MINUTES BioMedBridges Kick off meeting · MINUTES: Kick-off Meeting BMB_AGM_12-02 5 – 6 March...

MINUTES: Kick-off Meeting BMB_AGM_12-02

5 – 6 March 2012 2012-05-21 1 of 21

ELIXIR/EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD

MINUTES

BioMedBridges Kick-off meeting

5-6 March 2012

Wellcome Trust Conference Centre, Hinxton, U.K.

As approved by the BioMedBridges Coordinator


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Contents

List of participants ..................................................................................................... 3

Day 1 Monday, 5 March 2012 ................................................................................ 3

BioMedBridges overview and discussion ............................................................... 5

Report from the Executive Steering Committee ..................................................... 5

Committees and meeting schedule ............................................................... 5 Ethics requirements ............................................................................... 6 BioMedBridges website ............................................................................... 7 Project management ............................................................................... 7 Sustainability ............................................................................... 8 Metrics ............................................................................... 8

Presentation from construction Work Packages .................................................... 8

WP3: ESFRI BMS Standards Description and Harmonisation ............................... 8 WP4: Technical Integration ................................................................................... 10 WP5: Secure Access ............................................................................................. 12

Day 2 Tuesday, 6 March 2012 ............................................................................. 15

Presentations from Use Case Work Packages ...................................................... 15

WP6: Interoperability of large scale datasets from different biological scales ...... 15 WP7: Crossing the species bridge between mouse and human........................... 15 WP8: Personalised Medicine: integrating complex data sets to understand disease

pathogenesis and improve biomarker and treatment selection .................. 16 WP9: From cells to molecules: integrating structural data .................................... 16 WP10: Integrating disease-related data and terminology from samples of different

types ............................................................................................................ 17 WP11: Technology watch ...................................................................................... 18 WP12: Training ...................................................................................................... 19 WP2: Outreach and in-reach ................................................................................. 20

Any other issues ....................................................................................................... 21

Communication ............................................................................. 21 Interactions with other EU projects ............................................................. 21 Future AGMs ............................................................................. 21


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List of participants

Coordinator

Janet Thornton (EMBL-EBI)

Participants

ELIXIR/EBI INSTRUCT

Nicola Slater (EMBL-EBI) Chris Morris (STFC)

Lindsey Croswell (EMBL-EBI) Martin Wynn (STFC)

Helen Parkinson (EMBL-EBI) Narayanan Krishnan (STFC)

Alvis Brazma (EMBL-EBI) Dave Stuart (Uni. Oxford)

Ewan Birney (EMBL-EBI) Susan Daenke (Uni. of Oxford)

Ardan Patwardhan (EMBL-EBI) Lucia Banci (CERM)

Andrew Lyall (EMBL-EBI) Claudia Andreini (CERM)

Soeren Brunak (DTU)

Ugis Sarkans (EMBL-EBI) BBMRI

Stephanie Suhr (EMBL-EBI) Jan-Eric Litton (KI)

Heimo Mueller (MUG)

EATRIS Klaus Kuhn (TUM)

Frank De Man (VUMC) Sanela Kurtovic (KI)

Jan-Willem Boiten (CTMM) Martin Fransson (KI)

Henrik Edgren (FIMM) Morris Swertz (UMCG)

Krister Helbing (TMF)

Roland Krause (TMF) ECRIN

Juha Muilu (FIMM) Christian Ohmann

Töresin Karakoyun

Infrafrontier

Christoph Lengger (HZM) EMBRC

Frauke Neff (HZM) Rolf Apweiler

Martin Hrabé de Angelis Chuck Cook

Michael Raess Remo Sanges

EU-OPENSCREEN

Ronald Kuehne


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e-Infrastructures Euro-BioImaging

Neil Geddes Antje Keppler

Bob Jones Stephan Klein

Steven Newhouse

Dai Davies

Kimmo Koski

Tommi Nyrönen

Scientific Advisory Board

Bartha Maria Knoppers

Larry Hunter

Lee Harland

Babis Savakis

Eero Vuorio


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Day 1 Monday, 5 March 2012

BioMedBridges overview and discussion

The BioMedBridges Coordinator, Janet Thornton, welcomed the

participants and introduced the agenda and purpose of the meeting.

