AROBIO'Advanced Reasoning On Biological data

Integrated through Ontologies'

11:00-11:15: Welcome, ICT call review: Martin Kuiper11:15-12:45: General outline of the project: Martin Kuiper

Series of short presentations: state-of-the-art, proposed workVIB: Cell Cycle Ontology – Erick AntezanaDKFZ: Databases and knowledge management – Juergen EilsUGent: Databases and reasoning – Peter DawyndtLUB: Reasoning – Marijke KeetCNIO: Text mining – Carlos RodriguezVIB: Text curation – Steven Vercruysse / Vladimir Mironov

12:45 – 13:15 lunch

Afternoon: Off-site contributions:13:15-13:30: UNIMAN: Carole Goble 13:30-13:45: BIOALMA: Christian Blaschke13:45-14:00: PubGene: Tor-Kristian Jenssen14:00-14:15: NTNU: Finn Drablos/Hans Krokan

Agenda:

Breakout sessions / telecons:14:30 – 15:15 ApexWP3: VIB – DKFZ - NTNU - PubGene: Mironov, Vercruysse, Kuiper, Eils, Drablos, WP4: CNIO – NTNU – PubGene - bioalma: Rodriguez, Drablos, Kuiper, Vercruysse

15:15 – 16:00 ApexWP1: VIB – UNIMAN: Antezana, Mironov, EganaWP2: UNIMAN – CNIO – LUB - bioalma: Goble, Rodriguez, Antezana

14:30 – 16:00 bioitWP5: VIB – UGent – DKFZ: Mironov, Blonde, Dawyndt, Eils WP6: VIB - Ugent – UNIMAN - LUB: Antezana, De Baets, Keet,

16:00 - 17:00: Current status of the proposal, action points, timelines, deadlines, communication

Agenda:

Architecture

Other DBsVisualization/UI

Knowledge-based system

Expert domain knowledgeLiterature curation/mining

ComputationalReasoning

WP 1 2 3 4 5 6

1 VIB X x x x

2 UGENT x x

3 UNIMAN x X x

4 CNIO X

5 DKFZ x X

6 LUB x X

7 NTNU x -x-

8 PUBGENE X x

9 BIOALMA x

Workpackage assignment

Background

Call title: ICT Call 1

• Call identifier: FP7-ICT-2007-1

• Date of publication: 22 December 2006

• Closure date: May 8, 2007, at 17:00, Brussels local time

• Indicative budget: 1019 M€

Target:

Challenge 4: Digital libraries and content

ICT-2007.4.2: Intelligent Content and Semantics CP, NoE, CSA

Here: Small and medium-scale focused research projects – STREPs

• CP 40 M€ of which a minimum of 17 M€ to IP and a minimum of 10 M€ to STREP

• 150 pre-proposals !

STEP

2.2 Small and medium-scale focused research projects (STREPs)PurposeSmall and medium-scale focused research projects (STREPs) are objective-driven research projects, which aim at generating new knowledge, including new technology, or common resources for research in order to improve European competitiveness, or to address major societal needs.They have clearly defined scientific and technological objectives directed at obtaining specific results, which could be applicable in terms of development or improvement of products, processes, services or policy.STREPs target a specific research objective in a sharply focused approach. They have a fixed overall work plan where the principal deliverables are not expected to change during the lifetime of the project.

Partners: at least 3, project duration: 18 – 36 months

STREP

STREP

Objective ICT-2007.4.2 (ICT-2007.4.4): Intelligent Content and Semantics

Objective ICT-2007.4.2 (ICT-2007.4.4): Intelligent Content and Semantics

d) Actions geared towards community building, intended to stimulate cross-disciplinary approaches and a more effective user/supplier dialogue, and other measures, including field validation and standards, aimed at a faster uptake of research results. Usability and technology assessment studies, economic analyses and roadmaps to chart the democratisation of personal and community based multimedia production and management tools.

e) Semantic foundations: probabilistic, temporal and modal modelling and approximate reasoning through objective-driven research moving beyond current formalisms. Theoretical results will be matched by robust and scalable reference implementations. Usability and performance will be tested through large scale ontology mediated Web integration of heterogeneous, evolving and noisy or inconsistent data sources ranging from distributed multimedia repositories to data streams originating from ambient devices and sensors, supporting real time resolution of massive numbers of queries and the induction of scientific hypotheses or other forms of learning.

Objective ICT-2007.4.2 (ICT-2007.4.4): Intelligent Content and Semantics

f) Advanced knowledge management systems for information-bound organisations and communities, capable of extracting actionable meaning from structured and unstructured information and social interaction patterns, and of making it available for activities ranging from information search through conceptual mapping to decision making. Such systems will exploit semantics embedded in multimedia objects, data streams and ICTbased processes, and rely on formal policies to manage user access as well as audit trails in support of dynamic virtual organisations. Research advances will be embedded within end-to-end systems using computer-tractable knowledge in support of dynamic data andapplication integration, automation and interoperation of business processes, automated diagnosis and problem-solving in a variety of domains. Robustness, scalability and flexibility will be tested in real-life settings, together with interworking with legacy systems

Objective ICT-2007.4.2 (ICT-2007.4.4): Intelligent Content and Semantics

Expected impact• These activities will make digital resources that embody creativity and semantics easier and more cost-effective to produce, organize, search, personalise, distribute and (re)use, across the value chain.• Creators will be able to design more participative and communicative forms of content.• Publishers in creative industries, enterprises and professional sectors will increase their productivity with innovative content of greater complexity and ease of repurposing.• Organisations will be able to automate the collection and distribution of digital content and machine-tractable knowledge and share them with partner organisations in trusted collaborative environments.• Scientists will operate more efficiently by automating the link between data analysis, theory and experimental validation.

