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David R, Rybina A, Burel J, Heriche J, Audergon P, Boiten J, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Grüning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras J, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, Sánchez‐Pla A, Sansone S, Sarkans U, Serrano‐Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P. "Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling. EMBO J 2023; 42:e115008. [PMID: 37964598 PMCID: PMC10690449 DOI: 10.15252/embj.2023115008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 11/16/2023] Open
Abstract
The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.
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Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas DΕ, Dave K, Dilger M, Exner T, Geerke DP, Grafström R, Gray A, Hancock JM, Hollert H, Jeliazkova N, Jennen D, Jourdan F, Kahlem P, Klanova J, Kleinjans J, Kondic T, Kone B, Lynch I, Maran U, Martinez Cuesta S, Ménager H, Neumann S, Nymark P, Oberacher H, Ramirez N, Remy S, Rocca-Serra P, Salek RM, Sallach B, Sansone SA, Sanz F, Sarimveis H, Sarntivijai S, Schulze T, Slobodnik J, Spjuth O, Tedds J, Thomaidis N, Weber RJ, van Westen GJ, Wheelock CE, Williams AJ, Witters H, Zdrazil B, Županič A, Willighagen EL. ELIXIR and Toxicology: a community in development. F1000Res 2023; 10:ELIXIR-1129. [PMID: 37842337 PMCID: PMC10568213 DOI: 10.12688/f1000research.74502.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.
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Affiliation(s)
- Marvin Martens
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Rob Stierum
- Risk Analysis for Products In Development (RAPID), Netherlands Organisation for applied scientific research TNO, Utrecht, 3584 CB, The Netherlands
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 EN, The Netherlands
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Hristo Aladjov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Kasia Arturi
- Department Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, 8600, Switzerland
| | | | - Pavel Babica
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Palacky University Olomouc, Olomouc, 77146, Czech Republic
| | | | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Evan E. Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Dimitrios Ε. Damalas
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Kirtan Dave
- School of Science, GSFC University, Gujarat, 391750, India
| | - Marco Dilger
- Forschungs- und Beratungsinstitut Gefahrstoffe (FoBiG) GmbH, Freiburg im Breisgau, 79106, Germany
| | | | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Vrije Universiteit, Amsterdam, 1081 HZ, The Netherlands
| | - Roland Grafström
- Department of Toxicology, Misvik Biology, Turku, 20520, Finland
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Alasdair Gray
- Department of Computer Science, Heriot-Watt University, Edinburgh, UK
| | | | - Henner Hollert
- Department Evolutionary Ecology & Environmental Toxicology (E3T), Goethe-University, Frankfurt, D-60438, Germany
| | | | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Fabien Jourdan
- MetaboHUB, French metabolomics infrastructure in Metabolomics and Fluxomics, Toulouse, France
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Pascal Kahlem
- Scientific Network Management SL, Barcelona, 08015, Spain
| | - Jana Klanova
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Todor Kondic
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Boï Kone
- Faculty of Pharmacy, Malaria Research and Training Center, Bamako, BP:1805, Mali
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, 50411, Estonia
| | | | - Hervé Ménager
- Institut Français de Bioinformatique, Evry, F-91000, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, F-75015, France
| | - Steffen Neumann
- Research group Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, A-6020, Austria
| | - Noelia Ramirez
- Institut d'Investigacio Sanitaria Pere Virgili-Universitat Rovira i Virgili, Tarragona, 43007, Spain
| | | | - Philippe Rocca-Serra
- Data Readiness Group, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Reza M. Salek
- International Agency for Research on Cancer, World Health Organisation, Lyon, 69372, France
| | - Brett Sallach
- Department of Environment and Geography, University of York, UK, York, YO10 5NG, UK
| | | | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, 08003, Spain
| | | | | | - Tobias Schulze
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, 04318, Germany
| | | | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, SE-75124, Sweden
| | - Jonathan Tedds
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Ralf J.M. Weber
- School of Biosciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Gerard J.P. van Westen
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, 2333 CC, The Netherlands
| | - Craig E. Wheelock
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm SE-141-86, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Antony J. Williams
- Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | | | - Barbara Zdrazil
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Anže Županič
- Department Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
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Hancock JM, Escobar MA. An evaluation of von Willebrand factor (recombinant) therapy for adult patients living with severe type 3 von Willebrand disease. Expert Rev Hematol 2023; 16:157-161. [PMID: 36861346 DOI: 10.1080/17474086.2023.2184339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION Von Willebrand Factor (VWF) containing concentrates have been used for the treatment of von Willebrand Disease (VWD) for many years. Recently, however, a novel recombinant VWF (rVWF or vonicog alpha, VONVENDI [US], VEYVONDI [Europe]) has arrived to the market for the treatment of VWD. Initially, rVWF was approved by the U.S. Food and Drug Administration (FDA) for the on-demand treatment and control of bleeding episodes and for the perioperative management of bleeding for patients with VWD. More recently, however, the FDA has approved rVWF for routine prophylaxis to prevent bleeding episodes for those patients with severe type 3 VWD receiving on-demand therapy. AREAS COVERED This review will focus on recent phase III trial results from NCT02973087 regarding the use of long-term routine twice weekly prophylaxis with rVWF for the prevention of bleed events in patients with severe type 3 VWD. EXPERT OPINION A novel rVWF concentrate may have greater hemostatic potential over prior plasma-derived VWF concentrates and is now FDA approved for use in routine prophylaxis for patients with severe type 3 VWD in the United States. This greater hemostatic potential may be due to the presence of ultra-large VWF multimers and a more favorable high-molecular-weight multimer pattern compared to prior pdVWF concentrates.
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Affiliation(s)
- John M Hancock
- Gulf States Hemophilia and Thrombophilia Center, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Miguel A Escobar
- Gulf States Hemophilia and Thrombophilia Center, the University of Texas Health Science Center at Houston, Houston, Texas, USA
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Martins dos Santos V, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R, Dominguez Del Angel V, Ferk P, Fey D, Goble C, Golebiewski M, Gruden K, Heil KF, Hermjakob H, Kahlem P, Klapa MI, Koehorst J, Kolodkin A, Kutmon M, Leskošek B, Moretti S, Müller W, Pagni M, Rezen T, Rocha M, Rozman D, Šafránek D, Sheriff RSM, Suarez Diez M, Van Steen K, Westerhoff HV, Wittig U, Wolstencroft K, Zupanic A, Evelo CT, Hancock JM. Systems Biology in ELIXIR: modelling in the spotlight. F1000Res 2022; 11:ELIXIR-1265. [PMID: 36742342 PMCID: PMC9871403 DOI: 10.12688/f1000research.126734.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.
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Affiliation(s)
- Vitor Martins dos Santos
- Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands,
| | - Mihail Anton
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, SE-41258, Sweden
| | - Barbara Szomolay
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Ilja Arts
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Polonca Ferk
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - Dirk Fey
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, 4, Ireland
| | - Carole Goble
- Department of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
| | | | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Pascal Kahlem
- Scientific Network Management SL, Barcelona, 08015, Spain
| | - Maria I. Klapa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
| | - Jasper Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
| | - Alexey Kolodkin
- ISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands,Competence Center for Methodology and Statistics; Transversal Translational Medicine, Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, L-1445, Luxembourg
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands,Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | | | - Wolfgang Müller
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Marco Pagni
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tadeja Rezen
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Damjana Rozman
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - David Šafránek
- Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - Rahuman S. Malik Sheriff
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Suarez Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
| | - Kristel Van Steen
- BIO3 - Systems Genetics, GIGA-R Medical Genomics, University of Liege, Liege, 4000, Belgium,BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | | | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Katherine Wolstencroft
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, 2333 CA, The Netherlands
| | - Anze Zupanic
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - John M. Hancock
