Suzanna E Lewis
Affiliation: University of California
- Reactome: a knowledge base of biologic pathways and processesImre Vastrik
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Genome Biol 8:R39. 2007..Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets...
- Calling on a million minds for community annotation in WikiProteinsBarend Mons
Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
Genome Biol 9:R89. 2008..We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org...
- Apollo: a sequence annotation editorS E Lewis
Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94720 3200, USA
Genome Biol 3:RESEARCH0082. 2002..FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects...
- Gene Ontology: looking backwards and forwardsSuzanna E Lewis
Department of Molecular and Cell Biology, University of California, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
Genome Biol 6:103. 2005..Its most significant achievement lies in uniting many independent biological database efforts into a cooperative force...
- Uberon, an integrative multi-species anatomy ontologyChristopher J Mungall
Genomics Division, Lawrence Berkeley National Laboratory, 1 Cycltotron Road MS 64 121, Berkeley, CA 94720, USA
Genome Biol 13:R5. 2012..It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org...
- Integrating phenotype ontologies across multiple speciesChristopher J Mungall
Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Genome Biol 11:R2. 2010..We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology...
- The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental detailsNicole L Washington
Lawrence Berkeley National Laboratory, Genomics Division, 1 Cyclotron Road MS64 121, Berkeley, CA 94720, USA
Database (Oxford) 2011:bar023. 2011..modENCODE data can be found at http://www.modencode.org...
- Annotation of the Drosophila melanogaster euchromatic genome: a systematic reviewSima Misra
Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
Genome Biol 3:RESEARCH0083. 2002....
- The Human Phenotype Ontology project: linking molecular biology and disease through phenotype dataSebastian Kohler
Institute for Medical Genetics and Human Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke s Hospital, Cambridge CB2 2QQ, UK, Universite Paul Sabatier, Faculte de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre MAHSC, Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada
Nucleic Acids Res 42:D966-74. 2014..We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. ..
- Linking human diseases to animal models using ontology-based phenotype annotationNicole L Washington
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
PLoS Biol 7:e1000247. 2009....
- Systematic determination of patterns of gene expression during Drosophila embryogenesisPavel Tomancak
Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
Genome Biol 3:RESEARCH0088. 2002..Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription...
- Standardized description of scientific evidence using the Evidence Ontology (ECO)Marcus C Chibucos
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USAInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, School of Medicine
Database (Oxford) 2014:. 2014..ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org. ..
- JBrowse: a dynamic web platform for genome visualization and analysisRobert Buels
Department of Bioengineering, University of California, Berkeley, California, USA
- Sequence ontology annotation guideKaren Eilbeck
Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, California 94729 3200, USA
Comp Funct Genomics 5:642-7. 2004..First we show where the terms needed to describe the gene's features are located in SO and their relationships to one another. We then show line by line how to format the file to construct a SO compliant annotation of this gene...
- The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across speciesChristopher J Mungall
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
Nucleic Acids Res . 2016..Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species...
- The Sequence Ontology: a tool for the unification of genome annotationsKaren Eilbeck
Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
Genome Biol 6:R44. 2005....
- EGASP: the human ENCODE Genome Annotation Assessment ProjectRoderic Guigo
Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
Genome Biol 7:S2.1-31. 2006..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
- The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspectiveJoshua S Kaminker
Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
Genome Biol 3:RESEARCH0084. 2002..We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species...
- Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI projectChris F Taylor
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nat Biotechnol 26:889-96. 2008
- Modelling data across labs, genomes, space and timeJason R Swedlow
Division of Gene Regulation and Expression, Wellcome Trust Biocentre, Faculty of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
Nat Cell Biol 8:1190-4. 2006..Here, we use imaging applications to illustrate the purpose of the various implementations of data specifications and the requirement for open, standardized, data formats to facilitate the sharing of critical digital data and metadata...
- National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledgeDaniel L Rubin
Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA
OMICS 10:185-98. 2006....
- The RNA Ontology Consortium: an open invitation to the RNA communityNeocles B Leontis
RNA 12:533-41. 2006....
- The minimum information about a genome sequence (MIGS) specificationDawn Field
Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
Nat Biotechnol 26:541-7. 2008..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...