3rd International Workshop on Linked Science 2013—Supporting Reproducibility, Scientific Investigations and Experiments (LISC2013)
When: October 21st, 2013
Where: Sydney Masonic Conference & Function Centre, Sydney, Australia
Collocated with the 12th International Semantic Web Conference (ISWC2013).
Submission Deadline Extended: July 12th, 2013 at 23:59 (UTC−10:00 Hawaii Time zone)
Notification of Acceptance: August 9th, 2013
Workshop URI: http://linkedscience.org/events/lisc2013
Results: Results of Workshop discussion session
9.00 – 10.00 Keynote by Carole Goble
Results may vary: reproducibility, open science and all that jazz.
Abstract:How could we evaluate research and researchers? Reproducibility underpins the scientific method: at least in principle if not practice. The willing exchange of results and the transparent conduct of research can only be expected up to a point in a competitive environment. Contributions to science are acknowledged, but not if the credit is for data curation or software. From a bioinformatics view point, how far could our results be reproducible before the pain is just too high? Is open science a dangerous, utopian vision or a legitimate, feasible expectation? How do we move bioinformatics from one where results are post-hoc “made reproducible”, to pre-hoc “born reproducible”? And why, in our computational information age, do we communicate results through fragmented, fixed documents rather than cohesive, versioned releases? In this talk, which I gave as a keynote at the 2013 joint conference Intelligent Systems in Molecular Biology / European Conference on Computational Biology, I will explore these questions drawing on 20 years of experience in both the development of technical infrastructure for Life Science and the social infrastructure in which Life Science operates.[slides]
10.00-10:30 Paper session I
- Timo Willemsen, Anton Feenstra and Paul Groth. Building Executable Biological Pathway Models Automatically from BioPAX [preprint] [slides]
10.30 -11.00 break
11.00 – 12.45 Paper session II
- Nico Adams, Armin Haller, Alexander Krumpholz and Kerry Taylor. A Semantic Lab Notebook – Report on a Use Case Modelling an Experiment of a Microwave-based Quarantine Method [preprint]
- Jun Zhao, Graham Klyne, Matthew Gamble and Carole Goble. A Checklist-Based Approach for Quality Assessment of Scientific Information [preprint] [slides]
- Michiel Hildebrand, Rinke Hoekstra and Jacco van Ossenbruggen. Using Semantic Web Technologies to Reproduce a Pharmacovigelance Case Study [preprint] [slides]
13.45-15.30 Paper session III
- Guillermo Palma, Maria-Esther Vidal, Louiqa Raschid and Andreas Thor. Exploiting Semantics from Ontologies and Shared Annotations to Find Patterns in Annotated Linked Open Data [preprint] [slides]
- Cameron Mclean, Mark Gahegan and Fabiana Kubke. Capturing intent and rationale for Linked Science: design patterns as a resource for linked laboratory experiments [preprint] [slides]
- Niels Ockeloen, Antske Fokkens, Serge Ter Braake and Piek Vossen. BiographyNet: Managing Provenance at multiple levels and from different perspectives [preprint] [slides]
16.00-17.30 Co-writing session: how can linked science techniques solve problems in scientific reproducibility 2+45 minutes
- 1st 45 minutes: produce reproducibility problem/potential linked science technology matrix in breakout groups
- 2nd 45 minutes: merging matrices into consensus view and/or paper ideas/blog post
Scientific communication has a long history of relying heavily upon publications and presentations, producing an estimate of millions of publications worldwide per year. The results described in these articles are often backed by large amounts of diverse data produced by complex experiments, computer simulations, and observations of physical phenomena. Because of this avalanche of data, it is increasingly hard to validate, reproduce, reuse and leverage scientific findings. In addition, although publications, methods and datasets are very related, they are not equally accessible nor seamlessly interlinked. One notable exception is molecular biology research where journals require deposit of sequences in data banks as a condition of publication. Even where data is discoverable and accessible, significant challenges remain in data reuse and sharing, in facilitating the necessary correlation, integration and synthesis of data across levels of theory, techniques and disciplines.