- main S&T innovation, progress beyond state of the art

-positioning vis-a-vis other recent/ongoing projects and competing approaches

- genesis, previous collaborations, precursor projects

- actual or prospective application space, main players and existing/emerging products, market/social trends

-main concrete/exploitable project outputs, longer term derivatives and by-products

- public outputs and their (proactive!) dissemination

- impact (scientific, technical and/or economic), exploitation channels and prospects

-milestones, self-evaluation and progress/success indicators as a project

- characterisation of successive "demonstrators" (bigger? faster? more colourful?)

-risk analysis and mitigation (technical, managerial, due to obsolence)

-- technology assessment and metrics, in terms of components/subsystems and their performance (in the broad sense of the word)

- use cases/case studies: rationale, technical and non-technical challenges, commonalities/specificities, degree of involvement of user organisations

Attention points:

-field validation (technical, functional, user/organisation related); note that tests/trials must be adequately planned and resourced

- dissemination, including beyond purely scientific circles; strategy and underlying logic, target groups … not just a list of conferences

- awareness programme vis-a-vis relevant industrial, commercial, professional … circles

- participating organisations: what they put in / intend to get out i.e. motivation, role & function, intended use/exploitation of results

-skills matrix, project requirements vs expertise available within the consortium

- key personnel (name and background, role in the project, availability %), especially when the person in question is to be involved > 30% of his time

- project manager (same as above plus experience with multi-party/multi-nation endeavours), deputy/backup project manager, members of project office when known.

Attention points:

Info:

• http://cordis.europa.eu/fp7/dc/index.cfm

We have registered the project at the electronic project submission

site, the username/password to CONNECT TO: https://www.epss-fp7.org/"https://www.epss-fp7.org

un: QFT7XWD3CZpw: reasoning101

WIFI: FSVM_wireless

Username: user1 or user2

Password: 12345

4.2. Final checks before submission• Do you have the authorisation of all the members of the consortium to submit this proposal on their behalf?• Are you using the correct Part A forms and Part B format as given in this document?• Is your Part B in portable document format (PDF), including no material in other formats? If you have in error registered for the wrong call or funding scheme, discard that registration (usernames and passwords) and reregisterand re-submit correctly. If there is no time to do this, or the call deadline has already passed, notify the EPSS Helpdesk.• Have you printed out your Part B, to check that it really is the file you intend to submit, and that it is complete, printable and readable? After the call deadline it will not be possible to replace your Part B file• Is your Part B file within the size limit of 10 Mbytes?• Have you virus-checked your computer? The attempted submission of files containing a virus is automatically blocked.

4.3. The deadline: very important!• Have you, as coordinator, taken the responsibility to submit your proposal?• Have you made yourself familiar with the EPSS in good time?• Have you allowed time to submit a first version of your proposal well in advance of the deadline (at least several days before), and then to continue to improve it with regular resubmissions?• Have you pressed ‘SUBMIT’ after your final version?

• In the unlikely event of a failure of the EPSS service due to breakdown of the Commission server during the last 24 hours of this call, the deadline will be extended by a further 24 hours. This will be notified by e-mail to all proposal coordinators who had registered for this call by the time of the original deadline, and also by a notice on the Call page on CORDIS and on the website of the EPSS.

General Concept, objectives, abstract Slow response – please improve.. Deliverables / milestonesDeadlines Textual contributions !!!Work packages WP1 more detailed information on the contribution of UNIMAN tasks distribution between VIB and UNIMAN WP2 too many tasks some tasks seem to belong to WP1 some tasks may look too ambitious WP3/4 Definition of visualisationReconcile text mining CNIO/UNIMANdefine the scope and task distribution involvement of UNIMAN in WP4 WP5/WP6 need urgently definition Persistence of user comments / personalised workspace

To be discussed

What we need from you:WP Coordinator tasks:• Describe the state-of-the-art in the area concerned, and the advance

that the proposed project would bring about. If applicable, refer to the results of any patent search you might have carried out.

• Summary of WP discussions by Friday April 20• Receive/extract input from other WP coordinators by Tuesday April 24

(if not: others don’t contribute)• Finish WPs by Friday April 27By 3 May: • VIB: assemble and submit the first version of the proposal • all participants: fill in A forms Further need:• Legal representative / okaying the proposal• Financial administration to complete the budget

We wait for corrections and amendments till 6 May We submit the final version of the proposal 7 May