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia,
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Cokan KB, Hancock JM, Spindelböck W, Režen T, Juvan P, Rozman D. Matching mouse models to specific human liver disease states by comparative functional genomics of mouse and human datasets. Biochim Biophys Acta Gene Regul Mech 2022; 1865:194785. [PMID: 34971790 DOI: 10.1016/j.bbagrm.2021.194785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Omics has broadened our view of transcriptional and gene regulatory networks of multifactorial diseases, such as metabolism associated liver disease and its advanced stages including hepatocellular carcinoma. Identifying liver disease biomarkers and potential treatment targets makes use of experimental models, e.g. genetically engineered mice, which show molecular features of human pathologies but are experimentally tractable. We compared gene expression profiling data from human to our studies on transgenic mice with hepatocyte deletion of Cyp51 from cholesterol synthesis with the aim of identifying the human liver disease state best matched by the Cyp51 knockout model. Gene Expression Omnibus was used to identify relevant human datasets. We identified enriched and deregulated genes, pathways and transcription factors of mouse and human disease samples. Analysis showed a closer match of the Cyp51 knockout to the female patient samples. Importantly, CYP51 was depleted in both mouse and female human data. Among the enriched genes were the oxysterol-binding protein-related protein 3 (OSBPL3), which was enriched in all datasets, and the collagen gene COL1A2, which was enriched in both the mouse and one human dataset. KEGG and Reactome analyses revealed the most enriched pathway to be ECM-receptor interaction. Numerous transcription factors were differentially expressed in mice of both sexes and in the human female dataset, while depleted HNF4α and RXRα:PPARα-isoform1 were a hallmark in all cases. Our analysis exposed novel potential biomarkers, which may provide new avenues towards more personalized approaches and different targets in females and males. The analysis was only possible because of availability of open data resources and tools and broadly consistent annotation.
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Affiliation(s)
- Kaja Blagotinšek Cokan
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - John M Hancock
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Walter Spindelböck
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Juvan
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA. Disentangling the complexity of low complexity proteins. Brief Bioinform 2021; 21:458-472. [PMID: 30698641 PMCID: PMC7299295 DOI: 10.1093/bib/bbz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/19/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Abstract
There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Lisanna Paladin
- Department of Biomedical Science, University of Padova, Padova, Italy
| | - Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Sophia Petrosian
- Biological Computation and Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Borbála Hajdu-Soltész
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Annika Urbanek
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Aleksandra Gruca
- Institute of Informatics, Silesian University of Technology, Gliwice, Poland
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Christos A Ouzounis
- Biological Computation and Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS-UMR, Institut de Biologie Computationnelle, Universite de Montpellier, Montpellier, France.,Institute of Bioengineering, University ITMO, St. Petersburg, Russia
| | - John M Hancock
- Earlham Institute, Norwich, UK.,ELIXIR Hub, Welcome Genome Campus, Hinxton, UK
| | - Silvio C E Tosatto
- Department of Biomedical Science, University of Padova, Padova, Italy.,CNR Institute of Neuroscience, Padova, Italy
| | - Zsuzsanna Dosztanyi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Mainz, Germany
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7
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Salgado D, Armean IM, Baudis M, Beltran S, Capella-Gutierrez S, Carvalho-Silva D, Dominguez Del Angel V, Dopazo J, Furlong LI, Gao B, Garcia L, Gerloff D, Gut I, Gyenesei A, Habermann N, Hancock JM, Hanauer M, Hovig E, Johansson LF, Keane T, Korbel J, Lauer KB, Laurie S, Leskošek B, Lloyd D, Marques-Bonet T, Mei H, Monostory K, Piñero J, Poterlowicz K, Rath A, Samarakoon P, Sanz F, Saunders G, Sie D, Swertz MA, Tsukanov K, Valencia A, Vidak M, Yenyxe González C, Ylstra B, Béroud C. The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Res 2020; 9. [PMID: 34367618 PMCID: PMC8311797 DOI: 10.12688/f1000research.24887.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2020] [Indexed: 02/02/2023] Open
Abstract
Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established
human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.
