Chemical databases: curation or integration by user-defined equivalence?

There is a wealth of valuable chemical information in publicly available databases for use by scientists undertaking drug discovery. However finite curation resource, limitations of chemical structure software and differences in individual database applications mean that exact chemical structure equivalence between databases is unlikely to ever be a reality. The ability to identify compound equivalence has been made significantly easier by the use of the International Chemical Identifier (InChI), a non-proprietary line-notation for describing a chemical structure. More importantly, advances in methods to identify compounds that are the same at various levels of similarity, such as those containing the same parent component or having the same connectivity, are now enabling related compounds to be linked between databases where the structure matches are not exact

Extraction of Transcript Diversity from Scientific Literature

Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/

The impact of NQT induction programmes on the enhancement of teacher expertise, professional development, job satisfaction or retention rates: a systematic review of research literature on induction

This report is the result of a preliminary study undertaken by the Induction Review Group between January and March 2003 which essentially involved a mapping exercise to identify the range and type of research studies addressing the research question, ‘How does current research characterise the impact of induction programmes on new teachers in relation to enhancing teaching expertise, professional development, job satisfaction and retention rates?’ Results of the initial in-depth review are reported in Chapter 4. The Review Group plans further refinements of the mapping exercise and other in-depth reviews drawing on it

Combining quantifications for flexible query result ranking

Databases contain data and database systems governing such databases are often intended to allow a user to query these data. On one hand, these data may be subject to imperfections, on the other hand, users may employ imperfect query preference specifications to query such databases. All of these imperfections lead to each query answer being accompanied by a collection of quantifications indicating how well (part of) a group of data complies with (part of) the user's query. A fundamental question is how to present the user with the query answers complying best to his or her query preferences. The work presented in this paper first determines the difficulties to overcome in reaching such presentation. Mainly, a useful presentation needs the ranking of the query answers based on the aforementioned quantifications, but it seems advisable to not combine quantifications with different interpretations. Thus, the work presented in this paper continues to introduce and examine a novel technique to determine a query answer ranking. Finally, a few aspects of this technique, among which its computational efficiency, are discussed

Imagining Corporate Sustainability as a Public Good Rather than a Corporate Bad

Corporations have been criticized for their environmental misdeeds for over a century, so it is not surprising that many view corporate approaches to sustainability with skepticism. Reports of green-washing and other forms of misleading advertising by a handful of corporations only serve to reinforce this negative perception.The Kay Bailey Hutchison Center for Energy, Law, and Busines

The Evaluation Of Molecular Similarity And Molecular Diversity Methods Using Biological Activity Data

This paper reviews the techniques available for quantifying the effectiveness of methods for molecule similarity and molecular diversity, focusing in particular on similarity searching and on compound selection procedures. The evaluation criteria considered are based on biological activity data, both qualitative and quantitative, with rather different criteria needing to be used depending on the type of data available