Biomedical subjects

C Goble

Publications and source records attributed to C Goble.

4 recordsLinked to original sources

PubMed2001

A classification of tasks in bioinformatics.

MOTIVATION: This paper reports on a survey of bioinformatics tasks currently undertaken by working biologists. The aim was to find the range of tasks that need to be supported and the components needed to do this in a general query system. This enabled a set of evaluation criteria to be used to assess both the biology and mechanical nature of general query systems. RESULTS: A classification of the biological content of the tasks gathered offers a checklist for those tasks (and their specialisations) that should be offered in a general bioinformatics query system. This semantic analysis was contrasted with a syntactic analysis that revealed the small number of components required to describe all bioinformatics questions. Both the range of biological tasks and syntactic task components can be seen to provide a set of bioinformatics requirements for general query systems. These requirements were used to evaluate two bioinformatics query systems.

Computational Biology↗

PubMed1998

TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources.

The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a 'knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model. The Concept Model and Source Model provide a level of indirection that shields the user from source details, providing a high level of source transparency. Source independent, declarative queries formed from terms in the Concept Model are transformed into a set of source dependent, executable procedures. Query formulation, translation and execution is demonstrated using a working example.

Artificial Intelligence↗

PubMed1996

The mouse X-linked developmental mutant, tattered, lies between DXMit55 and Xkh and is associated with hyperkeratinization.

The X-linked mouse mutant phenotype, tattered (Td), is associated with prenatal lethality of males and has been mapped previously to the proximal region of the mouse X chromosome. We report here a refined position for Td and demonstrate that it lies in the approximately 0.9-cM interval between DXMit55 and Xkh. This enables us to predict that the human homologue lies either between CLCN5 and the evolutionary breakpoint that lies between GATA1 and PFC or distal to XK and proximal to the evolutionary breakpoint that lies between XK and DMD. Histological analysis of dorsal skin taken from 5-day-old heterozygous animals revealed that the mutation was associated with patches of hyperkeratinzation in the epidermis and in the hair follicles, accompanied by a mild inflammatory infiltrate in the underlying dermis.

Animals↗

PubMed1995

Survey and critique of time and medical records.

Although medical records are an example of a temporal database application, they are not satisfactorily supported by existing temporal and non-temporal data models. A new model and corresponding algebra is needed that can support the requirements of medical records. In this paper we identify the requirements medical records impose on a temporal model and highlight the discrepancies in existing models in light of these needs. We conclude the paper with a brief outline of how we approach the development of an extendible, temporal model for supporting medical record-based applications.

Medical Records↗