martedì 14 dicembre 2010

SWAT4LS-2010 aftermath

SWAT4LS-2010 took place in Berlin on Dec. 10th, preceded two tutorials days on the 8th and 9th. Proceedings of the workshop are being assembled on CEUR and Nature Precedings (provisional proceedings are available here). Slides from the presentations and from tutorials are being posted on Nature Precedings.
We will post here more details on this edition of the workshop.

giovedì 18 novembre 2010

Progam is out!

The list of selected communication at the 2010 editions of SWAT4LS is online.

lunedì 15 novembre 2010

Hackathon is sold out

The (mini)hackathon / tutorial day at SWAT4LS is now full.
There are still less then ten places for the workshop, and a few more for the tutorial day on Thursday.

Soon we will publish a provisional-final program!

lunedì 1 novembre 2010

Ulf Leser to participate at the SWAT4LS panel

Ulf Leser will joing Chris Bizer, Jonas Almeida and Chris Baker for the SWAT4LS panel discussion.

The tentative title of the panel discussion is: "The Future of Semantic Web and Linked data in Life Sciences"

lunedì 11 ottobre 2010

Deadline for paper submission extended

Due to several requests,

we are extending the papers submission deadline to Friday 15th.
We would invite authors to submit an abstract by their original deadline (Ocrober 12th), marking it as provisional.
A few additional days may be arranged for exceptional cases. Please contact

lunedì 20 settembre 2010

Registrations to SWAT4LS are now open

Registrations to SWAT4LS are now open and accessible at:

Places are limited. We suggest to book in advance. A limited number of additional places will be made available after the early registration deadline.

sabato 11 settembre 2010

Ontotext to sponsor SWAT4LS 2010

SWAT4LS is generously sponsored by Ontotext

Ontotext is a leading technology company that develops robust engines for analysis and management of text and data. It is a proven, competent and cost-effective, partner in:

  • Development of tools and solutions based on semantic technologies

  • Software engineering, performance optimization, ontology design

  • Analysis, evaluation, feasibility studies based on cutting-edge expertise

Our life sciences and health care platform facilitates semantic integration of heterogeneous data sources by employing inference rules and state-of-the-art text mining algorithms. The platform is capable of telling whether “kidney malfunction” is an adverse event or a symptom and will not be confused by the multiple coding systems. We offer customer specific information extraction services that will enrich you internal company knowledge with new facts that are “hidden” in the unstructured experimental data, clinical trials and literature. Our platform supports very powerful search that enable efficient reasoning over structures and extracted information, thus fostering discovery of previously unidentified correlations between varied biological, medical and chemical entities.

Ontotext delivers highly efficient and scalable semantic infrastructure that significantly reduces the cost of combining internal company knowledge with public information. Building a system to integrate and efficiently query 5 billion statements of semantic data on a USD 10K hardware is no longer a dream – it is Ontotext!

Ontotext /
135 Tsarigradsko Shosse, Sofia 1784, Bulgaria
T: +359 2 974 6160,

domenica 5 settembre 2010

Jonas Almeida to Keynote at SWAT4LS

Jonas Almeida will give a keynote at SWAT4LS.

Title: Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).

Summary: In response to the increasingly data intensive and increasingly heterogeneous sources involved in large scale biomedical initiatives, such as The Cancer Genome Atlas (TCGA), NCI's Specialized Programs of Research Excellence (SPOREs) and NHLBI's Proteomics Centers, we have had to move to abstract logical frameworks to develop applications that make use of more distributed computational resources. As a result, we embarked on a 6 year effort to increase the abstraction level of our data structures by relying on the diadic predicated nature of RDF (Wang 2005) to facilitate both our ability to represent fast changing biological data and to let the domain experts themselves participate in its constant re-definition (Almeida 2006). Fast forward to 2010 and a Knowledge Organization System, S3DB (Almeida 2010) is in place as a logical framework for a computational ecosystem assessable via SPARQL endpoints, such as In the process we found out, like many others, that the collaborative involvement of domain experts puts peculiar pressures on the software development environment. Specifically, that it clashes with the conventional stand alone executable application model we were used to. In response we moved to use code injection (javascript) and other distributed features of the modern web browser as a development platform, as in clinical trial initiatives such as and visualization of biomolecular data as in, and distributed computing in

Wang X, R Gorlitsky, and JS Almeida (2005) From XML to RDF: How Semantic Web Technologies Will Change the Design of ‘Omic’ Standards. Nature Biotechnology, Sep;23(9):1099-103 [PMID:16151403].

Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa, P Eleutério, JA Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) Data integration gets 'Sloppy'. Nature Biotechnology 24(9):1070-1071. [PMID:16964209].

Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315]

martedì 31 agosto 2010

A special issue in BMC Bioinformatics will be dedicated to the SWAT4LS 2010 workshop

We are planning to edit a special issue in BMC Bioinformatics dedicated to the 2010 edition of the workshop. The call for this special issue will be open to all authors of accepted contribution to SWAT4LS.

venerdì 20 agosto 2010

venerdì 13 agosto 2010

Christopher Baker to present a keynote at SWAT4LS 2010

Christopher Baker: A renaissance for the point mutation: from legacy data to semantic web service

Christopher Baker is currently the Innovatia Research Chair and Associate Profesor at the University of New Brunswick, Canada. Up until 2008 he was the head of the Semantic Technology Group at the Data Mining Department, I2R, (A-STAR) where his team developed KnowleSuite, now licensed from I2R by Knorex Pte Ltd, in Singapore. Chris has considerable experience in Biomedical Informatics and Semantic Technologies and was co-editor of the book Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences published by Springer in 2007. In 2005, his team won the Semantic Web Challenge (2nd prize) at the International Semantic Web Conference. He now serves on the Editorial Board of the Journal of Biomedical Semantics and is an invited expert for the W3C's Semantic Web in Health Care and Life Sciences Interest Group (HCLSIG). Chris holds PhD in Microbiology from the University of Wales, Cardiff (1996).

Further keyonotes are awaiting confirmation and will be announced later

martedì 27 luglio 2010

SWAT4LS is endorsed by NCBO and the W3C consortium

The 2010 edition of SWAT4LS is endorsed by The national center for Biomedical Ontologies and by the W3C consortium.

lunedì 26 luglio 2010

sabato 24 luglio 2010


A preliminary versione of the scientific program committee has been announced.
SWAT4LS is endorsed by the regional W3C office.

domenica 6 giugno 2010

SWAT4LS-2010 Website is on

A preliminary website with information for SWAT4LS 2010 is online at:

More information will be published as soon as available.

venerdì 7 maggio 2010

Announcing SWAT4LS-2010, December 10th, Berlin

The third edition of SWAT4LS (Semantic Web Applications and Tools for Life Sciences) will be held in Berlin, on Friday December 10th, 2010.
We are planning to propose 1-2 days of tutorials and related events (8-9 December). More information will be coming shortly.

venerdì 19 febbraio 2010

The call for the special issue in JBS is open

The call for the special issue of the BMC Journal of Biomedical Semantics dedicated to the SWAT4LS workshop is now open. Authors of contributions at the workshop and keynotes have been invited to submit an extended version of their submission or presentation, revised in the light of the discussion held at the workshop. The deadline for submission is March 22, 2010, and the submissions are managed via easychair.

All authors have been provided all necessary details. For any question, please write to info at

mercoledì 20 gennaio 2010

SWAT4LS-09 Proceedings are out!

Proceedings of the 2009 edition of SWAT4LS are out and available at: