Barend Mons

The FAIR Guiding Principles for scientific data management and stewardship

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

The value of data

Data citation and the derivation of semantic constructs directly from datasets have now both found their place in scientific communication. The social challenge facing us is to maintain the value of traditional narrative publications and their relationship to the datasets they report upon while at the same time developing appropriate metrics for citation of data and data constructs.

Distribution of information in biomedical abstracts and full-text publications

MOTIVATION Full-text documents potentially hold more information than their abstracts, but require more resources for processing. We investigated the added value of full text over abstracts in terms of information content and occurrences of gene symbol--gene name combinations that can resolve gene-symbol ambiguity. RESULTS We analyzed a set of 3902 biomedical full-text articles. Different keyword measures indicate that information density is highest in abstracts, but that the information coverage in full texts is much greater than in abstracts. Analysis of five different standard sections of articles shows that the highest information coverage is located in the results section. Still, 30-40% of the information mentioned in each section is unique to that section. Only 30% of the gene symbols in the abstract are accompanied by their corresponding names, and a further 8% of the gene names are found in the full text. In the full text, only 18% of the gene symbols are accompanied by their gene names.

Word Sense Disambiguation in the Biomedical Domain: An Overview

There is a trend towards automatic analysis of large amounts of literature in the biomedical domain. However, this can be effective only if the ambiguity in natural language is resolved. In this paper, the current state of research in word sense disambiguation (WSD) is reviewed. Several methods for WSD have already been proposed, but many systems have been tested only on evaluation sets of limited size. There are currently only very few applications of WSD in the biomedical domain. The current direction of research points towards statistically based algorithms that use existing curated data and can be applied to large sets of biomedical literature. There is a need for manually tagged evaluation sets to test WSD algorithms in the biomedical domain. WSD algorithms should preferably be able to take into account both known and unknown senses of a word. Without WSD, automatic metaanalysis of large corpora of text will be error prone.

Text mining for biology - the way forward: opinions from leading scientists

This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the next steps are, and what role future BioCreative evaluations can play. The responses identify several broad themes, including the possibility of fusing literature and biological databases through text mining; the need for user interfaces tailored to different classes of users and supporting community-based annotation; the importance of scaling text mining technology and inserting it into larger workflows; and suggestions for additional challenge evaluations, new applications, and additional resources needed to make progress.

In vitro formation of ookinetes and functional maturity of Plasmodium berghei gametocytes.

In vitro formation of Plasmodium berghei ookinetes was studied. Gametocytes produced in vitro were obtained from heart and tail blood of Swiss mice and from blood removed from mosquitoes directly after feeding on these mice. In vitro produced gametocytes were obtained from short-term cultures of the erythrocytic stages of P. berghei. Reproducible ookinete production was obtained in medium RPMI 1640, pH 7.8-8.0, using in vivo and in vitro produced gametocytes. The morphology of developmental stages of ookinetes and degenerate forms at the light microscope level is described. More ookinetes were produced in medium RPMI 1640 compared to MEM and ookinete yield--defined as the ratio between the number of in vitro produced ookinetes/10(5) erythrocytes and the number of exflagellations/10(5) erythrocytes in the infected blood--increased with lower erythrocyte densities in the cultures within the range of dilutions tested. A linear relationship existed between gametocytaemia and the number of ookinetes produced. The methods for in vitro ookinete formation and for estimating ookinete yields enabled us to study aspects of functional maturity of gametocytes independent of mosquitoes. The numbers of exflagellating gametocytes and in vitro ookinete yields in tail blood corresponded with those in heart blood and blood ingested by mosquitoes, suggesting a random distribution of functionally mature gametocytes within the vertebrate host.

Synchronized erythrocytic schizogony and gametocytogenesis of Plasmodium berghei in vivo and in vitro

Both asexual and sexual development of Plasmodium berghei was synchronized without chemical intervention using in vitro culture techniques. Combined in vivo and in vitro experiments were performed on the relationship between age, morphology and maturity of gametocytes. Schizogony took 22-23 h in the experiments. At 26 h post-invasion (p.i.) the first males became capable of exflagellation. By 20 h p.i. the first gametocytes were recognizable in Giemsa-stained smears but the sex was hardly distinguishable until maturity (26 h p.i.). Survival time of gametocytes was estimated at 26 h in vitro (half-life 13 h) and the same survival time was suggested for gametocytes in vivo. Schizonts of P. berghei apparently disappeared from the peripheral circulation upon maturity, rupturing almost immediately. Mature schizonts in vitro persisted up to 48 h p.i. in non-agitated cultures. No evidence was collected for sequestration of any sub-population of gametocytes.

Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes

MOTIVATION The advent of high-throughput experiments in molecular biology creates a need for methods to efficiently extract and use information for large numbers of genes. Recently, the associative concept space (ACS) has been developed for the representation of information extracted from biomedical literature. The ACS is a Euclidean space in which thesaurus concepts are positioned and the distances between concepts indicates their relatedness. The ACS uses co-occurrence of concepts as a source of information. In this paper we evaluate how well the system can retrieve functionally related genes and we compare its performance with a simple gene co-occurrence method. RESULTS To assess the performance of the ACS we composed a test set of five groups of functionally related genes. With the ACS good scores were obtained for four of the five groups. When compared to the gene co-occurrence method, the ACS is capable of revealing more functional biological relations and can achieve results with less literature available per gene. Hierarchical clustering was performed on the ACS output, as a potential aid to users, and was found to provide useful clusters. Our results suggest that the algorithm can be of value for researchers studying large numbers of genes. AVAILABILITY The ACS program is available upon request from the authors.

Plasmodium vivax: in vitro growth and reinvasion in red blood cells of Aotus nancymai.

Plasmodium vivax was maintained in experimentally infected Aotus nancymai. Positive monkeys were used as donors for culture material. After leucocyte removal with two different methods, including the classic CF11 method and a commercially available filter, parasites were grown under continuous shaking conditions in standard RPMI 1640, containing 20% human AB + serum. When mature schizonts were present, artificially induced reticulocytes from monkeys pretreated with the hemolytic drug phenylhydrazine HCl were added. Addition of reticulocytes and shaking were both necessary to realize a significant reinvasion under in vitro conditions. A strong positive correlation between the percentage of reticulocytes and in vitro invasion was demonstrated, and a preferential invasion into reticulocytes was demonstrated in vivo and in vitro using blood films stained with brilliant cresyl blue and counterstained with Giemsa.

Constructing an associative concept space for literature-based discovery

Scientific literature is often fragmented, which implies that certain scientific questions can only be answered by combining information from various articles. In this paper, a new algorithm is proposed for finding associations between related concepts present in literature. To this end, concepts are mapped to a multidimensional space by a Hebbian type of learning algorithm using co-occurrence data as input. The resulting concept space allows exploration of the neighborhood of a concept and finding potentially novel relationships between concepts. The obtained information retrieval system is useful for finding literature supporting hypotheses and for discovering previously unknown relationships between concepts. Tests on artificial data show the potential of the proposed methodology. In addition, preliminary tests on a set of Medline abstracts yield promising results.