An evaluation of the performance of three semantic background knowledge sources in comparative anatomy

In this paper we evaluate the performance and usefulness of three semantic background knowledge sources for predicting synonymous anatomical terms across species boundaries. The reference sources under evaluation are UMLS, FMA-OBO and WordNet, which are applied to the anatomical ontologies of mouse and zebrafish. Our results show that the use of specialized knowledge sources leads to highly accurate predictions, verified through complete manual curation, which can be further improved by combining multiple of said sources. We argue that these three references complement each other in terms of granularity and specificity. From our results we conclude that these references can be used to create reliable ontology mappings with minimal human supervision

Evidence for RNA recombination between distinct isolates of Pepino mosaic virus.

Genetic recombination plays an important role in the evolution of virus genomes. In this study we analyzed publicly available genomic sequences of Pepino mosaic virus (PepMV) for recombination events using several bioinformatics tools. The genome-wide analyses not only confirm the presence of previously found recombination events in PepMV but also provide the first evidence for double recombinant origin of the US2 isolate

Methods for interpreting lists of affected genes obstained in a DNA microarray experiment

Background - The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results - Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion - It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experimen

Computer applications in protein and nucleic acid sequence analysis

Contains fulltext : mmubn000001_076770931.pdf (publisher's version ) (Open Access)Promotor : H. Bloemendal169 p

Chimera: construction of chimeric sequences for phylogenetic analysis

Chimera allows the construction of chimeric protein or nucleic acid sequence files by concatenating sequences from two or more sequence files in PHYLIP formats. It allows the user to interactively select genes and species from the input files. The concatenated result is stored to one single output file in PHYLIP or NEXUS formats

Evolution of web services in bioinformatics

Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformaticians have experimented with several strategies to try to integrate data sets and tools. Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task. Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects. This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited for automatic workflow generation to a dynamic network of XML-based web services that can easily be used to create pipelines

A comparison of database systems for XML-type data

Background: In the field of bioinformatics interchangeable data formats based on XML are widely used. XML-type data is also at the core of most web services. With the increasing amount of data stored in XML comes the need for storing and accessing the data. In this paper we analyse the suitability of different database systems for storing and querying large datasets in general and Medline in particular. Results: All reviewed database systems perform well when tested with small to medium sized datasets, however when the full Medline dataset is queried a large variation in query times is observed. Conclusions: There is not one system that is vastly superior to the others in this comparison and, depending on the database size and the query requirements, different systems are most suitable. The best all-round solution is the Oracle 11~g database system using the new binary storage option. Alias-i's Lingpipe is a more lightweight, customizable and sufficiently fast solution. It does however require more initial configuration steps. For data with a changing XML structure Sedna and BaseX as native XML database systems or MySQL with an XML-type column are suitable

An evaluation of the performance of three semantic background knowledge sources in comparative anatomy

In this paper we evaluate the performance and usefulness of three semantic background knowledge sources for predicting synonymous anatomical terms across species boundaries. The reference sources under evaluation are UMLS, FMA-OBO and WordNet, which are applied to the anatomical ontologies of mouse and zebrafish. Our results show that the use of specialized knowledge sources leads to highly accurate predictions, verified through complete manual curation, which can be further improved by combining multiple of said sources. We argue that these three references complement each other in terms of granularity and specificity. From our results we conclude that these references can be used to create reliable ontology mappings with minimal human supervision