Open PHACTS Deliverable 8.3 Concept for OPS Community Workshop

Open PHACTS

Deliverable 8.3

Concept for OPS Community workshop

Prepared by UniVie, RSC Approved by AZ, LUMC, Pfizer, RSC, UniVie

August 2011 Version 1.0

Project title: An open, integrated and sustainable chemistry, biology and pharmacology knowledge resource for drug discovery Instrument: IMI JU Contract no: 115191

Start date: 01 March 2011 Duration: 3 years

Nature of the Deliverable Report x Prototype Other Dissemination level Public dissemination level x For internal use only

Open Deliverable: Concept for OPS Community Deliverable: 8.3 PHACTS workshop Authors: Richard Kidd, Anika Robl IMI - 115191 Version: 1.0 2 / 10

Definitions  Partners of the Open PHACTS Consortium are referred to herein according to the following codes:

Pfizer – Pfizer limited – Coordinator UNIVIE – Universität Wien – Managing entity of IMI JU funding DTU – Technical University of Denmark – DTU UHAM – University of Hamburg, Center for Bioinformatics BIT – BioSolveIT GmbH PSMAR – Consorci Mar Parc de Salut de Barcelona LUMC – Leiden University Medical Centre RSC – Royal Society of Chemistry VUA – Vrije Universiteit Amsterdam CNIO – Spanish National Cancer Research Centre UNIMAN – University of Manchester UM – University of Maastricht ACK – ACKnowledge USC – University of Santiago de Compostela UBO – Rheinische Friedrich-Wilhelms-Universität Bonn AZ – AstraZeneca GSK – GlaxoSmithKline Esteve – Laboratorios del Dr. Esteve, S.A. Novartis – Novartis ME – Merck Serono HLU – H. Lundbeck A/S E.Lilly – Eli Lilly

 Grant Agreement: The agreement signed between the beneficiaries and the IMI JU for the undertaking of the Open PHACTS project.

 Project: The sum of all activities carried out in the framework of the Grant Agreement.

 Work plan: Schedule of tasks, deliverables, efforts, dates and responsibilities corresponding to the work to be carried, out as specified in the Grant Agreement.

 Consortium: The Open PHACTS Consortium composed of the above-mentioned legal entities.

 Project Agreement: Agreement concluded amongst Open PHACTS 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.

1 Introduction

Open PHACTS will organize 6-monthly workshops with the aim of addressing the project’s key developments and/or challenges with the wider community of potential OPS users. During the WP 7, 8, 9 cluster meeting in Vienna on May 03-04, 2011 it was agreed that sustainable data sharing, and specifically the current perceived hurdles, licensing and sustainability models, should be the topic of the first workshop – specifically to engage those who we want to make their data available to OPS. This workshop has both practical education and application goals around buy-in for data suppliers into OPS, puts in some groundwork at this early stage for models around future sustainability, and delivers team/community building in a memorable and constructive format.

The workshop will be co-organised by GEN2PHEN and will be held in Volendam (The Netherlands) on September 19 and 20, 2011. Its main topic will be "Solving bottlenecks in data sharing in the Life Sciences". The first day will focus on tutorials by licensing and sustainability experts and the second day participants will board traditional Dutch sailing ships and, divided into 3 groups and assisted by the experts, work in Masterclasses on developing a bullet point licensing/sustainability plan for their own data sources.

The issues at hand:

 How can data be shared in a sustainable manner?  Which licensing models are available for (and applicable) IP in distributed and/or academia driven projects?  How to negotiate Consortium Agreements and Project Agreements?  What are sustainability strategies and business models in open source/open access/open data scenarios?

2 Goals of the Workshop

Goals for Open PHACTS:

 Lower barriers for data sharing into OPS – primarily for those outside the consortium, but including some consortium data holders  Start discussions about sustainability models as OPS becomes operational  Team and community building for the influencers outside the consortium. This is our first real opportunity to get the wider data-holding community behind the project

Goals for attendees:

 Have these issues addressed in tutorials by experts.  Participants assisted to applying principles learned to their own projects, databases and tools.  Participants helped to create bullet point IP licensing and sustainability plan.

3 Sustainability and costs

 NBIC will sponsor € 4.000,- for the dinner on Monday  Gen2Phen will sponsor € 15.000  because of that there will be no conference fee  travel and lodging expenses have to be paid by the participants themselves, except of SAB members and John Wilbanks (keynote speaker)  how to share costs: as local coordinator LUMC will carry all costs with reimbursement after the event

4 Organisation team and approach

 We have formed a small organisational team consisting of Albert Mons, Mascha Jansen, Daniela Past, Anika Robl and Eva Molero.  Form a small group of 'legal and business experts' under the guidance of John Wilbanks and Magali Poinot and make them talk to each other before the workshop, so that they are all on the same page and can assist subgroups on day two in getting things straight.

