Frank

Future Generation Computer Systems, Vol. 25, No. 5. (10 May 2009), pp. 528-540. Scientific workflow systems have become a necessary tool for many applications, enabling the composition and execution of complex analysis on distributed resources. Today there are many workflow systems, often with overlapping functionality. A key issue for potential users of workflow systems is the need to be able to compare the capabilities of the various available tools. There can be confusion about system functionality and the tools are often selected without a proper functional analysis. In this paper we extract a taxonomy of features from the way scientists make use of existing workflow systems and we illustrate this feature set by providing some examples taken from existing workflow systems. The taxonomy provides end users with a mechanism by which they can assess the suitability of workflow in general and how they might use these features to make an informed choice about which workflow system would... - Frank

The Microsoft Biology Foundation (MBF) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework. Currently it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological Web services such as NCBI BLAST. MBF is available under an open source license - Frank

Nucl. Acids Res. (15 September 2009), gkp760. Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model based on the principle of community intelligence. Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Previously, we described the creation of Gene Wiki stubs' for approximately 9000 human genes. Here, we describe ongoing systematic improvements to these articles to increase their utility. Moreover, we retrospectively examine the community usage and improvement of the Gene Wiki, providing evidence of a... - Frank

Genome Biology, Vol. 8, No. 4. (30 April 2007), 404. Gene annotation, as measured by links to the biomedical literature and funded grants, is governed by a power law, indicating that researchers favor the extensive study of relatively few genes. This emphasizes the need for data-driven science to accomplish genome-wide gene annotation. Andrew Su, John Hogenesch - Frank

The Web of data for e-commerce. A hands-on introduction to the GoodRelations Ontology, RDFa and Yahoo! SearchMonkey - slides - Frank

Nat Biotech, Vol. 27, No. 10. (01 October 2009), pp. 921-924. Networks in biology can appear complex and difficult to decipher. We illustrate how to interpret biological networks with the help of frequently used visualization and analysis patterns. Daniele Merico, David Gfeller, Gary Bader - Frank

Nucleic acids research (23 October 2009), gkp886. Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/. This article reports on new features in ChEBI since the last NAR report in 2007, including substructure and similarity searching, a submission tool for authoring of ChEBI datasets by... - Frank