All posts by tomi.kauppinen

Program of LISC2013 Sydney on October 21st, 2013 published

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).

PROGRAM

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.

 

10.00-10:30 Paper session I

  • Timo Willemsen, Anton Feenstra and Paul Groth. Building Executable Biological Pathway Models Automatically from BioPAX

10.30 -11.00 break

11.00 – 12.45 Paper session II

  • 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
  • Cameron Mclean, Mark Gahegan and Fabiana Kubke. Capturing intent and rationale for Linked Science: design patterns as a resource for linked laboratory experiments
  • Jun Zhao, Graham Klyne, Matthew Gamble and Carole Goble. A Checklist-Based Approach for Quality Assessment of Scientific Information

12.45-13.45 Lunch

13.45-15.30 Paper session III

  • 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
  • Niels Ockeloen, Antske Fokkens, Serge Ter Braake and Piek Vossen. BiographyNet: Managing Provenance at multiple levels and from different perspectives
  • Michiel Hildebrand, Rinke Hoekstra and Jacco van Ossenbruggen. Using Semantic Web Technologies to Reproduce a Pharmacovigelance Case Study

15.30-16.00 Break

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

Closing

Seven papers accepted to Linked Science 2013

We are happy to announce that we have accepted the following seven papers to be presented in the Linked Science 2013 (LISC2013)  workshop in Sydney, Australia in October 2013:

  • Timo WillemsenAnton Feenstra and Paul Groth. Building Exceutable Biological Pathway Models Automatically from BioPAX
  • 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
  • Jun Zhao, Graham Klyne, Matthew Gamble and Carole Goble. A Checklist-Based Approach for Quality Assessment of Scientific Information
  • Michiel HildebrandRinke Hoekstra and Jacco van Ossenbruggen. Using Semantic Web Technologies to Reproduce a Pharmacovigilance Case Study
  • Guillermo Palma, Maria-Esther VidalLouiqa Raschid and Andreas Thor. Exploiting Semantics from Ontologies and Shared Annotations to Find Patterns in Annotated Linked Open Data
  • Cameron Mclean, Mark Gahegan and Fabiana Kubke. Capturing intent and rationale for Linked Science: design patterns as a resource for linked laboratory experiments
  • Niels Ockeloen, Antske Fokkens, Serge Ter Braake and Piek Vossen. BiographyNet: Managing Provenance at multiple levels and from different perspectives

On behalf of the organizing committee of LISC2013,
Tomi Kauppinen

 

Linked Science 2013 workshop will be arranged in Sydney, Australia late October

We will organize the 3rd International Workshop on Linked Science 2013 (LISC2013) in Sydney, Australia on October 21st or 22nd.

The specific theme of the Linked Science workshop this year will be “Supporting Reproducibility, Scientific Investigations and Experiments”.  Workshop will be collocated with the 12th International Semantic Web Conference (ISWC2013).

The chairs of the workshop are Tomi KauppinenJun ZhaoPaul GrothCarsten KeßlerLine C. PouchardCarole GobleYolanda GilMarieke van Erp and Jacco van Ossenbruggen.

Please check the LISC2013 web site for more information about submission themes and deadlines.

Looking forward to rejoin the Linked Science community in Sydney!

 

TEACH Vocabulary Extended

We just published a new version of the TEACH vocabulary, which enables richer descriptions of courses as Linked Data. The vocabulary now supports quite a few new features, including classes and properties for defining assignments of courses. Here are some examples which illustrate the use of some of the new classes and predicates:

Moreover, now TEACH has quite a few classes as well: CourseAssignmentMaterialTeacherStudentGroupStudentModuleStudyProgram,
LectureBuilding and Room. Future work includes fine tuning of domain and range specifications. Moreover, classes and  properties will be better linked to other vocabularies.

