centre website. Although much of the content is publically available, and is therefore visible to all visitors, some is only accessible to users who have been granted the appropriate permissions. Files uploaded to the Knowledge Centre are stored on a secure server and cannot be accessed without going through the website and are subject to the same access control as other content. Users attempting to access content without appropriate permission are presented with an ‘Access Denied’ message.
© Copyright 2009 GEN2PHEN Consortium
D 8.2 Launch of the GEN2PHEN Knowledge Centre
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Security: PU Version: v3.0 –
Final
Author(s): Adam Webb (ULEIC)
Page 17 of 17
3. Initial uptake and usage
The Knowledge Centre has seen steady growth in users and visits since its low-profile launch late May 2009. The site currently has 102 registered users, of which approximately one third are GEN2PHEN partners. Despite the recent launch, the site records an average of 210 unique visitors per week.
4. Summary
This first version of the GEN2PHEN Knowledge Centre provides an extensive and fully-featured interactive site for the G2P community. Furthermore, through the partners’ zone, the website provides a secure project resource centre with facilities to expose certain components to the public. The considerable groundwork involved in creating this initial version has established a versatile and extensible framework allowing the seamless introduction of additional features envisioned for the Knowledge Centre. These include holistic G2P search facilities, catalogues of G2P resources and the provision of GEN2PHEN generated resources and training tools to the general public.
© Copyright 2009 GEN2PHEN Consortium
This document is © 2009 by acaciareiche - all rights reserved.
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© 2009
GEN2PHEN Project
.
The
GEN2PHEN Knowledge Centre
has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)
under grant agreement number 200754 - the GEN2PHEN project.