In the 3rd International Workshop on Linked Science (LISC2013) we aim to discuss and present results of new ways of applying Semantic Web technologies to the publishing, sharing and interlinking of scientific data and methods, and to the reasoning over such resources to discover interesting new links to validate, reuse and reproduce scientific research. The theme of this year’s workshop is “Supporting Reproducibility, Scientific Investigations and Experiments”. We will focus on scientific investigations and experiments that use Linked Data and semantic technologies to represent their data and methods and enable their knowledge discovery, reuse and validation.
LISC2013 will be a mixture of paper and demo presentations and break-out sessions. Workshop participants will also be expected to contribute informally to discussions as well as bring up their own topics of interest. LISC2013 is a continuation of the 1st International Workshop on Linked Science 2011 (LISC2011) and 2nd International Workshop on Linked Science 2012 (LISC2012).
We invite two kinds of submissions:
- Research papers. These should not exceed 12 pages in length.
- Position papers. Novel ideas, experiments, and application visions from multiple disciplines and viewpoints are a key ingredient of the workshop. We therefore strongly encourage the submission of position papers. Position papers should not exceed 4 pages in length.
The research papers can include optional materials. Example of these materials are tutorials that explain more in detail scientific study setting of the research paper. Note that based on numerous requests we decided to accept also other optional materials than just tutorials. Supplementary materials will be published online at LinkedScience.org and linked to the according workshop paper. The tutorial materials will be published at LinkedScience.org/tutorials. Accepted papers will be published at CEUR workshop series.
Submissions should be formatted according to the Lecture Notes in Computer Science guidelines for proceedings available at http://www.springer.com/computer/lncs?SGWID=0-164-7-72376-0. Papers should be submitted in PDF format. The optional tutorial materials are submitted as a zip (preferably wordpress friendly html including all figures). Submissions are done via Easychair: https://www.easychair.org/conferences/?conf=lisc2013.
At least one author of each accepted paper must register for the workshop. All workshop participants have to register for the main conference, ISWC2013, as well.
TOPICS OF INTEREST:
In all three categories, the submissions are expected in (but not restricted to) the following topics:
- Linked Data- based scientific experiments
- Dissemination and integration of scientific resources (data, methods, etc) using the Semantic Web
- Linked Citizen Science
- Scientific Information Retrieval
- Formal representations of scientific data
- Ontologies for scientific information
- Reasoning mechanisms for interlinking scientific datasets and other resources
- Integration of quantitative and qualitative scientific information
- Ontology-based visualization of scientific data
- Semantic similarity in science applications
- Semantic integration of crowd sourced scientific data
- Provenance, quality, privacy and trust of scientific information
- Support for data publishing for sharing and reuse
- Case studies on linked science, i.e., astronomy, biology, environmental and socio- economic impacts of global warming, statistics, environmental monitoring, cultural heritage, etc.
- Replication of SW experiments
- Reproduction of SW approaches & results
- Incentives for reproducing work by others & making own work reproducible
- Use of SW technology to support replication & reproduction
The Workshop Proceedings will be published online.
July 10th, 2013: Paper submission deadline August 9th, 2013: Notification of Accepted Papers
- October 21st or 22nd, 2013: Linked Science 2013 Workshop
Tomi Kauppinen is a postdoctoral researcher in the Department of Media Technology at the Aalto University School of Science in Finland. During 2010-2012 he was a postdoctoral researcher in Germany in the Semantic Interoperability Lab (MUSIL) at the Institute for Geoinformatics at the University of Muenster in Germany. He holds a PhD (2010) from the Aalto University with a thesis on reasoning about change and time, and interacting with the reasoning results. He co-chaired the First and Second International Workshops on Linked Science 2011 and 2012 at the International Semantic Web Conferences, and led the breakout session for Vocabularies for Science at Science Online London 2011 organized by Nature. His research focuses on information usability–especially the semantics, visualization, linkage and interaction aspects. His current projects are opening and linking of scientific and educational data in in the the LinkedScience.org- project and in the Linked Open Aalto- project. You can find him on twitter: @LinkedScience
Jun Zhao is a Project Lead at the University of Oxford. She holds a PhD in Computer Science from the University of Manchester. Her current research interests are provenance, trust of data, Semantic Web applications for integrating biological data resources, and provenance-based information quality assessment. She has been the provenance lead in the UK data.gov.uk project and currently she is the Oxford lead of the EU Wf4Ever project, providing cutting edge models and technologies to support the reproducibility of scientific workflows. She is an active member of the W3C Provenance Working Group and the Health Care Life Science Interest Group. She has been leading organizer and invited speaker of many national and international workshops.
