Semantic Web Application and Tools 4 Life Science

BMC Bioinformatics special issue is out

2012-01-25T09:49:00.001-08:00

The BMC Bioinformatics special issue dedicated to the 2010 edition of SWAT4LS is now out and available at http://www.biomedcentral.com/bmcbioinformatics/supplements/13/S1.

SWAT4LS Submissions view

2011-12-12T15:45:00.001-08:00

In time, we will post the ratings and impressions on the workshop. In the meantime, here is the visualization of words in accepted submissions!

The SWAT4LS-2011 Program is out!

2011-11-14T16:54:00.000-08:00

Still, missing a poster and demo list... but the full program of SWAT4LS is out and available at: http://www.swat4ls.org/workshops/london2011/scientific-programme/

SWAT4LS Posters to be deposited in the Faculty of 1000

2011-10-04T07:50:00.000-07:00

The SWAT4LS Workshop 2011 , in cooperation with Faculty of 1000 (http://f1000.com/), invites poster/oral presenters at this meeting to deposit their poster(s)/slides(s) into the new open access poster repository, F1000 Posters (http://posters.f1000.com/) to enable those who could not make the meeting to see your novel work. F1000’s expert Faculty of 10,000 members will then view these submissions to identify those they wish to select for positive evaluation in the award winning F1000 service. To deposit your poster, simply go to http://posters.f1000.com/deposit and upload your poster file.

Proceedings of SWAT4LS in ACM

2011-09-29T09:24:00.000-07:00

The proceedings of SWAT4LS-2011 will be published by ACM. SWAT4LS is now co-organized with ACM (Special Interest Group in Bioinformatics).
This takes the place of CEUR proceedings, and will require a change in the formatting style, from LNCS to ACM. Details will be provided on the website.

SWAT4LS is now in cooperation with ACM

2011-09-15T07:39:00.000-07:00

SWAT4LS is now in cooperation with ACM (ACM Bioinformatics SIG)

Registrations to SWAT4LS are now open!

2011-09-13T12:08:00.000-07:00

Click Here to Register

Online event registration with TicketLeap

Registration to the hackathon is handled separately through the DevCSI website.

Submissions are open

2011-09-13T11:07:00.000-07:00

Submission to SWAT4LS-2011 are now open at https://www.easychair.org/conferences/?conf=swat4ls2011.

The deadline for papers submission is October 7th, the deadline for Poster and Demos submission is October 31st.

Prof. Douglas Kell to keynote at SWAT4LS

2011-07-27T17:19:00.000-07:00

Prof. Douglas Kell (1 - 2) will present a short keynote at SWAT4LS.

Prof. Wendy Hall to Keynote at SWAT4LS

2011-06-24T09:36:00.001-07:00

Prof. Wendy Hall will be a keynote at swat4ls 2011.

Tetsuro Toyoda to Keynote at SWAT4LS-2011

2011-06-13T10:00:00.000-07:00

We are delighted to announce that Tetsuro Toyoda, Director of the Bioinformatics And Systems Engineering division of RIKEN (Yokohama), Japan, will keynote at SWAT4LS 2011.

TITLE: Future Biology is Semantic Information Science
Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 7.5 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System or a “Virtual Laboratory Centre,” providing numerous virtual labs for semantic-web-based data management and collaboration of various purposes. SciNetS.org is thus designed to discover novel relationships between data, because automatic intelligent agent generates for each data item a summary content displaying the linked information via Semantic Web. We demonstrate we successfully used the SciNetS interface across 26 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers.

Tetsuro Toyoda was born in Tokyo, Japan, in 1968. He graduated from the Faculty of Pharmaceutical Sciences at the University of Tokyo in 1992, and obtained his PhD in 1997 from the same university. He started as a researcher at the Institute of Medical Molecular Design in 1997, and joined RIKEN as team leader in the Genomic Sciences Center in 2001. He became director of the RIKEN Bioinformatics and Systems Engineering Division when it was established in 2008. His expertise is in bioinformatics and computer-aided rational design of biomolecules, including rational database-supported drug design based on protein structural information and rational genome design in synthetic biology for biomass engineering. He promotes Japan’s database integration projects as a member of several national database committees.

