Frederic B. Bastian

Swiss Institute of Bioinformatics · Department of Ecology and Evolution, University of Lausanne

Background The RIKEN BRC develops and maintains the RIKEN BioResource MetaDatabase to help users explore appropriate target bioresources for their experiments and prepare precise and high-quality data infrastructures. The Swiss Institute of Bioinformatics develops two RDF datasets across multi species for the study of gene expression and orthology:...

Background, enhancing interoperability of bioinformatics knowledge bases is a high priority requirement to maximize data reusability, and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange v...

Background: Enhancing interoperability of bioinformatics knowledge bases is a high-priority requirement to maximize data reusability and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange v...

With the new era of genomics, an increasing number of animal species are amenable to large-scale data generation. This had led to the emergence of new multi-species ontologies to annotate and organize these data. While anatomy and cell types are well covered by these efforts, information regarding development and life stages is also critical in the...

RNA-Seq is a powerful technique to provide quantitative information on gene expression. While many applications focus on estimated expression levels, it is also important to determine which genes are actively transcribed, and which are not. The problem can be viewed as simply setting a biologically meaningful threshold for calling a gene expressed....

A full-fledged data exploration system must combine different access modalities with a powerful concept of guiding the user in the exploration process, by being reactive and anticipative both for data discovery and for data linking. Such systems are a real opportunity for our community to cater to users with different domain and data science expert...

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable refe...

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of n...

PURPOSE The purpose of OncoMX ¹ knowledgebase development was to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types. METHODS Cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expres...

Cancer biomarkers have become integral components of many clinical protocols and research studies. Nonetheless there still is an urgent need for more accurate, less invasive, and cost-effective biomarker tests to advance precision oncology. Despite considerable success in the preclinical setting, most candidate biomarker tests have yet to receive r...

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence t...

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence ta...

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of S...

Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess the confidence in annotations. Although several resources already provide confidence information ab...

Background Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to re...

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This art...

Background / Purpose: Bgee (a dataBase for Gene Expression Evolution) is a database to automatically compare gene expression patterns between animal species. Bgee addresses difficulties such as complex anatomies and diverse sources of data, by the use of ontologies and the explicit representation of homology. Main conclusion: The current curat...

Background / Purpose: Bgee (a dataBase for Gene Expression Evolution) requires curating relations of historical homology between anatomical structures of different species, to be able to define which organs are comparable between species. Main conclusion: The Bgee team have created an annotation file, defining homology relations between anatom...

As part of the development of the database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types and different sources, notably Affymetrix data from GEO and ArrayExpress, and RNA-Seq data from SRA. During our quality control procedure, we have identified duplicated content in GEO and ArrayExpr...

Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species. vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of g...

The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration’s (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions wit...

Background / Purpose: The study of the evolution of developmental processes has shown that a major source of change in the evolution of phenotypes is changes in gene expression. Comparing gene expression patterns between animals thus is a major step to understand their evolution. This approach requires dedicated bioinformatics tools to perform hi...

The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species. We present a new algorithm, and its implementation in the software Homolo...

The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we aim to establish homology relations between ontologies describing different species. We present a new algorithm, and its implementation in the softwar...

Generating Homology Relationships by Alignment of Anatomical Ontologies

Gene expression patterns are a key feature in understanding gene function, notably in development. Comparing gene expression patterns between animals is a major step in the study of gene function as well as of animal evolution. It also provides a link between genes and phenotypes. Thus we have developed Bgee, a database designed to compare express...