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Affiliation(s)
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael Baudis
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Salvador Capella-Gutierrez
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona, Spain
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | | | - Joaquin Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud, CDCA, Hospital Virgen del Rocio, Sevilla, Spain
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Bo Gao
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Leyla Garcia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.,ZB MED Information Centre for Life Sciences, Cologne, Germany.,ELIXIR Hub, Hinxton, UK
| | - Dietlind Gerloff
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Attila Gyenesei
- Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Nina Habermann
- Genome Biology, European Molecular Biological Laboratory, Heidelberg, Germany
| | | | | | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Thomas Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jan Korbel
- Genome Biology, European Molecular Biological Laboratory, Heidelberg, Germany
| | | | - Steve Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain
| | - Brane Leskošek
- Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia
| | | | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Katalin Monostory
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Janet Piñero
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | | | | | - Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | | | - Daoud Sie
- Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kirill Tsukanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies, Barcelona, Spain
| | - Marko Vidak
- Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia
| | - Cristina Yenyxe González
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Marseille, France.,Département de Génétique Médicale et de Biologie Cellulaire, APHM, Hôpital d'enfants de la Timone, 13385 Marseille, France
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8
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Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro MA, Hancock JM, Dosztányi Z, Paladin L, Necci M, Piovesan D, Tosatto SCE, Promponas VJ, Grynberg M, Gruca A. PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. Nucleic Acids Res 2020; 48:W77-W84. [PMID: 32421769 PMCID: PMC7319588 DOI: 10.1093/nar/gkaa339] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/08/2020] [Accepted: 05/01/2020] [Indexed: 12/25/2022] Open
Abstract
Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToLoCo - PLAtform of TOols for LOw COmplexity-a meta-server that integrates and collects the output of five different state-of-the-art tools for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies. In addition, the union or intersection of the results of the search on a query sequence can be obtained. By developing the PlaToLoCo meta-server, we provide the community with a fast and easily accessible tool for the analysis of LCRs with additional information included to aid the interpretation of the results. The PlaToLoCo platform is available at: http://platoloco.aei.polsl.pl/.
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Affiliation(s)
- Patryk Jarnot
- Department of Computer Networks and Systems, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | | | - Laszlo Dobson
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, Hungary.,Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
| | - Matthew Merski
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - John M Hancock
- ELIXIR, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös LorándUniversity, Budapest, Pázmány Péter stny 1/c 1117, Budapest, Hungary
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, P.O. Box 20537, Nicosia, CY 1678, Cyprus
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Aleksandra Gruca
- Department of Computer Networks and Systems, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
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9
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Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Res 2020; 9. [PMID: 32566135 PMCID: PMC7284151 DOI: 10.12688/f1000research.20559.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.
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Affiliation(s)
- Christine Orengo
- Structural and Molecular Biology Department, University College, London, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Shoshana Wodak
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Vincent Zoete
- Department of Oncology, Lausanne University, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandre M J J Bonvin
- Bijvoet Center, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Arne Elofsson
- Science for Life Laboratory, Stockholm University, Solna, S-17121, Sweden
| | - K Anton Feenstra
- Dept. Computer Science, Center for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit, Amsterdam, 1081 HV, The Netherlands
| | - Dietland L Gerloff
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Thomas Hamelryck
- Bioinformatics center, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | | | | | - Adam Hospital
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | | | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Hamburg, D-20146, Germany
| | - Claudio Soares
- Instituto de Tecnologia Química e Biológica Antonio Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Pierre Tuffery
- Ressource Parisienne en Bioinformatique Structurale, Université de Paris, Paris, F-75205, France
| | - Gabor Tusnady
- Membrane Bioinformatics Research Group, Institute of Enzymology, Budapest, H-1117, Hungary
| | | | - Tiina Salminen
- Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, FI-20500, Finland
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, CZ-25250, Czech Republic
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10
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Ison J, Ménager H, Brancotte B, Jaaniso E, Salumets A, Raček T, Lamprecht AL, Palmblad M, Kalaš M, Chmura P, Hancock JM, Schwämmle V, Ienasescu HI. Community curation of bioinformatics software and data resources. Brief Bioinform 2019; 21:1697-1705. [PMID: 31624831 PMCID: PMC7947956 DOI: 10.1093/bib/bbz075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/13/2019] [Accepted: 05/30/2019] [Indexed: 11/13/2022] Open
Abstract
The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.