Tutorial on Analyzing and Visualizing Linked Data with R at ESWC2013

Tutorial on Analyzing and Visualizing Linked Data with R 2013 (LODR2013)

When: May 26 or May 27, 2013
Where: Montpellier, France
Duration: half-day
Collocated with the Extended Semantic Web Conference (ESWC2013)—Semantics and Big Data

The openly available R package SPARQL allows to directly connect to Linked Data and use the SPARQL querying language for selecting interesting part of data for analysis. Thus it enables to meet massive and rich data sets with the analytical power of the R language and environment.

This approach and tools contribute to Linked Science and Open Science movements to support the transparency of science and to conduct transdisciplinary research.

In this tutorial we will introduce the idea and concepts about Linked Science, and show via illustrative examples about how to practically query and analyze Linked Data from within R environment for visual and statistical analysis. Tutorial materials will be published online.

Teachers of the tutorial are

Tutorial on Interconnecting Linked Open Data and R on November 29th in Paris

When: November 29th, 2012
Where:  Centre de Recherche des CordeliersParis, France
Duration: 4h
Collocated with International workshop on the Semantic Web applications and tools for Life sciences (SWAT4LS)

The openly available R package SPARQL allows to directly connect to Linked Data and use the SPARQL querying language for selecting interesting part of data for analysis. Thus it enables to meet massive and rich data sets with the analytical power of the R language and environment.

This approach and tools contribute to Linked Science and Open Science movements to support the transparency of science and to conduct transdisciplinary research.

In this tutorial we will introduce the idea and concepts about Linked Science, and show via illustrative examples about how to practically query and analyze Linked Data from within R environment for statistical analysis.

Tutorial materials:
Teachers of the tutorial are
  • Dr. Tomi Kauppinen (Department of Media Technology, Aalto University School of Science, Finland),
  • Dr. Willem Robert van Hage (VU University Amsterdam, the Netherlands) and
  • Benedikt Gräler (University of Münster, Germany).
  • Biniyam Tilahun (University of Münster, Germany)

Nine Papers Accepted for the Linked Science 2012

We are pleased to announce that we accepted the following papers for publication and presentation at the 2nd International Workshop on Linked Science 2012—Tackling Big Data (LISC2012):

The selection process was competitive with the acceptance rate of 47%: we received 19 submissions and accepted these 9 papers.

The 2nd International Workshop on Linked Science 2012—Tackling Big Data (LISC2012) will be held within the 11th International Semantic Web Conference (ISWC2012) in Boston, USA on November 12th, 2012.

The more detailed workshop programme will be announced in September at the workshop web pages at LinkedScience.org/events/lisc2012/ and via twitter hashtag  #LISC2012 and twitter feed @LinkedScience.

 

Tutorial on Linked Science at EKAW2012

Tutorial on Linked Science 2012 (TOLSCI2012)

When: October 7th, 2012
Where: Galway City, Ireland
Tutorial at the International Conference on Knowledge Engineering and Knowledge Management (EKAW 2012)

Tutorial URI: http://linkedscience.org/events/tolsci2012/

Linked Science is an approach to interconnect scientific assets in order to enable transparent, reproducible and transdisciplinary research. Tutorial on Linked Science 2012 (TOLSCI2012) will be a half day tutorial comprising of different aspects of Linked Science: semantic description of scientific data (e.g. observations and measurements), existing vocabularies, bridging of statistical analysis and Linked Data, and license and copyright issues about data.

Through exercises and the introductory talk the aim of TOLSCI2012 is to stimulate transdisciplinary discussions among researchers and publishers from various backgrounds on semantic integration of scientific information.

The main part of the tutorial will concentrate in a hands-on session in order to learn how to describe, access and analyze scientific data about scientific observations, and especially how to get only that part of data which is of interest for a given research question.

We will teach

  • how Linked Data solves the access part, and
  • how SPARQL allows to query only a subset of the data.

In particular, the participants will learn in a hands-on session

  • how Linked Data can be connected with the help of the SPARQL package for statistical analysis in R, and
  • how and which visualization techniques and tools are available for interacting with the data.

All tutorial materials will be published online.

