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"tag:"ontology""


Title and summary Date/time
1
Ontology-based data integration
As data repositories grow both in size and in number, data integration becomes an ever more pressing challenge. In bioinformatics data integration, bio-ontologies have long been used to assist in data integration pipelines mainly through their provision ...
26-Sep-2013
09:25:00
2
Exploiting disjointness axioms in semantic similarity
Semantic similarity is used in many applications to exploit the knowledge contained in ontologies and give a measure of relatedness for two ontology terms, say A and B. Typically, structural features of the ontology are used in this computation, such as ...
16-Sep-2013
14:06:00
3
The OntoQuery utility
Do you love the Protege DLquery facility and wish it was available in web-based form?Well, now it is!Recently developed and implemented for ChEBI, but compatible with most OWL bio-ontologies, OntoQuery is a little utility that offers syntax ...
06-Sep-2013
15:35:00
4
A very short introduction to BFO
Following on from my last post, here is an attempt to give an introduction to Basic Formal Ontology (BFO) that conveys the "bare minimum"basics needed for adoption, but avoids overly technical or philosophical language. Disclaimer:this post ...
30-Nov-2012
12:13:00
5
Challenges in ontology education and training for scientists
On the 9th September, Barry Smith and Igave a bio-ontology tutorial in advance of the ECCB conference held inBasel, Switzerland. We had a modest but comfortable group of around 20 registrants, which filled our allocated tutorial room very nicely, with ...
10-Oct-2012
13:19:00
6
Report on the ICBO Workshop on Mental Functioning Ontology
On the 22nd July 2012, a day before the start of the International Conference onBiomedical Ontology, we held a workshop devoted to discussion of standardisation, alignment and improvement of various ontology efforts in the domain of mental functioning. ...
07-Sep-2012
10:46:00
7
Report on the International Conference on Biomedical Ontology
Last week, the third International Conference on Biomedical Ontology was held at the medical university in Graz, Austria, thanks to the hospitality of local chair Stefan Schulz and his helpful team. The scientific conference chairs for the 2012 edition ...
31-Jul-2012
17:31:00
8
The OWLTools library
I'm a big fan of the OWLAPI. I've been using it for years to do useful things with OWLontologies in Java. It's a comprehensive and powerful reference library for working with all aspects of the OWL language, and the repository also includes ...
01-Jun-2012
12:20:00
9
The many faces of 'neurotransmitter'
Neurotransmitters are the molecular messengers that travel across synapses between neurons, allowing communication to take place between individual cells. They consist of small chemical entities -- mostly amino acids (also the building blocks of ...
16-May-2012
14:00:00
10
Different theories, one ontology?
Scientific ontologies aim to represent what is agreed upon by a consensus of scientific researchers. They aim to represent the best of scientific knowledge in a particular domain. (with thanks to xkcd) This objective is open to several objections. One ...
30-Apr-2012
17:11:00
11
ChEBI and MeSH
Every now and then, thankfully not that frequently, somebody asks me "What's the point of ChEBI, when MeSH already does chemical classification?"...
18-Apr-2012
09:45:00
12
Why good ontology is good for science
Ontology has become the method of choice throughout most of biology and biomedicine for constructing and maintaining standardisations of the terminology used in database annotations. This was the primary motivation for the development of the Gene ...
25-Mar-2012
18:28:00
13
BioAssay Ontology for EU-OPENSCREEN
On Thursday, 8th March, Ivisited the Center for Computational Science at the University of Miami. Note, not computer science but computational science:the center is a broad-ranging interdisciplinary think-tank for projects that need to use innovative ...
10-Mar-2012
13:12:00
14
5th Interdisciplinary Ontology conference in Tokyo
Tokyo is a magical place, no doubt about it. The bustle and size of the city renders surprising the beauty, cleanliness and overall pleasant atmosphere. The Japanese are wonderfully friendly and polite. The seafood is unrivalled. Almost every corner ...
27-Feb-2012
11:33:00