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Affiliation(s)
- Jon Ison
- National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800 Kongens Lyngby, Denmark
| | - Hervé Ménager
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Bryan Brancotte
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Erik Jaaniso
- ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia
| | - Ahto Salumets
- ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia
| | - Tomáš Raček
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.,Faculty of Informatics, Masaryk University, Botanická 68a, 602 00 Brno, Czech Republic
| | - Anna-Lena Lamprecht
- Department of Information and Computing Sciences, Utrecht University, Utrecht, Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Matúš Kalaš
- Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
| | - Piotr Chmura
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen
| | - John M Hancock
- ELIXIR-Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Hans-Ioan Ienasescu
- National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800 Kongens Lyngby, Denmark
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11
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Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res 2019; 8. [PMID: 31824649 PMCID: PMC6880265 DOI: 10.12688/f1000research.20136.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2019] [Indexed: 01/20/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK
| | - M Madan Babu
- MRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France
| | - Alan Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Zsuzsanna Dosztanyi
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | | | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Isabella C Felli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - John M Hancock
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Jen Harrow
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Desmond Higgins
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Balint Mészáros
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Marco Necci
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Roberta Pierattelli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Patrick Ruch
- HES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Pedro Romero
- University of Wisconsin-Madison, Madison, WI, 53706-1544, USA
| | | | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Malvika Sharan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Denis C Shields
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Joel L Sussman
- Department of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel
| | | | - Peter Tompa
- VIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium
| | - Michael Turewicz
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany
| | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic
| | - Wim F Vranken
- VUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Bonnie Ann Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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12
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Horro C, Cook M, Attwood TK, Brazas MD, Hancock JM, Palagi P, Corpas M, Jimenez R. BioCIDER: a Contextualisation InDEx for biological Resources discovery. Bioinformatics 2017; 33:2607-2608. [PMID: 28407033 PMCID: PMC5870719 DOI: 10.1093/bioinformatics/btx213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/11/2017] [Indexed: 11/13/2022] Open
Abstract
Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded. Availability and Implementation BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence.
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Affiliation(s)
- Carlos Horro
- Elixir Department, Earlham Institute, Norwich Research Park Innovation Centre, Norwich NR4 7UH, UK
| | - Martin Cook
- ELIXIR Hub, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Teresa K Attwood
- School of Computer Science, The University of Manchester, Manchester M13 9PL, UK
| | - Michelle D Brazas
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada
| | - John M Hancock
- Elixir Department, Earlham Institute, Norwich Research Park Innovation Centre, Norwich NR4 7UH, UK
| | - Patricia Palagi
- SIB Training Group, SIB Swiss Institute of Bioinformatics, Lausanne 1005, Switzerland
| | - Manuel Corpas
- Repositive, Future Business Centre, Kings' Hedges Road, Cambridge CB4 2HY, UK
| | - Rafael Jimenez
- ELIXIR Hub, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
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13
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Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G. ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR. F1000Res 2017; 6. [PMID: 28781748 PMCID: PMC5521157 DOI: 10.12688/f1000research.11837.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2017] [Indexed: 11/20/2022] Open
Abstract
ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics.
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Affiliation(s)
- L Larcombe
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - R Hendricusdottir
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - T K Attwood
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - F Bacall
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - N Beard
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - L J Bellis
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - W B Dunn
- Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - A Nenadic
- The Software Sustainability Institute, University of Manchester, Manchester, M13 9PL, UK
| | - C Orengo
- University College London, London, WC1E 6BT, UK
| | - B Overduin
- Edinburgh Genomics, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - S-A Sansone
- Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK
| | - M Thurston
- Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK
| | - M R Viant
- Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - C L Winder
- Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - C A Goble
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - C P Ponting
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - G Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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14
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Eckes AH, Gubała T, Nowakowski P, Szymczyszyn T, Wells R, Irwin JA, Horro C, Hancock JM, King G, Dyer SC, Jurkowski W. Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data. F1000Res 2017; 6:465. [PMID: 28529710 PMCID: PMC5428495 DOI: 10.12688/f1000research.11301.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/16/2017] [Indexed: 11/20/2022] Open
Abstract
The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users. BIP opens up the opportunity to apply integrative, cross-project analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.