5 Agenda and keynote speakers

Monday September 19, 2011 (Hotel Spaander)

12.00 – 13.00 Registration, lunch/coffee/tea

13.00 – 13.30 Opening: introduction (Barend Mons) / Open PHACTS (Bryn Williams Jones) / GEN2PHEN (Anthony Brookes)/ program overview and goals workshop (Day Chairs Richard Kidd, RSC and Barend Mons, LUMC/NBIC)

13.30 – 13.50 short presentations by data owners about ‘their issues’

13.30-13.35 Pubchem by Evan Bolton 13.35-13.40 BIOBASE by Frank Schacherer 13.40-13.50 OPS Open PHACTS by Christine Chichester

13.50 – 14.15 Keynote 1: ‘Introduction of IMI Ju’, Ann Martin, Principal Scientific Manager Knowledge Management

14.15 - 14.40 Keynote 2: ‘Data licensing and sustainability from IMI’s perspective’, Magali Poinot, IMI legal counsel (may be changed)

14.40 – 15.15 Keynote 3: ‘Open Access and Open Source: no free lunch!’ Jan Velterop, Open PHACTS consortium and AQknowledge

15.15 – 15.45 Coffee break

15.45 – 16.30 Keynote 4: ‘ Forms of OPEN Sharing that avoid data disclosure, and methods to make CONTROLLED sharing equivalent to OPEN sharing’ Anthony J Brookes, GEN2PHEN Co-ordinator

16.30 – 17.15 Keynote 5: ‘Open Source licensing and sustainability models for effective data sharing in the Life Sciences’, John Wilbanks, Creative Commons and SageBioNetworks

17.15 – 18.00 Plenary discussion about topics keynotes

18.00- 18.15 Wrap up and housekeeping (explanation program day 2)

18.15 – 19.15 Drinks and networking

19.15 – 22.00 Dinner (Room: Grande Serre)

Tuesday September 20, 2011 (on sailing ships)

7.45: Departure from hotel lobby to harbor (walking distance)

8.00 – 09.30 Breakfast on board, prepare for sailing and departure

9.30 – 12.00 Workshop under guidance of speakers and/or other experts

12.00 – 13.00 Skipper’s lunch on deck (weather permitting!)

13.00 – 15.00 Workshop continued

15.00 – 16.30 Sailing race at Markermeer and return to harbor (drinks and snacks)

16.30 – 17.30 Brief summary presentations of results from workshops (including 20 minute presentation by Open PHACTS licensing group)

17.30 - 18.00 Closing reception

6 Audience/participants

The workshop is by invitation only, the number of participants is limited to 100. Participants will initially only be OPS consortium members, Faculty and Associated Partners. The most important (for the project) are representatives from the priority data sources, then other Faculty members (as the influencers). It is not expected that all consortium members would need to send multiple representatives, though this may be appropriate for some. The following people will be invited to participate in the first Open PHACTS Workshop:

Organisation first name name TopQuadrant (member of SAB of OPS) Dean Allemang Univ. Santiago (OPS Consortium) Filipe Areias Phenosystems (GEN2PHEN) David Atlan European Institute of System Biology and Medicine (EISBM) Stephane Ballereau GSK, Open Innovation Michael Barnes TraIT Jeroen Belien AstraZeneca (OPS Consortium) Niklas Blomberg Eli Lilly (OPS Consortium) Micheal Bodkin TraIT Jan-Willem Boiten (PubChem), NCBI Evan Bolton TNO Jildau Bouwman University of Leicester (GEN2PHEN) Anthony Brookes Institute Molecular Medicine Finland (FIMM) (GEN2PHEN) Myles Byrne Univ. Santiago (OPS Consortium) Marian Castro Leiden Univ. Medical Center (OPS Consortium) + ConceptWiki Christine Chichester (VIVO) Mike Conlon

Eli Lilly (OPS Consortium) Hans Constandt Univ. Santiago (OPS Consortium) Emiliano Cuadrado University of Leicester (GEN2PHEN) Raymond Dalgleish EBI/ChEMBL Bernard de Bono Leiden Univ. Medical Center (GEN2PHEN) Johan den Dunnen Orphanet/Inserm Ferdinand Dhombres Fundació IMIM (GEN2PHEN) Carlos Díaz Bio2RDF, Carleton University, Ottawa, Canada (CWA) Michel Dumontier Univ. Vienna (OPS Consortium) Gerhard Ecker Univ. Maastricht (OPS Consortium) Chris Evelo Karolinska Institute (GEN2PHEN) Martin Fransson Univ. Vienna (OPS Consortium) Franz Gatterer Univ. Manchester (OPS Consortium) Carole Goble San Diego University Jeff Grethe Global Health Equity Foundation Athol Harrison Pistoia Ian Harrow Leiden Univ. Medical Center (OPS Consortium) Rob Hooft Leiden Univ. Medical Center (OPS Consortium) Mascha Jansen RSC (OPS Consortium) Richard Kidd Elsevier Adriaan Klinkenberg NBIC Ruben Kok BioSolve IT Christian Lemmen PSMAR Oriol Lopez Massaguer Technical Univ. of Denmark (OPS Consortium) Ole Lund (HCLS,W3C) (CWA) Scott Marshall IMI Ann Martin University of Aveiro (GEN2PHEN) Sérgio Matos VUMC Gerrit Meijer Fundació IMIM (GEN2PHEN) Eva Molero Leiden Univ. Medical Center (OPS Consortium) Barend Mons Leiden Univ. Medical Center (OPS Consortium) Albert Mons Univ. Vienna (OPS Consortium) Daniela Past Univ. Manchester (OPS Consortium) Steve Pettifer INSERM (GEN2PHEN) Anna Pigeon Novartis (OPS Consortium) Maxim Popov Eagle Genomics Glenn Proctor NBIC Theo Reijmers Univ. Vienna (OPS Consortium) Anika Robl University of Oxford Susanna Sansone BIOBASE (GEN2PHEN) Frank Schacherer Leiden Univ. Medical Center (OPS Consortium) + Sequenomics Erik Schultes IUPHAR Joanna Sharman Univ. Hamburg (OPS Consortium) Katrin Stierand British Library (GEN2PHEN) Allan Sudlow Rijks Universiteit Groningen Morris Swertz

Technical Univ. of Denmark (OPS Consortium) Olivier Taboureau Biocomputing Platforms (GEN2PHEN) Päivi Tikka-Kleemola Univ. Amsterdam (OPS Consortium) Frank van Harmelen Science & Technology Experts Pool Bart van Mierlo Erasmus University Medical Center/EU-ADR/CALBC (CWA) Erik van Mulligen (LUMC/BBMRI) (CWA) Gertjan van Ommen Netherlands Metabolomics Centre Merlijn van Rijswijk Leiden Univ. Medical Center (OPS Consortium) Willeke van Roon-Mom Acknowledge (OPS Consortium) Jan Velterop Data Dyrad (GEN2PHEN) Todd Vision Carealliance Peter Walgemoed John Hopkins University Jing Wang Stanford University/NCBO (CWA) Trish Whetzel Univ. Maastricht (OPS Consortium) Kim Wiersma Creative Commons/Sage Bionetworks (CWA) John Wilbanks DataCite (GEN2PHEN) J Max Wilkinson RSC (OPS Consortium) + ChemSpider Antony Williams Pfizer (OPS Consortium) Bryn Williams-Jones CNG Data Sharing Diana Zelenika UBO (OPS Consortium) Marc Zimmerman NMC/NBIC Gooitzen Zwanenburg SIB Ron Appel ETRIKS Charles Auffrey (Nature genetics, VIVO, Gen2Phen) (CWA) Myles Axton Orphanet Segolene Ayme SIB/SwisProt Amos Bairoch Biowisdom Gordon Baxter Pipeline Alfred Berkeley CrossRef Geoffrey Bilder Fabian Boes University of Indiana/sciencemaps, VIVO (CWA) Katy Borner PDB Phil Bourne LUMC/BBMRI Jasper Bovenberg Biowisdom Paul Bradley ResearchCrossroads Kyle Brown (PubChem), NCBI Steve Bryant CaBIG NCI Ken Buetow Merck Miguel Camargo PLoS (CWA) Richard Cave EU-Openscreen Jon Chambers board Tim Clark EBI Dominic Clark BMC Matthew Cockerill EUR Franciska de Jong ALPSP Sarah Durrant