She presented the aims and challenges of the BioMedBridges project,

its management structure and the tasks and deliverables of WP1

Management.

Stephanie Suhr was introduced as the BioMedBridges Project

Manager who would officially assume her position at EBI on 2 April

2012.

Report from the Executive Steering Committee

Committees and meeting schedule

DECISION

The Executive Steering Committee will meet once a year in person at the AGM.

The Executive Steering Committee will hold teleconferences every three months, as

far as possible in the afternoon of the first Tuesday of the month in question.

The Technical Coordination Committee will hold teleconferences every month.

The Scientific Advisory Board (SAB) will attend the AGMs and provide feedback to

the Steering Committee at end of each meeting.

The technical contacts at the different Research Institutions (RIs) will provide

information to e-Advisory task force concerning their respective requirements.


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ACTION Who?

Two persons from each of the ten mature RIs to be nominated to take

part in Executive Steering Committee. This should be the

PI/coordinator (or representative if necessary) and a nominated

deputy.

BMS

Coordinators

Organise teleconferences to be held by the Executive Steering

Committee every three months.

S. Suhr

Set up monthly teleconferences of Technical Coordination

Committee.

S. Suhr

Identify further dates for the first AGM; hold 11-12 March 2013 until

finalised.

C. Ohmann,

S. Suhr

e-Advisory Task Force and BBMRI (biobanking lexicon) to provide

information on existing lexicon.

N. Geddes,

BBMRI

Collate information for the e-Advisory board, prepare reports. E. Birney,

A. Lyall

Ethics requirements

DECISION

An „Ethics and Legal Advisory Committee‟ was established, comprising the following

members:

Janet Thornton (Chair)

Representatives from ECRIN, BBMRI, EATRIS, EMBRC (to

represent environmental research)

Ethics Adviser (WTSI)

Legal EU advisor (to be appointed)

The committee will be tasked with monitoring the potential for unforeseen usage of

data which requires ethical approval.

The committee‟s reports should be submitted to the Executive Steering Committee

for approval.


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ACTION Who?

Provide list of potential candidates for the position of legal advisor to

the Ethics Advisory Committee.

J.-E. Litton

Nominate representative for Ethics Committee (EMBRC to represent

environment).

EATRIS and

EMBRC

Coordinators

Once the committee has been established, organise teleconference.

Agenda to include item on Deputy Chair for the group.

S. Suhr

Send ethics documents to the Executive Steering Committee and the

Scientific Advisory Board.

A. Lyall

BioMedBridges website

DECISION

The website will be both a project management tool and the public face of

BioMedBridges.

ACTION Who?

Collect information on the contact person for each RI‟s website to

help ensure effective dissemination of information.

WP2

Develop an initial website as soon as possible. EBI

Project management

DECISION

Each WP leader (with their deputies) is responsible for writing reports, which will then

be collated and submitted to the EC by the BioMedBridges project manager.

All types of information on the project should be collected, positive and “negative” –

including bridges built, bridges tried and failed, bridges not tried


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Sustainability

DECISION

A session on sustainability will be scheduled at the AGM in 2014, half way through

the project. The Executive Steering Committee is responsible for this.

Sustainability should be tackled in month 24.

Metrics

DECISION

The metrics to monitor progress and impact of the project that have to be developed

should be technical/scientific rather than political.

The e-Advisory task force should contribute to the development of metrics.

ACTION Who?

Collect metrics information from all infrastructures. S. Suhr

Executive Steering Committee to discuss metrics (e-Advisory task

force could advise on this); put on agenda for next meeting.