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Affiliation(s)
| | - Tomasz Gubała
- Earlham Institute, Norwich, NR4 7UZ, UK.,Academic Computer Centre CYFRONET, AGH University of Science and Technology, Kraków, 30-059, Poland
| | - Piotr Nowakowski
- Earlham Institute, Norwich, NR4 7UZ, UK.,Academic Computer Centre CYFRONET, AGH University of Science and Technology, Kraków, 30-059, Poland
| | | | | | | | | | | | - Graham King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
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15
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Eckes AH, Gubała T, Nowakowski P, Szymczyszyn T, Wells R, Irwin JA, Horro C, Hancock JM, King G, Dyer SC, Jurkowski W. Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data. F1000Res 2017; 6:465. [PMID: 28529710 DOI: 10.12688/f1000research.11301.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/07/2017] [Indexed: 11/20/2022] Open
Abstract
The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for scientists and breeders. BIP opens up the opportunity to apply big data analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.
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Affiliation(s)
| | - Tomasz Gubała
- Earlham Institute, Norwich, NR4 7UZ, UK
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Kraków, 30-059, Poland
| | - Piotr Nowakowski
- Earlham Institute, Norwich, NR4 7UZ, UK
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Kraków, 30-059, Poland
| | | | | | | | | | | | - Graham King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
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16
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Abstract
ELIXIR is the European infrastructure established specifically for the sharing and sustainability of life science data. To provide up-to-date resources and services, ELIXIR needs to undergo a continuous process of refreshing the services provided by its national Nodes. Here we present the approach taken by ELIXIR-UK to address the advice by the ELIXIR Scientific Advisory Board that Nodes need to develop “
mechanisms to ensure that each Node continues to be representative of the Bioinformatics efforts within the country”. ELIXIR-UK put in place an open and transparent process to identify potential ELIXIR resources within the UK during late 2015 and early to mid-2016. Areas of strategic strength were identified and Expressions of Interest in these priority areas were requested from the UK community. Criteria were established, in discussion with the ELIXIR Hub, and prospective ELIXIR-UK resources were assessed by an independent committee set up by the Node for this purpose. Of 19 resources considered, 14 were judged to be immediately ready to be included in the UK ELIXIR Node’s portfolio. A further five were placed on the Node’s roadmap for future consideration for inclusion. ELIXIR-UK expects to repeat this process regularly to ensure its portfolio continues to reflect its community’s strengths.
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Affiliation(s)
| | - Alf Game
- Tatterdemalion Solutions, Marlborough, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Carole A Goble
- School of Computer Science, University of Manchester, Manchester, UK
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17
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Vihinen M, Hancock JM, Maglott DR, Landrum MJ, Schaafsma GCP, Taschner P. Human Variome Project Quality Assessment Criteria for Variation Databases. Hum Mutat 2016; 37:549-58. [PMID: 26919176 DOI: 10.1002/humu.22976] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/25/2016] [Accepted: 02/12/2016] [Indexed: 12/28/2022]
Abstract
Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184, Lund, Sweden
| | - John M Hancock
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Donna R Maglott
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, 20892
| | - Melissa J Landrum
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, 20892
| | - Gerard C P Schaafsma
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184, Lund, Sweden
| | - Peter Taschner
- Generade Center of Expertise Genomics and University of Applied Sciences Leiden, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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18
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Hancock JM. Circles within circles: commentary on Ghosal et al. (2013) "Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits". Front Genet 2015; 5:459. [PMID: 25610452 PMCID: PMC4285795 DOI: 10.3389/fgene.2014.00459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 12/15/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- John M Hancock
- Department of Physiology, Development and Neuroscience, University of Cambridge Cambridge, UK
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19
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Chesnel K, Trevino M, Cai Y, Hancock JM, Smith SJ, Harrison RG. Particle size effects on the magnetic behaviour of 5 to 11 nm Fe3O4nanoparticles coated with oleic acid. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/521/1/012004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Hancock JM. Commentary on Shimoyama et al. (2012): three ontologies to define phenotype measurement data. Front Genet 2014; 5:93. [PMID: 24795755 PMCID: PMC4006037 DOI: 10.3389/fgene.2014.00093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/03/2014] [Indexed: 01/17/2023] Open
Affiliation(s)
- John M Hancock
- Department of Physiology, Development and Neuroscience, University of Cambridge Cambridge, UK
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21
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Affiliation(s)
- John M Hancock
- Department of Physiology, Development and Neuroscience, University of Cambridge Cambridge, UK
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22
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Abstract
The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35-45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.
