In The News Papers Semantics and Ontologies

I Spy an Ontology Helper

Here is what they have to say about their product, OntologyWidget, in the abstract (hosted on BioMed Central) from BMC Bioinformatics:

"We have developed OntologyWidget, an easy-to-use ontology search and
display tool that can be used on any web page by creating a simple html
description. OntologyWidget provides a rapid auto-complete search
function paired with an interactive tree display. We have developed the
web service layer that communicates between the web page interface and
a database of ontology terms. We are currently storing and maintaining
40 of the ontologies on the site as well as
a few others."

It piqued my interest, and so I had a play with their "sandbox" website. I was interested, as I'm part of the development team for SyMBA, a multi-omics high-throughput data archive. However, we plan to make OBI available to our users, which is in OWL format, and so OntologyWidget wouldn't be useful "out of the box". However, I like that someone's done what I'd have to do in a web front end anyway, which would save me some hassle if it can be made to work with OWL files. It's released with the MIT Open Source License, which I'm not all that familiar with myself, but which (one assumes) means that others can work on it. The other worry I have is that the paper has only just been published, yet their website states that: "Current version is 1.00. Last updated November 6 2006 – see included documentation for details
". So, perhaps they are updating the ontologies weekly (as they state in the paper), but they don't seem to have updated the code in 10 months or so. Perhaps it's an error on the web page.

I have to say that anything that makes adding ontology terms more easily usable is a fantastic idea, and I'm really glad to see it. We need to have more and easier usage of ontologies. I'll have a little look into this, and see if I like it.

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Meetings & Conferences Papers Standards

eGenomics III GSC Meeting Report Published

The 3rd Genomic Standards Consortium meeting report  has been published by Comparative and Functional Genomics. There is more information available from the GSC blog.

The aim of the Genomic Standards Consortium (GSC) is to support the community-based development of a genomic standard that
captures a richer set of information about complete genomes and metagenomic datasets. The GSC is currently working together towards the "Minimum Information about a Genome Sequence" specification.

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CISBAN Papers Software and Tools Standards

Newcastle University Technical Report: CISBAN DPI

A Technical Report for the School of Computing Science of Newcastle University was released last month describing the CISBAN DPI, an implementation of the FuGE Milestone 3 STK. You can find and download that technical report here:

The Abstract follows:

The Centre for Integrated Systems Biology of Ageing and Nutrition has
developed a Data Portal and Integrator (CISBAN DPI) that is based on
the FuGE Object Model and which archives, stores, and retrieves raw
high-throughput data. Until now, few published systems have
successfully integrated multiple omics data types and information about
experiments in a single database. The CISBAN DPI is the first published
implementation of FuGE that includes a database back-end, expert and
standard interfaces, and utilizes a Life Science Identifier (LSID)
Resolution and Assigning service to identify objects and provide
programmatic access to the database. Having a central data
repository prevents deletion, loss, or accidental modification of
primary data, while giving convenient access to the data for
publication and analysis. It also provides a central location for
storage of metadata for the high-throughput data sets, and will
facilitate subsequent data integration strategies.


Functional Genomics, High-Throughput
Experiments, FuGE, LSID, Experimental Workflows, Databases, Data
Standards, Data Sharing, Metadata, Data Integration.

CS-TR: 1016 Implementing the FuGE Object Model: a Systems Biology Data Portal and Integrator
Lister, A. L., Jones, A. R., Pocock, M., Shaw, O., Wipat, A.
School of Computing Science, Newcastle University, Apr 2007

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