SWAT4LS-2011

2011-06-05T17:34:00.000-07:00

Pre announcement:
SWAT4LS 2011 will be held in London, Dec. 7-9 2011.
It will be articulated in 1 day hackathon, 1 day tutorial and 1 day workshop.
We are finalizing the venue(s) (central London) and the details of the Hackathon (co-organized with the Open Knowldge Foundation Working Group), Tutorials and Keynotes.
More information will be posted soon on this blog. You can also follow a new lanyrd page:
http://lanyrd.com/2011/swat4ls/

Special issue in Journal of Biomedical Semantics is out!

2011-03-07T05:19:00.000-08:00

The special issue in the Journal of Biomedical Semantics dedicated to the SWAT4LS-2009 workshop has been published today and is available here.

The call for SWAT4LS special issue in BMC Bioinformatics is now open

2011-03-03T16:43:00.000-08:00

We are pleased to inform you that the call for the special issue of BMC Bioinformatics dedicated to the SWAT4LS-2010 workshop is now open.
As a contributor to this workshop, you are invited to submit a new version of your contribution, revised and extended according to the discussion held at the workshop.

The agenda for this call is the following:

Paper registration (abstracts only): 15th April

Paper submission deadline: 22nd April

Notification of acceptance: 13th June

Camera ready papers: 4th July

Submissions can be sent using easychair.org (http://www.easychair.org/conferences/?conf=swat4ls2010bmcbioinf) and should be formatted according to BMC guidelines. There is not a page limit for submissions, but we would ask you not to exceed 25 pages, unless necessary.

SWAT4LS Proceedings are out!

2011-02-08T10:21:00.000-08:00

The Proceedings of the 2010 edition of SWAT4LS are now available at: http://CEUR-WS.org/Vol-698/

SWAT4LS-2010 aftermath

2010-12-14T08:57:00.000-08:00

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.

Progam is out!

2010-11-18T08:03:00.000-08:00

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

Hackathon is sold out

2010-11-15T05:44:00.000-08:00

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!

Ulf Leser to participate at the SWAT4LS panel

2010-11-01T06:54:00.000-07:00

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"

Deadline for paper submission extended

2010-10-11T09:33:00.000-07:00

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 info@swat4ls.org

Registrations to SWAT4LS are now open

2010-09-20T03:36:00.001-07:00

Registrations to SWAT4LS are now open and accessible at: http://swat4ls2010.eventbrite.com/.

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

Ontotext to sponsor SWAT4LS 2010

2010-09-11T08:37:00.000-07:00

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 / www.ontotext.com
135 Tsarigradsko Shosse, Sofia 1784, Bulgaria
T: +359 2 974 6160, info@ontotext.com

Jonas Almeida to Keynote at SWAT4LS

2010-09-05T09:40:00.000-07:00

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 http://tcga.s3db.org. 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 http://aguia.googlecode.com and visualization of biomolecular data as in http://cnviewer.googlecode.com, and distributed computing in http://quanah.googlecode.com.

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]

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

2010-08-31T08:29:00.001-07:00

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.

Franz Inc. to sponsor SWAT4LS 2010

2010-08-20T02:24:00.000-07:00

Franz Inc. is sponsoring SWAT4LS 2010

Christopher Baker to present a keynote at SWAT4LS 2010

2010-08-13T08:41:00.000-07:00

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

SWAT4LS is endorsed by NCBO and the W3C consortium

2010-07-27T16:25:00.000-07:00

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

7th Berlin Semantic Web Meetup to be held in conjunction with SWAT4LS

2010-07-26T10:21:00.000-07:00

The 7th Berlin Semantic Web Meetup - Semantic Healt Care and Life Sciences will be held in conjunction with SWAT4LS, on Thursday Dec 9th, starting at 17:00.

SWAT4LS News

2010-07-24T20:20:00.000-07:00

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

SWAT4LS-2010 Website is on

2010-06-06T07:40:00.001-07:00

A preliminary website with information for SWAT4LS 2010 is online at: swat4ls.org/2010.

More information will be published as soon as available.

Announcing SWAT4LS-2010, December 10th, Berlin

2010-05-07T01:56:00.000-07:00

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.

The call for the special issue in JBS is open

2010-02-19T07:30:00.000-08:00

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 swat4ls.org

SWAT4LS-09 Proceedings are out!

