Archive for category semantic web

The Semantic Web of Life Science

This summary was born out of a question  on Twitter and percolated to FriendFeed, which was “Who is using RDF and integrating other resources at the minute and what are those resources? From this question, several resources were highlighted.

UniProt. The comprehensive resource of protein information is available as an RDF distribution and each Protein record has a corresponding RDF download option.

Phil pointed out Semantic Systems Biology, As systems biology is largely concerned with representing networks and interactions at a systems level, a language like RDF would seem an obvious choice to represent this type of knowledge, to aid semantic description and data integration.

Melanie pointed out the following resources such as Bio2RDF. This project aims to RDF-ize numerous public life-science resources using what they call a three step approach which they have developed. The following image illustrates some of the resources that are included in Bio2RDF.

Bio2RDF Cloud

Bio2RDF Cloud

The NeuroCommons project seeks to make all scientific research materials – research articles, annotations, data, physical materials – as available and as usable as they can be. As a result they have an RDF triple store which they encourage you to either contribute to or download and use.

For a more general overview of resources that exist as an RDF implementation, the Linked Open Data cloud provides a graphical summary of the resources that exists and the relationships between them.

If you know of any more life-science resources or projects using RDF, then please do comment below.  Egon has indicated he is working on RDF-ing the NMRShiftDB and ChEMBL’s Starlight, and Andrew Clegg is considering a project proposal involving RDF. As a result a very interesting discussion ensued on FF.

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CFP: Bio-Ontologies 2008: Knowledge in Biology

Call for Papers for Bio-Ontologies 2008. Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008.

Key Dates to remember:

  • Submission due: Friday 2nd May
  • Notifications: Friday 23rd May
  • Final Version Due: Friday 30th May
  • Workshop: Sunday 20th July

Introduction

Bio-Ontologies has existed as a SIG at ISMB for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year’s reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology.

So, for example:

  • Semantic and/or Scientific wikis.
  • Multimedia blogs
  • Folksonomies
  • Tag Clouds
  • Collaborative Curation Platforms
  • Collaborative Ontology Authoring and Peer-Review Mechanisms

are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies.

  • Biological Applications of Ontologies
  • Reports on Newly Developed or Existing Bio-Ontologies
  • Tools for Developing Ontologies
  • Use of Ontologies in Data Communication Standards
  • Use of Semantic Web technologies in Bioinformatics
  • Implications of Bio-Ontologies or the Semantic Web for drug discovery
  • Current Research In Ontology Languages and its implication for Bio-Ontologies

Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs DURING ISMB. Bio-Ontologies is on the Sunday parallel to the main conference.

Submissions

Submissions are now open and can be submitted through easychair.
Instructions to Authors

We are inviting two types of submissions.

Short papers, up to 4 pages.
Poster abstracts, up to 1/2 page.

Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic.

Organisers

  • Phillip Lord, Newcastle University
  • Susanna-Assunta Sansone, EBI
  • Nigam Shah, Stanford
  • Matt Cockerill, BioMedCentral

Programme Committee

The programme committee, organised alphabetically is:

  • Mike Bada, University of Colorado
  • Judith Blake, Jackson Laboratory
  • Frank Gibson, Newcastle University
  • Cliff Joslyn, Pacific National Laboratory
  • Wacek Kusnierczyk, Norwegian University of Science and Technology
  • Robin MacEntire, GSK
  • Helen Parkinson, EBI
  • Daniel Rubin, Stanford University
  • Alan Ruttenberg, Science Commons
  • Robert Stevens, University of Manchester
  • and the conference organisers.

Templates

Submission templates are available from the Bio-Ontologies website.

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goPubmed

In catching up with my reading lists of 2007 I was alerted to gopubmed via Deepak’s post. Gopubmed described itself as an ontology based literature search making use of both the Gene ontology and Mesh terms. There is also the ability to provide feedback or rather act as a curator for the search results. I have already noticed  some mis-match in author details.  In general though the interface  is a vast improvement on pubmed’s tiered interface and the ability to refine the searches looks interesting. I have added gopubmed to  my search engines within firefox and will have a play to see if it is any good. RSS feeds on search terms would be top of the wish list. Anybody used it in anger?

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Semantic Web for e-science

BMC bioinformatics has released a special issue supplement on the Semantic e-science for biomedicine. It contain six papers on “the-state-of-the-art”  concerning the use of semantic web technologies in the life-sciences or biomedicine.   The topics covered range from modelling networks and pathways to,  intriguingly “traditional Chinese Medicine”.

One of the papers Advancing translational medicine research with the semantic web presents an overview of the W3C Semantic Web Health Care and Life Sciences Interest Group (HCLSIG).  This paper describes the work of HCLSIG and a use-case example covering the achievements as well as the future directions of the group. Unlike many “Semantic Web” papers I have read before it presents a well grounded view of the technologies and challenges of the semantic web in biomedince and does not proclaim to solve the bio-data problem by applying a new set of technologies to the issues.

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