Paul Groth is an assistant professor in the Knowledge Representation and Reasoning Group at the VU University of Amsterdam. He holds a Ph.D. in Computer Science from the University of Southampton (2007) and has done research at the University of Southern California. His research focuses on mechanisms for enabling multi-institutional systems. This includes research in data provenance, scientific workflow and knowl- edge sharing with over 50 publications in these areas. Paul is co-chair of the W3C Provenance Working Group developing a standard for provenance interchange. Currently, he is a key contributor to Open Phacts (www.openphacts.org), a project to develop a provenance-enabled platform for pharmacological information. You can find him on twitter: @pgroth
Carsten Keßler is a post-doc researcher at Institute for Geoinformatics (ifgi), University of Muenster, Germany, where he finished his PhD on context-aware semantics-based information retrieval in 2009. In ifgi’s semantic interoperability lab (MUSIL), he currently coordinates the Linked Open Data University of Muenster (LODUM) project and is a member of the Linked- Science.org team. He also leads a 2-year project on Linked Data for eScience Services funded by the German Research Foundation. Besides his activities at the university, Carsten is a consultant for the United Nations Office for the Coordination of Humanitarian Affairs (UN OCHA) in the development of the Humanitarian eXchange Language (HXL). In fall 2013, Carsten will join the faculty at Hunter College, NYC, as assistant professor for geographic information science.
Line C. Pouchard is an Information Scientist in the Scientific Data Group at Oak Ridge National Laboratory, US Department of Energy. With Tomi Kauppinen and Carsten Keßler, she co-chaired the Linked Science 2011 at ISWC in Bonn and Linked Science 2012 at ISWC in Boston. Her recent work includes implementing semantic technologies to improve observation data discovery in the Earth and Atmospheric Sciences for the NASA-sponsored ORNL DAAC (Distributed Active Archive Center for Biogeochemical Dynamics). Her long-term research interests have focused on ontologies and the implementation of frameworks for scientific applications of interest to the Departments of Energy and Defense. These interests have been applied to the scientific domains of climate and earth sciences, fusion, medical modeling, and homeland security. She is an active participant to several leading ORNL efforts contributing to other agencies, including the NSF-sponsored DataONE (Integration and Semantics Working-Group) and Remote Data Visualization and Analytics. DataONE (Data Observation Network for Earth) is developing infrastructure, strategies, and practices for decade-long sustainable data management, publication, archive, and curation services for the digital data supporting earth, environmental, and ecology research.
Carole Goble is Professor of Computer Science at the University of Manchester where she directs a mixed team of researchers, computational scientists and software engineers that specialise in e-Science. Her research interests lie in the acceleration of reproducible scientific innovation through scientific automation, knowledge management, social interaction and new models of publishing. Her myGrid group is responsible for a widely used workflow system (Taverna), virtual research environments (myExperiment, SEEK, BioCatalogue, MethodBox) and instrumenting scientific tools with semantics. She currently leads: the technical development of the EU projects BioDiversity Virtual e-Laboratory and Wf4Ever digital library project on the preservation and reproducibility of workflow-based research using Research Objects; the work package on Concept and Identity management on EU project OpenPHACTS which is building an Open Linked Data environment for drug discovery. Carole was the EIC of the Journal of Web Semantics for 7 years and is the General Chair of ISWC 2014. In 2008 she was awarded the Microsoft Jim Gray award for outstanding contributions to e-Science.