S. Suhr

WPLs to discuss metrics after Executive Steering Committee, then

add to agenda for discussion at AGM.

S. Suhr

Presentation from construction Work Packages

WP3: ESFRI BMS Standards Description and Harmonisation

J.-E. Litton (BBMRI) gave a presentation on the importance of standards and

the need to monitor quality. This was followed by a presentation from

H. Parkinson (ELIXIR) on the objectives, tasks and challenges of WP3.


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Challenges

WP is cross-cutting: input to WP4, consumer of outputs

Many partners, few resources

Finding focus

Provide useful resources for the wider community

Avoid reinventing the wheel

Restricted resources, especially medical terminologies

If WP3 fails, WP4 usability would be compromised

Objectives

WP3 will support WP4 test by implementation into WPs 6-10

Tasks

Inclusion of relevant community standards

Register new standards

Re-usable extendable resource to the wider community

WP3 will map, survey and evaluate existing resources for use by

BioMedBridges.

Measures of Success

WP3 partners successfully engaged

WP6-10 connected with WP3 usable resources from WP3

WP4 supported, tech implementation enabled

Non-BioMedBridges applications

Following a presentation by S. Klein (Euro-BioImaging) on the challenges and

initiatives of WP3 from a Euro-BioImaging perspective, M. Swertz (BBMRI)

mentioned that the issues had already been faced and many had been

discussed nationally. He added that there are no formal data access templates

in the Netherlands; however, there are some best practices.

Comments

With respect to the harmonisation of standards, there seem to be many

different ideas concerning which standards should be included. It was

advised that this would depend on the aims of the use cases.

Harmonisation of standards should have the overall effect of reducing

their number.


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There will be a curation research conference (NORDBID) in June that

has similar goals. It was suggested that a BioMedBridges

representative attends.

Costs should be minimised by figuring out what is already available.

How will things change with new EU regulations on data sharing?

The potential scale of the task is huge and there is a need to prioritise.

It is important to work with the use case WPs to shape priorities before

submitting a proposal to other partners.

It is important not to forget the international dimension of the task; most

project participants are involved in international activities.

Important not to focus solely on medicine, also include e.g. mice.

The WP should first focus on constructing bridges between the

partners involved in the project.

It should be clarified which region the use case data is based on to

make sure standards in all countries and areas are covered.

Take into consideration that some open access data is not harmonised.

WP4: Technical Integration

Ewan Birney presented an overview of the tasks of WP4. He mentioned that

the technical integration required for BioMedBridges is compatible with

ongoing technical integration work at EBI.

Challenges

Large number of types of data and amount of data

Next generation reads are exceeding Moore‟s law

WP4 is about implementing standards from WP3 via REST-based web

services, for browsing and programmatic access

Will eventually employ semantic web technologies and pilot use; WP11

technology watch will feed into this.

Plan

A survey will be sent to the technical contact at each RI – questions will

include:

What data would your RI like to share and consume?


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For your data – provide a current web page which describes

one data item

Do you have an internet accessible programmatic system now

for access to this data?

If not, will you be implementing one?

Is there documentation on it?

Technical groups will be asked to provide a REST-based service for

their data with WP3 blessed XML of data items.

A harmonised RDF dump of open data available at RIs will be provided

first. Technically more ambitious items will follow later.

The technical solution of WP4 should be wrappable inside a WP5

framework.

Questions and Comments

IMI would like to harmonise RDF exposure; L. Harland stated his

interest in data publishing in RDF format.

E. Birney advised that the data does not necessarily have to be in XML

format, which could be changed to suit the RI area‟s natural format. In

any case, the format would have to be approved by WP3.

The Executive Steering Committees is responsible for making sure that

data is used in compliance of the ethics requirements.

