Assessing Potential Spawning and Nursery Habitat Availability in the River Rhine for the Critically Endangered European Sturgeon.

Information about reproductive habitat and migration pathways is of paramount importance to restore migratory fish species. This study assesses the availability of spawning and nursery habitats for the European sturgeon () in the delta and lower Rhine (covering over 350 river kilometres) as part of a larger feasibility assessment for a future restoration of this critically endangered species. The general approach has three steps: (1) the identification of the species' specific habitat requirements, based on a systematic literature review; (2) the collection and preprocessing of data from two countries, including the 1D and 2D modelling of water depths and flow velocities; and (3) GIS-based mapping of spawning and nursery habitat.

Calling on a million minds for community annotation in WikiProteins.

WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data.

Training multidisciplinary biomedical informatics students: three years of experience.

Objective: The European INFOBIOMED Network of Excellence recognized that a successful education program in biomedical informatics should include not only traditional teaching activities in the basic sciences but also the development of skills for working in multidisciplinary teams.

Design: A carefully developed 3-year training program for biomedical informatics students addressed these educational aspects through the following four activities: (1) an internet course database containing an overview of all Medical Informatics and BioInformatics courses, (2) a BioMedical Informatics Summer School, (3) a mobility program based on a 'brokerage service' which published demands and offers, including funding for research exchange projects, and (4) training challenges aimed at the development of multi-disciplinary skills.

Measurements: This paper focuses on experiences gained in the development of novel educational activities addressing work in multidisciplinary teams.

Automatic mining of the literature to generate new hypotheses for the possible link between periodontitis and atherosclerosis: lipopolysaccharide as a case study.

Aim: The aim of the current report was to generate and explore new hypotheses into how, in a pathophysiological sense, atherosclerosis and periodontitis could be linked.

Material And Methods: Two different biomedical informatics techniques were used: an association-based technique that generated a ranked list of genes associated with the diseases, and a natural language processing tool that extracted the relationships between the retrieved genes and lipopolysaccharide (LPS).

Results: This combined approach of association-based and natural language processing-based literature mining identified a hit list of 16 candidate genes, with PON1 as the primary candidate.

Applied information retrieval and multidisciplinary research: new mechanistic hypotheses in complex regional pain syndrome.

Background: Collaborative efforts of physicians and basic scientists are often necessary in the investigation of complex disorders. Difficulties can arise, however, when large amounts of information need to reviewed. Advanced information retrieval can be beneficial in combining and reviewing data obtained from the various scientific fields.

Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification.

Gene and protein name identification in text requires a dictionary approach to relate synonyms to the same gene or protein, and to link names to external databases. However, existing dictionaries are incomplete. We investigate two complementary methods for automatic generation of a comprehensive dictionary: combination of information from existing gene and protein databases and rule-based generation of spelling variations.

Online tools to support literature-based discovery in the life sciences.

In biomedical research, the amount of experimental data and published scientific information is overwhelming and ever increasing, which may inhibit rather than stimulate scientific progress. Not only are text-mining and information extraction tools needed to render the biomedical literature accessible but the results of these tools can also assist researchers in the formulation and evaluation of novel hypotheses. This requires an additional set of technological approaches that are defined here as literature-based discovery (LBD) tools.

Chemical and biological profiling of an annotated compound library directed to the nuclear receptor family.

Nuclear receptors form a family of ligand-activated transcription factors that regulate a wide variety of biological processes and are thus generally considered relevant targets in drug discovery. We have constructed an annotated compound library directed to nuclear receptors (NRacl) as a means for integrating the chemical and biological data being generated within this family. Special care has been put in the appropriate storage of annotations by using hierarchical classification schemes for both molecules and nuclear receptors, which takes the ability to extract knowledge from annotated compound libraries to another level.

Thesaurus-based disambiguation of gene symbols.

Background: Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.

Results: We developed a simple thesaurus-based disambiguation algorithm that can operate with very little training data.

Contextual annotation of web pages for interactive browsing.

With the information on the World Wide Web and in specialized databases exploding, researchers and physicians are in dire need to browse efficiently though the large corpus of information resources in their field of interest. The focus is not any longer to find everything related to your interest, but it shifts to zooming in, based on context and expanding again in neighboring knowledge domains. This paper describes an attempt to develop a completely new, interactive way of browsing distributed corpora of information without the need for multiple different queries in different information resources.

A probabilistic similarity metric for Medline records: a model for author name disambiguation.

We present a model for automatically generating training sets and estimating the probability that a pair of Medline records sharing a last and first name initial are authored by the same individual, based on shared title words, journal name, co-authors, medical subject headings, language, and affiliation, as well as distinctive features of the name itself (i.e., presence of middle initial, suffix, and prevalence in Medline).

Using contextual queries.

Search engines generally treat search requests in isolation. The results for a given query are identical, independent of the user, or the context in which the user made the request. An approach is demonstrated that explores implicit contexts as obtained from a document the user is reading.

Ambiguity of human gene symbols in LocusLink and MEDLINE: creating an inventory and a disambiguation test collection.

Genes are discovered almost on a daily basis and new names have to be found. Although there are guidelines for gene nomenclature, the naming process is highly creative. Human genes are often named with a gene symbol and a longer, more descriptive term; the short form is very often an abbreviation of the long form.

Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomide.

The availability of scientific bibliographies through online databases provides a rich source of information for scientists to support their research. However, the risk of this pervasive availability is that an individual researcher may fail to find relevant information that is outside the direct scope of interest. Following Swanson's ABC model of disjoint but complementary structures in the biomedical literature, we have developed a discovery support tool to systematically analyze the scientific literature in order to generate novel and plausible hypotheses.