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Affiliation(s)
- Christopher Southan
- IUPHAR Database and Guide to Pharmacology Web Portal Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of EdinburghEdinburgh, UK
| | - John M. Hancock
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridge, UK
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23
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Hoehndorf R, Hancock JM, Hardy NW, Mallon AM, Schofield PN, Gkoutos GV. Analyzing gene expression data in mice with the Neuro Behavior Ontology. Mamm Genome 2013; 25:32-40. [PMID: 24177753 DOI: 10.1007/s00335-013-9481-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/02/2013] [Indexed: 12/13/2022]
Abstract
We have applied the Neuro Behavior Ontology (NBO), an ontology for the annotation of behavioral gene functions and behavioral phenotypes, to the annotation of more than 1,000 genes in the mouse that are known to play a role in behavior. These annotations can be explored by researchers interested in genes involved in particular behaviors and used computationally to provide insights into the behavioral phenotypes resulting from differences in gene expression. We developed the OntoFUNC tool and have applied it to enrichment analyses over the NBO to provide high-level behavioral interpretations of gene expression datasets. The resulting increase in the number of gene annotations facilitates the identification of behavioral or neurologic processes by assisting the formulation of hypotheses about the relationships between gene, processes, and phenotypic manifestations resulting from behavioral observations.
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Affiliation(s)
- Robert Hoehndorf
- Department of Computer Science, University of Aberystwyth, Old College, King Street, Aberystwyth, SY23 2AX, UK,
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24
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Simon MM, Greenaway S, White JK, Fuchs H, Gailus-Durner V, Wells S, Sorg T, Wong K, Bedu E, Cartwright EJ, Dacquin R, Djebali S, Estabel J, Graw J, Ingham NJ, Jackson IJ, Lengeling A, Mandillo S, Marvel J, Meziane H, Preitner F, Puk O, Roux M, Adams DJ, Atkins S, Ayadi A, Becker L, Blake A, Brooker D, Cater H, Champy MF, Combe R, Danecek P, di Fenza A, Gates H, Gerdin AK, Golini E, Hancock JM, Hans W, Hölter SM, Hough T, Jurdic P, Keane TM, Morgan H, Müller W, Neff F, Nicholson G, Pasche B, Roberson LA, Rozman J, Sanderson M, Santos L, Selloum M, Shannon C, Southwell A, Tocchini-Valentini GP, Vancollie VE, Westerberg H, Wurst W, Zi M, Yalcin B, Ramirez-Solis R, Steel KP, Mallon AM, de Angelis MH, Herault Y, Brown SDM. A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. Genome Biol 2013; 14:R82. [PMID: 23902802 PMCID: PMC4053787 DOI: 10.1186/gb-2013-14-7-r82] [Citation(s) in RCA: 335] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 06/07/2013] [Accepted: 07/31/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as the International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely used in mouse genetics studies. Here we perform a comprehensive genomic and phenotypic analysis of the two strains to identify differences that may influence their underlying genetic mechanisms. RESULTS We undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. We annotate 34 SNPs and 2 indels that distinguish C57BL/6J and C57BL/6N coding sequences, as well as 15 structural variants that overlap a gene. In parallel we assess the comparative phenotypes of the two inbred lines utilizing the EMPReSSslim phenotyping pipeline, a broad based assessment encompassing diverse biological systems. We perform additional secondary phenotyping assessments to explore other phenotype domains and to elaborate phenotype differences identified in the primary assessment. We uncover significant phenotypic differences between the two lines, replicated across multiple centers, in a number of physiological, biochemical and behavioral systems. CONCLUSIONS Comparison of C57BL/6J and C57BL/6N demonstrates a range of phenotypic differences that have the potential to impact upon penetrance and expressivity of mutational effects in these strains. Moreover, the sequence variants we identify provide a set of candidate genes for the phenotypic differences observed between the two strains.
