MOTIVATION: The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. RESULTS: The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API. AVAILABILITY AND IMPLEMENTATION: The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api . The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library . CONTACT: [email protected] ; [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Abstract Motivation: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task, numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial. Results: This survey focuses on classifying mappers through a wide number of characteristics. The goal is to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem. Availability: A regularly updated compendium of mappers can be found at http://wwwdev.ebi.ac.uk/fg/hts_mappers/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

Breast screening is the regular examination of a woman's breasts to find breast cancer earlier. The sole exam approved for this purpose is mammography. Usually, findings are annotated through the Breast Imaging Reporting and Data System (BIRADS) created by the American College of Radiology. The BIRADS system determines a standard lexicon to be used by radiologists when studying each finding. Although the lexicon is standard, the annotation accuracy of the findings depends on the experience of the radiologist. Moreover, the accuracy of the classification of a mammography is also highly dependent on the expertise of the radiologist. A correct classification is paramount due to economical and humanitarian reasons. The main goal of this work is to produce machine learning models that predict the outcome of a mammography from a reduced set of annotated mammography findings. In the study we used a data set consisting of 348 consecutive breast masses that underwent image guided or surgical biopsy performed between October 2005 and December 2007 on 328 female subjects. The main conclusions are threefold: (1) automatic classification of a mammography, independent on information about mass density, can reach equal or better results than the classification performed by a physician; (2) mass density seems to be a good indicator of malignancy, as previous studies suggested; (3) a machine learning model can predict mass density with a quality as good as the specialist blind to biopsy, which is one of our main contributions. Our model can predict malignancy in the absence of the mass density attribute, since we can fill up this attribute using our mass density predictor.

Abstract Inductive logic programming (ILP) is a sub‐field of machine learning that provides an excellent framework for multi‐relational data mining applications. The advantages of ILP have been successfully demonstrated in complex and relevant industrial and scientific problems. However, to produce valuable models, ILP systems often require long running times and large amounts of memory. In this paper we address fundamental issues that have direct impact on the efficiency of ILP systems. Namely, we discuss how improvements in the indexing mechanisms of an underlying logic programming system benefit ILP performance. Furthermore, we propose novel data structures to reduce memory requirements and we suggest a new lazy evaluation technique to search the hypothesis space more efficiently. These proposals have been implemented in the April ILP system and evaluated using several well‐known data sets. The results observed show significant improvements in running time without compromising the accuracy of the models generated. Indeed, the combined techniques achieve several order of magnitudes speedup in some data sets. Moreover, memory requirements are reduced in nearly half of the data sets. Copyright © 2008 John Wiley & Sons, Ltd.

One of the most well known successes of Inductive Logic Programming (ILP) is on Structure-Activity Relationship (SAR) problems. In such problems, ILP has proved several times to be capable of constructing expert comprehensible models that help to explain the activity of chemical compounds based on their structure and properties. However, despite its successes on SAR problems, ILP has severe scalability problems that prevent its application on larger datasets. In this paper we present LogCHEM, an ILP based tool for discriminative interactive mining of chemical fragments. LogCHEM tackles ILP's scalability issues in the context of SAR applications. We show that LogCHEM benefits from the flexibility of ILP, both by its ability to quickly extend the original mining model, and by its ability to interface with external tools. Furthermore, we demonstrate that LogCHEM can be used to mine effectively large chemoinformatics datasets, namely several datasets from EPA's DSSTox database and on a dataset based on the DTP AIDS anti-viral screen.

The amount of data collected and stored in databases is growing considerably for almost all areas of human activity. Processing this amount of data is very expensive, both humanly and computationally. This justifies the increased interest both on the automatic discovery of useful knowledge from databases, and on using parallel processing for this task. Multi relational data mining (MRDM) techniques, such as inductive logic programming (ILP), can learn rides from relational databases consisting of multiple tables. However, ILP systems are designed to run in main memory and can have long running times. We propose a pipelined data-parallel algorithm for ILP. The algorithm was implemented and evaluated on a commodity PC cluster with 8 processors. The results show that our algorithm yields excellent speedups, while preserving the quality of learning