Answering a comment that the main concern for EATRIS is how to

combine resources between imaging, biobanking and medical,

E. Birney advised that the scientific integration itself was not within the

scope of BioMedBridges. The objective of BioMedBridges was to lower

the barrier for others to do the integration, i.e. to put things in an

accessible form.

The security issues for the different RIs are:

ECRIN – There is an intellectual property issue. Most full clinical trial

data sets are not available, only for some compounds. Dummy data

could be provided (see also http://www.controlled-trials.com,

clinicaltrials.gov).

INSTRUCT – There is data that could be shared and data they would

like to share.


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Eu-Openscreen – There is a question whether there are other projects

with model systems. Need the approach of EUDAT but implementation

needs to be in BioMedBridges.

Infrafrontier – Need to link mice to medical and omics data as early as

possible. C. Lengger would be the technical contact.

EMBRC – helps organisations to organise their own data.

EU-Openscreen – It is possible to provide targets and books;

compound resolver.

Euro-BioImaging – Human data is more interesting for this WP. WP5

should address some concerns of medical WPs.

E. Vuorio (SAB, Finland) suggested asking the EC what projects they are

supporting that are handling such issues. He suggested that the technology

watch group might also help with this.

J. Thornton advised that it would not be possible to do everything during the

course of the project, but it would be important to at least demonstrate that it

can work and people can use it by end of project (i.e. search one infrastructure

and link to another).

ACTION Who?

WP4 will send out a requirements survey once the RIs have

communicated the names of their technical representatives.

E. Birney

List of data types produced from survey to be submitted to Ethical

Governance Committee.

E. Birney

Approach EU re projects involving technical integration BMB

Coordinator

WP5: Secure Access

C. Ohmann (ECRIN) presented the tasks and objectives of WP5 and the

partners involved. The objective of WP5 is to establish a security framework


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that is compliant with legal and ethical requirements on the national and

European level. A number of partners are involved; in some cases, there may

need to be two representatives from each partner.

WP5 will look to identify two representatives in each country, one for legal

issues and one technical. A large report on “regulations, privacy and security

requirements” is scheduled to be delivered in month 18. This will be the first

output on the overall infrastructure. WP5 covers three RIs at present, but the

complexity will increase.

Plans

Identify security requirements

What local systems exist, what data is going to be shared and how?

What kind of data and how to integrate?

Will work with all WPs, 3, 4, 5 and the use cases.

Identify WP members

Set up regular teleconference of WP5 (every 4 weeks)

Face to face meeting (June 2012?)

Questions and comments

It was confirmed that kn–anonymity had been piloted already. However,

it is best to use derivatives, as many rely on informed consent.

J. Thornton commented that it may not be possible for two

representatives to be found within the project who can provide

expertise on every country.

It is clarified that just a short summary of the main points for the

European level is needed.

The main data sets used will be retrospective, rather than WP5 asking

for data that meet the criteria.

An audit trail should be available of the use, i.e. o used what, for what,

and when.

Under the proposed new EU data regulations, which will be in effect

from 2015 onwards, things will be easier. Before that, someone would

have to have already approved the data for use. BioMedBridges must

be set up based on the current system and legal framework.


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A „Tool box‟ approach should be considered so that BioMedBridges is

prepared for the new EU regulations.

Need to consider how data can move from one risk category to another

depending on how it is used. A risk-based approach should be used.

The legal definition of terms such as coded, anonymised, anonymous

data differs.

Other projects – such as ENGAGE – that have already undergone the

ethics requirements process should be contacted.

ECRIN and B.M. Knoppers will investigate the possibility of

subcontracting a member of the Public Population Project in Genomics

(P³G) consortium to assist WP5.

ACTION Who?

Compile a list of privacy terms; produce a lexicon with definitions. WP5/S. Suhr

Ideas for WP5 proposed at the kick-off meeting to be written up by

WP5 and circulated for discussion.

