Archive for category bioinformatics
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
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
- 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 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.
- Phillip Lord, Newcastle University
- Susanna-Assunta Sansone, EBI
- Nigam Shah, Stanford
- Matt Cockerill, BioMedCentral
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.
Submission templates are available from the Bio-Ontologies website.
I described in an earlier post that data sharing in Neuroscience is relatively non-existent. Some commentary on the subject has appeared since then via the 2007 SfN Satellite Symposium on Data Sharing entitled Value Added by Data SharingLong-TermPotentiation of Neuroscience Research, published in Neuroinformatics. I was also excited to see an article published last week Data Sharing for Computational Neuroscienc, also in Neuroinformatics. However, there is a caveat or two. Apart from ignoring all the data representation issues presented in other domains such as bioinformatics, the re-use of data models such as FuGE, or contribution to ontology efforts such as OBI, all these articles are not open access! How ironic, or should that be how embarrassing. Phil also covers this issue in his blog.
Oh well, looks as if there is still a challenge in the domain of Neuroscience for access to valuable insights into information flow in the brain. Who want to know how the brain works anyway? You can always pay $32 to springer if you want to find out.
When finnished, I would have liked it to be published some where like Nature Preceedings, however they only accept proprietary Microsoft files and pdfs rather than XML documents. I also though of creating a Google code project for it, but it seems quite elaborate for something nobody else would be contributing to and once completed would be rather static. Any suggestions are very welcome.
A new blog has appeared over the last month entitled e-science ramblings. This blog is edited by Hugo Hiden who is the technical director of the North Eastern Regional e-Science centre which is based at Newcastle University.
As described in his first post:
The reason for this blog is, primarily, to document my experiences with writing a prototype e-Science research platform using Microsoft tools instead of the more traditional approach of fighting with Open Source. This way is easier, supposedly. The task I have set myself is to recreate, at a basic level, the software being developed by the CARMEN project.
I think this should be an interesting read both on the technical aspects and the usability of Microsoft products compared to open source software for e-science.
The full complement of the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI), Minimum Information About a Proteomics Experiment (MIAPE), recommended reporting guidelines are now available for community review on the Nature Biotechnology website.
The manuscripts range from the definition of the MIAPE concept to the individual guidelines themselves which cover, Mass Spectrometry, Mass Spectrometry Informatics, Gel Electrophoresis and Molecular Interaction experiments. A further paper on the PSI protein modification ontology (PSI-MOD) is also listed.
Several other Minimum reporting requirements are also listed from other domains such as genome sequences (MIGS) and in Situ Hybridization and Immunochemistry (MISFISHIE).
There is also a paper on the Functional Genomics Experiment Model (FUGE) which is an “extensible framework” or data model for standards in functional genomics, although equally extensible to most scientific experiments.
As this process of community review, hosted on the Nature Biotech website, is a relatively new process and open to anyone, both identified or anonymous, I would encourage anybody with the relevant knowledge to comment on the papers. A greater response from the community ultimately means the guidelines are actually representative of the domain and technology they represent.