Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation
- P. Lord, R. Stevens, A. Brass, C. Goble
- Computer Science, BiologyBioinform.
- 1 July 2003
This paper investigates the use of ontological annotation to measure the similarities in knowledge content or 'semantic similarity' between entries in a data resource and shows a simple extension that enables a semantic search of the knowledge held within sequence databases.
Semantic Similarity Measures as Tools for Exploring the Gene Ontology
- P. Lord, R. Stevens, A. Brass, C. Goble
- Computer Science, BiologyPacific Symposium on Biocomputing
- 1 December 2002
Detailed investigation of the properties of these information content based measures are presented, and various properties of GO are examined, which may have implications for its future design.
TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources.
- P. Baker, A. Brass, S. Bechhofer, C. Goble, N. Paton, R. Stevens
- Computer ScienceProceedings. International Conference on…
- 1 January 1998
A prototype system has been developed that includes a knowledge base of biological terminology, a model of the underlying data sources (the Source Model) and a 'knowledge-driven' user interface that shields the user from source details, providing a high level of source transparency.
Making sense of microarray data distributions
- D. Hoyle, M. Rattray, R. Jupp, A. Brass
- BiologyBioinform.
- 1 April 2002
It is shown that mRNA transcription data from a wide range of organisms and measured with a range of experimental platforms show close agreement with Benford's law and Zipf's law, and useful biological findings may result from analyzing microarray data at the level of entire intensity distributions.
TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources
- P. Baker, A. Brass, S. Bechhofer, C. Goble, N. Paton, R. Stevens
- BiologyIntelligent Systems in Molecular Biology
- 1 July 1998
UNLABELLED
TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) is an application that allows biologists to ask rich and complex questions over a range of bioinformatics…
Identification of the complete coding sequence and genomic organization of the Treacher Collins syndrome gene.
- J. Dixon, S. Edwards, I. Anderson, A. Brass, P. Scambler, M. Dixon
- BiologyGenome research
- 1 March 1997
Observations suggest that phosphorylation may be important for its role in early embryonic development and that it may play a role in nucleolar-cytoplasmic shuttling.
Transparent access to multiple bioinformatics information sources
- C. Goble, R. Stevens, A. Brass
- Computer ScienceIBM Systems Journal
- 1 February 2001
A domain ontology for molecular biology and bioinformatics is used in a retrieval-based information integration system for biologists, in which the ontology is used both to drive a visual query interface and as a global schema against which complex intersource queries are expressed.
Secondary and tertiary structures of hyaluronan in aqueous solution, investigated by rotary shadowing-electron microscopy and computer simulation. Hyaluronan is a very efficient network-forming…
- J. Scott, C. Cummings, A. Brass, Y. Chen
- BiologyBiochemical Journal
- 15 March 1991
The hyaluronan twofold helix was shown by computer simulation and energy calculations to be sterically capable of extensive duplex formation, probably driven by interactions between the large hydrophobic patches on alternate sides of the tape-like polymer, forming stable aggregates at biological temperatures in water.
Identification of a key integrin-binding sequence in VCAM-1 homologous to the LDV active site in fibronectin.
- J. Clements, P. Newham, M. Humphries
- Biology, ChemistryJournal of Cell Science
- 1 August 1994
The identification of a key alpha 4 beta 1-binding sequence in both domains 1 and 4 of VCAM-1 as the tetrapeptide Ile-Asp-Ser-Pro (IDSP), which is homologous to the LDVP and IDAP fibronectin peptides, provides a molecular explanation for the promiscuity of ligand binding by alpha 4 alpha 1.
Identification of Novel Genes in Intestinal Tissue That Are Regulated after Infection with an Intestinal Nematode Parasite
- R. Datta, M. Deschoolmeester, C. Hedeler, N. Paton, A. Brass, K. Else
- BiologyInfection and Immunity
- 1 July 2005
It is demonstrated that the gene expression profile of infected gut tissue differs according to whether the parasite is expelled or not, and this may suggest a role for tryptophan metabolism in the parasite survival strategy.
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