To register, visit: http://ekaw2012.ekaw.org/Registration.html

Teachers

  • Tomi Kauppinen is a postdoctoral researcher in the Muenster Semantic Interoperability Lab (MUSIL) at the Institute for Geoinformatics at the University of Muenster, Germany. He holds a PhD from the Aalto University, Finland with a thesis on reasoning about change and time. He chaired the First International Workshop on Linked Science 2011 at the International Semantic Web Conference (ISWC2011), the track on Interoperability and Semantics of the Geoinformatik 2011 conference, and led the breakout session for Vocabularies for Science at Science Online London 2011 organized by Nature. His research focuses on spatiotemporal and semantic modeling of processes such as deforestation, extreme weather events, changes in administrational borders, digital cultural heritage, and linked science. His current projects include opening and linking of scientific and educational data in LinkedScience.org-project and in the Linked Open Data University of Muenster (LODUM). He coordinates activities as a post-doc in the International Research Training Group on Semantic Integration of Geospatial Information.
  • Willem Robert van Hage is a researcher in the field of information integration on the web. His main research topics in the past years are geospatio-temporal semantics, ontology alignment, and ontology learning. He is a co-organizer of the Detection, Representation, and Exploitation of Events in the Semantic Web workshop (DeRiVE 2011) and since 2006 he has been a co-organizer of the Ontology Alignment Evaluation Initiative (OAEI), a collaborative benchmarking effort for the evaluation of on- tology alignment techniques. He has led the development of the Simple Event Model (SEM), an ontology for the description of events. In the past years he has worked on the combination of Semantic Web reasoning (RDF(S), OWL) and geospatio-temporal reasoning, developing a spatiotemporal indexing package for the popular SWI-Prolog programming language, which has led to a best paper award at the EKAW 2010 conference, and Semantic Web packages for SPARQL querying and RDF storage for the R statistical programming language. He is the coordinator of the interfaculty Web Science minor at the VU University Amsterdam.

Demo and Poster today @ESWC2012

Today on May 29th a poster and a demo will be presented at the 9th Extended Semantic Web Conference (ESWC2012) related to Linked Science and LODUM projects. The poster and the demo will be presented next to each other at the Posters and Demos session for your convenience.

The poster

is about  Sharing and Analyzing Remote Sensing Observation Data for Linked Science and presents the Linked Brazilian Amazon Rainforest project. Below is a figure illustrating how to interact with these large amounts of Linked Spatiotemporal Data to support understanding of the ecological, social and economical dimensions of sustainable development. For more information see also the Triangle of Sustainability project.

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The demo

is about the Linked Open Data University of Münster – Infrastructure and Applications (see also the data portal)The idea is to open up the university’s data silos, integrate the data, and make it easy to build applications on top of the data collection. The productivity map shown as a video below is an example of such an application. It renders the university buildings in 3D—the building height indicates the number of publications written by researchers working in the respective building. The KML file is also available for download—just open it up in Google Earth to explore the productivity map.

 

2nd International Workshop on Linked Science 2012—Tackling Big Data will be arranged in Boston, USA

The 2nd International Workshop on Linked Science 2012—Tackling Big Data (LISC2012) will be organized in November, 2012 in Boston, USA.

LISC2012 will be collocated with the 11th International Semantic Web Conference (ISWC2012). The submission deadline for the papers is July 31th, 2012.

Organizers of LISC2012 are

  • Tomi Kauppinen, Institute for Geoinformatics, University of Muenster, Germany. (co-chair)
  • Line C. Pouchard, Scientific Data Group, Oak Ridge National Laboratory, US Department of Energy, USA. (co-chair)
  • Carsten Keßler, Institute for Geoinformatics (ifgi), University of Muenster, Germany. (co-chair)
  • Paul Groth, VU University of Amsterdam, the Netherlands.
  • Natasha Noy, Stanford Medical Informatics, USA
  • Eric G. Stephan, U.S. Department of Energy, Pacific Northwest National Laboratory in Richland, Washington, USA
  • Jun Zhao, Life Science Interface, University of Oxford

More information is now available at the web page of the LISC2012 at LinkedScience.org/events/lisc2012.

You may also follow the twitter feed @LinkedScience and hashtag #LISC2012 for announcements and discussions.