2010-01-20T06:52:00.001-08:00

Proceedings of the 2009 edition of SWAT4LS are out and available at: http://ceur-ws.org/Vol-559.

SWAT4LS aftermath

2009-11-23T09:16:00.001-08:00

The 2009 edition of SWAT4LS was held on the November 20th in Amsterdam.
It was attended by 56 participants.
We collected some feedback (from about 60%) of the participants.

The scientific quality of the workshop was rated very good (top evaluation) from 28% , good by 66% and average by 6% of participants.

The most appreciated aspects have been the keynotes, the constructive atmosphere, the content and the limited size.

The most problematic aspects were related to the organization, in particular the difficulty to find the place (construction site) and the delays. These last point is related to another frequent complaint: the tight timing.

A vast majority of people indicated that they would like to see a longer workshop (2 days) with a tutorial session.

Among desiderata for the next workshop is in primis more technical/"how to" related content, which seems to fit the request for a tutorial session.

All participants expressed (if possible) the intention to participate to the next edition of the workshop.

Registrations are open!

2009-10-24T18:15:00.000-07:00

Registrations to SWAT4LS are now open. You can find instructions to register on the SWAT4LS website and on this website.
While registrations will be open up to and during the event (registrations on site are possible), we can only assure the availability of conference bags and/or related items for "very" early registrations.

The BMC Bioinformatics Supplement for SWAT4LS is out!

2009-10-01T04:29:00.000-07:00

The BMC Bioinformatics supplement dedicated to the 2008 edition of SWAT4LS (Semantic Web Applications and Tools for Life Sciences) has been published, and is accessible here.

Special issue in the Journal of Biomedical Semantics dedicated to SWAT4LS

2009-09-17T14:19:00.000-07:00

A selection of contribution from SWAT4LS will be invited to submit to a special issue if the new BMC Journal of Biomedical Semantics dedicated to the workshop. The call will be open in the beginning of 2010 (to be defined) for all participants to SWAT4LS (accepted papers, posters and demos).

SWAT4LS extended deadlines

2009-09-16T06:08:00.000-07:00

The deadlines for the submissions to SWAT4LS have been extended:

Submission openinig: 1 September 2009
Intention to submit (abstract only): 5 Ocober 2009
Submission of oral communications (papers): 12 October 2009
Submission for posters and demos: 15 October 2009
Communication of acceptance: 28 October 2009
Camera ready: 13 November 2009

SWAT4LS receives support from VL-e and NBIC

2009-09-16T06:05:00.000-07:00

The 2009 edition of SWAT4LS will be supported by the Virtual Laboratory for e-Science and by the Netherland Bioinformatics Center.

Keynote Speakers

2009-08-24T07:47:00.000-07:00

The keynote speakers for the 2009 edition of SWAT4LS will be:

Barend Mons,
Erasmus Medical Center, Rotterdam and Leiden University Medical Center

Michael Schroeder,
Biotechnology Center TU Dresden

Alan Ruttenberg,
Science Commons

Announcing SWAT4LS09

2009-07-28T15:46:00.000-07:00

SWAT4LS
Semantic Web Application and Tools for Life Sciences

SWAT4LS is a workshop that provides a venue to present and discuss benefits and limits of the adoption of Semantic Web technologies and tools in biomedical informatics and computational biology.
The first edition, held in Edinburgh in November 2008, received 40 submissions, of which 13 were accepted as oral communications, and part of them included in a special issue of BMC Bioinformatics dedicated to the workshop (in preparation).
The second edition of SWAT4LS will provide the same open and stimulating environment that brought together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and real experiences in the use of Semantic Web technologies in Life Sciences.

SWAT4LS Call for Papers

Topics of interest include, but are not limited to:

Standards, Technologies, Tools for the Semantic Web
    Semantic Web standards and new proposals (RDF, OWL, SKOS,... )
    Biomedical Ontologies and related tools
    Formal approaches to large biomedical knowledge bases
Systems for a Semantic Web for Bioinformatics
    RDF stores, Reasoners, query and visualization systems for life sciences
    Semantic biomedical Web Services
    Semantics aware Biological Data Integration Systems
Existing and prospective applications of the Semantic Web for Bioinformatics
    Semantics aware application tools
    Semantic collaborative research environments
    Case studies, use cases, and scenarios

For more details visit the SWAT4LS-09 website.