Harvard University-Santa Fe (CWA) Walter Fontana DataSHAPER Isabel Fortier Sage Bionetworks, Seattle Stephen Friend EHR4CR Ben Goldacre Health Equity Foundation Peter Gollnow Kinesis Kees Groen Hudson Alpha Chris Gunter Elsevier Vishal Gupta NGI Chretien Herben CNRS Marcel Hibert SCAI Martin Hofmann-Apitius Schrödinger Annette Höglund Dundee Andrew Hopkins Thomson Reuters Bruce Kiesel LUMC Eduard Klasen NextBio Ilya Kuperschmidt NGI Colja Laane Enovite Hans Le Fever NIH Izja Lederhendler DCC Liz Lyon Chem Computing Group Steve Maginn Wiley-Blackwell Jason Markos Neuroscience Information Framework (CWA) Maryann E. Martone TraIT Gerrit Meijer GIV Bill Melton NextBio Mike Meyers (NCBO)* (CWA) Mark Musen EPO (KEOPS) Stephane Nauche Clinical Semantics Group (CWA) Eric Neumann Cameron Neylon Accelrys Carmen Nitsche EBI/ChEMBL John Overington Scielo Abel Packer IMI Magali Poinot Nature PG/ORCID Howard Ratner Oxford University Graham Richards ETRIKS Anthony Rowe University Medical Center, Freiburg (BioTOp ontology) (CWA) Stephan Schultz Molecular Networks Christof H. Schwab Stanford University/NCBO (CWA) Nigam Shah Schrödinger Woody Sherman http://bts.ucsf.edu/pspg/faculty/pages/shoichet.html Brian Shoichet dot-n Marketta Silvera STM Association Eefke Smit MIT (CWA)/D space repositories (CWA) MacKenzie Smith

Eagle Genomics Will Spooner board Susie Stephens Stanford Victoria Stodden Erasmus Medical Center Miriam Sturkenboom (WikiGenes) (CWA) Andrew Su PLACEBO Giulio Superti-Furga LUMC Peter Bram t Hoen Aureus Sciences (http://www.aureus-sciences.com) Jason Theodosiou New York Hall of Science Stepehn Uzzo Los Alamos National Laboratory (CWA) Herbert van de Sompel Erasmus Medical Center Johan Van der Lei NuGO (confirmed via UNIMAAS) Ben van Ommen University of Colorado School of Medicine Karin Verspoor IDBS Andy Vines University of Turku/BBMRI/EBI Eero Vuorio Twobirds Maurits Westrik Pistoia John Wise Inte:Ligand/FU Berlin (KEOPS) - exemplars Gerhard Wolber Riken PDSP_DB : Bryan Roth DrugBank Already in ChemSpider David Wishart HMDB David Wishart ChEMBL John Overington NCI Database Markus Sitzmann

TCDB Transporters classification Milton H Saier, Jr. HGNC Elspeth Bruford UniProt Ioannis Xenarios IUPHAR Limited targets Graeme Milligan

KEGG Minoru Kanehisa ENSEMBL Flicked Paul Chebi Christoph Steinbeck BRENDA Dietmar Schomburg Chem2Bio2RDF David Wild Interpro Sarah Hunter Biocomputing Platforms Anni Ahonen-Bishopp INSERM Christophe Béroud EMBL-EBI Ewan Birney University of Leicester Paul Burton Cambon- INSERM Anne Thomsen Council of Scientific and Industrial Research (CSIR), India Debasis Dash LUMC Johan den Dunnen University of Manchester Andrew Devereau Editor GigaScience Journal (in partnership with BMC) Scott Edmunds GEN2PHEN Project Officer Iiro Eerola Swiss Institute of Bioinformatics Livia Famiglietti ______© Copyright 2011 Open PHACTS Consortium Open Deliverable: Concept for OPS Community Deliverable: 8.3 PHACTS workshop Authors: Richard Kidd, Anika Robl 10 / IMI - 115191 Version: 1.0 10

DataCite Adam Farquhar EMBL-EBI Paul Flicek Organisation for Economic Co-operation and Development Toby Green deCODE Hakon Gudbjartsson University of Leicester Robert Hastings Dryad UK / British Library Brian Hole Editor BMC Iain Hrynaszkiewicz Biocomputing Platforms Timo Kanninen CNG Data Sharing Mark Lathrop Karolinska Institute Jan-Eric Litton INSERM Laurence Mabile University of Helsinki Juha Muilu University of Aveiro Jose Luis Oliveira EMBL-EBI Helen Parkinson University of Patras George Patrinos DataCite Tom Pollard Foundation for Research and Technology (FORTH) George Potamias INSERM Emmanuelle Rial-Sebbag University of Oxford David Shotton Cold Spring Harbor Laboratory Lincoln Stein University of Menheim Jochen Taupitz University of Leicester Gudmundur Thorisson