WP5


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Day 2 Tuesday, 6 March 2012

Presentations from Use Case Work Packages

WP6: Interoperability of large scale datasets from different biological

scales

A. Keppler (Euro-BioImaging) presented the tasks and objectives of WP6. She

advised that a technical person to work on the work package was still to be

recruited. A teleconference between WP6 members and the technical contact

would be set up in the near future.


A. Keppler clarified that the images to be included in the

BioMedBridges project would be of tissues. Details would be discussed

at the next conference call.

WP7: Crossing the species bridge between mouse and human

Michael Krauss presented tasks and objectives of WP7. WP7 will build bridges

between human and mouse data. The WP involves Infrafrontier, ELIXIR,

BBMRI, and INSTRUCT. A contact point at each of the centres has been

identified, but more staff may need to be hired.

Next steps

Check existing ontologies, involve experts in workshops to improve and

enhance ontologies.

Provide sample data sets.


For anatomy, an ontology is already being built, although some

complicated anatomy ontology is not available and needs to be done.

Disease ontology for complex diseases is needed.


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Examples based on good, available data should be produced first and

the work should then be extended into other disease areas.

Establish first what is already available before deciding what can be

improved.

WP8: Personalised Medicine: integrating complex data sets to

understand disease pathogenesis and improve

biomarker and treatment selection

H. Edgren (EATRIS) presented the tasks and objectives of WP8. The work

package participants are FIMM, TUM, EMBL-EBI, KI, UDUS.

Next steps

WP8 has a list of questions they would like to get answered by each of

the core research infrastructures, with the aim of identifying what data

they can share that is relevant to WP8 and what the conditions for use

of these data are.

Once it is known what data is available, a specification will be

developed.

J.E. Litton (BBMRI) clarified that there are three phases: find case, find

samples, do science.


J. Thornton suggested that, instead of contacting the BioMedBridges

RIs, BBMRI may contact people who are involved in personalised

medicine in different countries.

WP9: From cells to molecules: integrating structural data

M. Winn presented the tasks and objectives of WP9. They are aiming to

develop database and software. The WP is due to start in January 2013. EBI

and CERM have people to work on the WP. STFC still needs to recruit

someone.


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Within the WP, there is bilateral interaction between INSTRUCT and ELIXIR.

More staff from INSTRUCT, ELIXIR, and maybe other RIs will be involved. A

connection to Euro-BioImaging may also be made.

M. Winn mentioned among possible ideas for metrics the accuracy of shape

measuring, usage of software distributed within INSTRUCT, usage of web

services, and evidence of usage by other RIs.

Next steps

Conduct a survey on the available software

Investigate how to include non-deposited information.


J. Thornton agreed that there were potential links with Euro-BioImaging

for WP9 in terms of volumes and tomography.

A suggestion was made to produce a draft document describing which

part of Euro-BioImaging overlaps with INSTRUCT.

Overall, simple cases should be examined first.

WP10: Integrating disease-related data and terminology from

samples of different types

A. Brazma presented the tasks and objectives of WP10. The WP will get

patient profiles and link them to genes. A reusable reference sample with

unique IDs will be created while minimising redundancy. The WP will

concentrate on specific diseases and select five to six biobanks within BBMRI

with the most open attitude towards their sample information usage.

Next steps

Meeting with WP participants in October

Discuss where linkage is possible and what kind of architecture can be

proposed

Feedback to WP3, 4 and 5

Present at next AGM.


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Comments and questions

A question was raised as to whether the work package intended to look

to identifying a higher level generic model to work with, rather than just

specific cases.

The work package will work with data they can easily obtain; focusing

on some full length papers. In most cases to be considered here there

is one disease to one gene.

K. Kuhn suggested that there are similarities in approach between

WP10 and WP8 and that it might be useful for these work packages to

work together.