Yolanda Gil is Director of Knowledge Technologies and Associate Division Director at the Information Sciences Institute of the University of Southern California, and Research Professor in the Computer Science Department. She received her M.S. and Ph. D. degrees in Computer Science from Carnegie Mellon University. Dr. Gil leads a group that conducts research on various aspects of Interactive Knowledge Capture. Her research interests include intelligent user interfaces, knowledge-rich problem solving, scientific and grid computing, and the semantic web. An area of recent interest is large-scale distributed data analysis through semantic workflows. Dr. Gil was elected to the Council of the American Association of Artificial Intelligence (AAAI), and served in the Advisory Committee of the Computer Science and Engineering Directorate of the National Science Foundation. She recently led the W3C Provenance Group, an effort to chart the state-of-the-art and posit standardization efforts in this area. In 2010 she was elected Chair of ACM SIGART, the Association for Computing Machinery’s Special Interest Group on Artificial Intelligence.
Marieke van Erp is a postdoctoral researcher in the Computational Lexicology & Terminology Lab at VU University Amsterdam. She has a PhD in computational linguistics focused on data cleaning and structuring from Tilburg University. She has been involved in research in NLP since 2005 and in Semantic Web since 2009. Her research is focused on applying natural language processing in semantic web applications. She recently joined the European NewsReader project, which aims to build structured indexes of events from large volumes of financial news. She has co-organised several international workshops and panels as well as meetups for computer scientists and cultural heritage professionals in the Netherlands.
Jacco van Ossenbruggen is a researcher in the Information Access group at CWI and an associate professor in the Web and Media group at VU University Amsterdam. He has a PhD in computer science from VU Amsterdam. His research interests focus on designing user interfaces for curated and uncurated Web data. Jacco is currently working on communicating the provenance of data generated by computer vision systems to marine biologists, and on replicating and reproducing ontology alignments made in an interactive setting. He has co-organised several international workshops in the area of web, semantic web, multimedia and hypertext.
- Mathieu d’Aquin, The Open University, UK
- Charalampos Bratsas, Aristotle University of Thessaloniki, Greece
- Boyan Brodaric, Natural Resources Canada, Canada
- Arne Bröring, 52◦ North, Germany
- Gully Burns, ISI, University of Southern California
- Oscar Corcho, UPM, Spain
- Stefan Dietze, L3S Research Center, Germany
- Ying Ding, Indiana University, USA
- Hannes Ebner, Royal Institute of Technology (KTH), Sweden
- Antske Fokkens, VU University, Amsterdam
- Asunción Gómez Pérez, Universidad Politécnica de Madrid
- Willem van Hage, Vrije Universiteit, the Netherlands
- Frank van Harmelen, VU University, Amsterdam
- Michiel Hildebrand, VU University, Amsterdam
- Rinke Hoekstra, Vrije Universiteit, the Netherlands
- Laura Hollink, VU University, Amsterdam
- Michael D. Huhns, University of South Carolina, USA
- Stratos Idreos, CWI, Amsterdam
- Krzysztof Janowicz, University of California, Santa Barbara, USA
- Craig A. Knoblock, University of Southern California, USA
- Werner Kuhn, University of Muenster, Germany
- Timothy Lebo, RPI, Troy, NY, USA
- Zoltán Miklós, University of Rennes 1, France
- Paulo Pinheiro da Silva, Pacific Northwest National Laboratory, USA
- Herbert van de Sompel, Los Alamos National Laboratory, USA
- Eric Stephan, Pacific Northwest National Laboratory, USA
- Mark Wilkinson, Centre for Plant Biotechnology and Genomics UPM-INIA, Madrid, Spain
- Bryn Williams-Jones, Connected Discovery & OpenPHACTS, UK
- Max Wilson, University of Nottingham, UK
- Amrapali Zaveri, University of Leipzig, Germany