Affiliation: Wellcome Trust Genome Campus
- The NHGRI GWAS Catalog, a curated resource of SNP-trait associationsDanielle Welter
European Bioinformatics Institute EMBL EBI, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA and Division of Policy, Communication and Education, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Nucleic Acids Res 42:D1001-6. 2014..This article presents a number of recent improvements to the Catalog, including novel ways for users to interact with the Catalog and changes to the curation infrastructure...
- MageComet--web application for harmonizing existing large-scale experiment descriptionsVincent Xue
Department of Computer Science, Hunter College, City University of New York, NY 10065, USA
Bioinformatics 28:1402-3. 2012..Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline...
- MIAME/Plant - adding value to plant microarrray experimentsPhilip Zimmermann
Swiss Federal Institute of Technology ETH Zurich, ETH Center, CH 8092 Zurich, Switzerland
Plant Methods 2:1. 2006..The power and value of systematic annotation of microarray data is convincingly demonstrated by data warehouses such as Genevestigator(R) or NASCArrays, and better experimental annotation will make these applications even more powerful...
- Anatomy ontologies and potential users: bridging the gapRavensara S Travillian
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
J Biomed Semantics 2:S3. 2011..To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations...
- Modeling biomedical experimental processes with OBIRyan R Brinkman
British Columbia Cancer Agency, Vancouver, Canada
J Biomed Semantics 1:S7. 2010..AVAILABILITY : OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl...
- Large scale comparison of global gene expression patterns in human and mouseXiangqun Zheng-Bradley
European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
Genome Biol 11:R124. 2010....
- XGAP: a uniform and extensible data model and software platform for genotype and phenotype experimentsMorris A Swertz
Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
Genome Biol 11:R27. 2010..Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans...
European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
BMC Bioinformatics 12:218. 2011..This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups...
- The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a buttonMorris A Swertz
Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen and Department of Genetics, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands
BMC Bioinformatics 11:S12. 2010..We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed...
- ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experimentsHelen Parkinson
Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Nucleic Acids Res 39:D1002-4. 2011..Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy...
- ArrayExpress--a public repository for microarray gene expression data at the EBIH Parkinson
European Bioinformatics Institute, EMBL EBI Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Nucleic Acids Res 33:D553-5. 2005..Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress...
- ArrayExpress--a public database of microarray experiments and gene expression profilesH Parkinson
European Bioinformatics Institute, EMBL EBI Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Nucleic Acids Res 35:D747-50. 2007..ArrayExpress supports community standards, including MIAME, MAGE-ML and more recently the proposal for a spreadsheet based data exchange format: MAGE-TAB. Availability: www.ebi.ac.uk/arrayexpress...
- The EMBL nucleotide sequence databaseG Stoesser
EMBL Outstation The European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 29:17-21. 2001..For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT...
- Minimum information about a microarray experiment (MIAME)-toward standards for microarray dataA Brazma
European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nat Genet 29:365-71. 2001..With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it...