WP11: Technology watch

N. Geddes (STFC) presented the objectives, partners, and deliverables of

WP11. He advised that WP11 intends to collate e-infrastructure requirements

and requirements for data and service bridges from WPs; they will inform

BioMedBridges about and leverage what already exists and work to identify

areas where there may already have been in-depth tech work. They will also

aim to identify possible future projects outside the remit of BioMedBridges and

create social links by laying the groundwork for future collaborations. They will

formally meet each year at the AGM.

The members of the task force are:

Ewan Birney

Dai Davies

Neil Geddes (Chair)

Bob Jones (CERN)

Kimmo Koski

Andrew Lyall

Steven Newhouse (EGI)

S. Newhouse (EGI) then presented an introduction to the e-infrastructure

landscape. He advised that the e-infrastructures are looking at priority areas

and opportunities, which will include: identity management, secure data

access and virtualisation.


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BioMedBridges to collate current estimates of data volumes and traffic.

Identify already existing contacts would be very useful.

ACTION Who?

Links to e-infrastructure documents to be included on BioMedBridges

website.

S. Suhr

WP12: Training

C. Brooksbank presented the aims and tasks of WP12. She stressed that all

WPs would need to be involved in identifying focus areas for the training and

workshops to be developed.

Objectives

Deliver short workshops to project participants on specific areas to

facilitate building of data bridges among the BMS RIs.

Produce documentation on the resources developed and give training

to end users.

Next steps

WP12 will gather information from the other WPs and coordinate.

A Scientific Training Officer to work on the work package will be

recruited by EBI.

Each WP must commit resources to developing the training courses.

WP12 will need a contact person for each WP.

There will be four workshops for project participants and two user

workshops.

WP12 will send out a short questionnaire to gather input on the „wants‟

and „haves‟.

There is also the possibility of recruiting experts from outside the

project.


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It may be useful to ask RIs what they already provide since they each

have their own workshops.

WP3, WP4, and WP5 should have a workshop each and the use cases

have one.

Additionally, it would be good to have a workshop on personalised data

(ethical/legal workshop).

B.M. Knoppers advised that the “HandsOn: Biobanks Conference and

International Biobanking Summit” to be held in Sweden in September

could be interesting to project partners.

L. Banci should be included in next call.

WP2: Outreach and in-reach

F. de Man presented the tasks and objectives of WP2. He advised that

EATRIS are in the process of recruiting someone to lead WP2.

He reported that WP2 will develop the branding and logo for BioMedBridges;

however, work on this task had been delayed. It is expected that it will be

completed by summer.


J. Thornton suggested that WP2 canvas each RI about their own PR

activities to find out what they are doing and then pick parts that are

applicable to all RIs. She added that it would also be important to

decide on the aim of the website and develop a strategic plan for it, e.g.

whether the website was going to be a tool for now or something that

would support the RIs going forward.

It was suggested that there is an INFSO project with a platform for e-

infrastructures that might be of use.

It was suggested that WP2 could also be tasked with informing people

of the BioMedBridges deliverables, as they are delivered.


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Any other issues

Communication

DECISIONS

A calendar of AGMs for each RI should be put together and a decision made

concerning how BioMedBridges is presented there. The item should be considered

by WP2

A newsletter of achievements and current events in BioMedBridges should be

produced by WP1 and WP2 together.

Interactions with other EU projects

ACTION Who?

WPs planning on using data sets that require ethics approval to

forward the information.

WPLs,

S. Suhr

Contact EC and discuss how to take the idea of conducting a survey

of related EU projects (such as P-medicine) forward. Specifically,

contact may be made with: Joint Programme Initiatives, Innovative

Medicines Initiative (IMI), Other ESFRI Clusters, OpenAire.

BMB

Coordinator

Future AGMs

DECISIONS

The first AGM in 2013 will be held in Düsseldorf.

AGM 2 in 2014 will be held in Florence at the offer of L. Banci.

AGM 3 in 2015 to be held in Brussels; Commission to be invited and hopefully attend

Future BioMedBridges AGMs will be open meetings to encourage wider exchange

with the community / different communities.

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