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Affiliation(s)
- Michelle M Simon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Simon Greenaway
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Jacqueline K White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Helmut Fuchs
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Valérie Gailus-Durner
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Sara Wells
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Tania Sorg
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Kim Wong
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Elodie Bedu
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Elizabeth J Cartwright
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, MN13 9PT, UK
| | - Romain Dacquin
- AniRA ImmOs phenotyping facility- SFR Biosciences Lyon Gerland- UMS3444/US8, 21 avenue Tony Garnier F-69007 Lyon, France
| | - Sophia Djebali
- AniRA ImmOs phenotyping facility- SFR Biosciences Lyon Gerland- UMS3444/US8, 21 avenue Tony Garnier F-69007 Lyon, France
| | - Jeanne Estabel
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Jochen Graw
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Developmental Genetics, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Neil J Ingham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Ian J Jackson
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Andreas Lengeling
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Veterinary Campus, Midlothian, EH25 9RG, UK
| | - Silvia Mandillo
- Consiglio Nazionale delle Ricerche- Cell Biology and Neurobiology Institute, Via E.Ramarini 32, 00015 Monterotondo Scala, Italy
| | - Jacqueline Marvel
- AniRA ImmOs phenotyping facility- SFR Biosciences Lyon Gerland- UMS3444/US8, 21 avenue Tony Garnier F-69007 Lyon, France
| | - Hamid Meziane
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Frédéric Preitner
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Oliver Puk
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Developmental Genetics, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Michel Roux
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Sarah Atkins
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Abdel Ayadi
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Lore Becker
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Andrew Blake
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Debra Brooker
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Marie-France Champy
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Roy Combe
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Petr Danecek
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Armida di Fenza
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Hilary Gates
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Anna-Karin Gerdin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Elisabetta Golini
- Consiglio Nazionale delle Ricerche- Cell Biology and Neurobiology Institute, Via E.Ramarini 32, 00015 Monterotondo Scala, Italy
| | - John M Hancock
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Wolfgang Hans
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Sabine M Hölter
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Tertius Hough
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Pierre Jurdic
- AniRA ImmOs phenotyping facility- SFR Biosciences Lyon Gerland- UMS3444/US8, 21 avenue Tony Garnier F-69007 Lyon, France
| | - Thomas M Keane
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Hugh Morgan
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, MN13 9PT, UK
| | - Frauke Neff
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Pathology, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - George Nicholson
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Bastian Pasche
- Mouse Metabolic Facility of the Cardiomet Center, University Hospital, and Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Laura-Anne Roberson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Jan Rozman
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Mark Sanderson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Luis Santos
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Mohammed Selloum
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Carl Shannon
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Anne Southwell
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Glauco P Tocchini-Valentini
- Consiglio Nazionale delle Ricerche- Cell Biology and Neurobiology Institute, Via E.Ramarini 32, 00015 Monterotondo Scala, Italy
| | - Valerie E Vancollie
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Henrik Westerberg
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Wolfgang Wurst
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Developmental Genetics, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
- Chair for Developmental Genetics, Technische Universität München, Arcisstr. 21, Munich, 80333, Germany
- Max Planck Institute of Psychiatry, Kraepelinstrasse 2, Munich, 80804, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Schillerstrasse 44, Munich, 80336, Germany
| | - Min Zi
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, MN13 9PT, UK
| | - Binnaz Yalcin
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
- Center for Integrative Genomics, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Karen P Steel
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
| | - Martin Hrabě de Angelis
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Yann Herault
- Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, France
| | - Steve DM Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, UK
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Hazelwood LD, Hancock JM. Functional modelling of planar cell polarity: an approach for identifying molecular function. BMC Dev Biol 2013; 13:20. [PMID: 23672397 PMCID: PMC3662592 DOI: 10.1186/1471-213x-13-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/30/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Cells in some tissues acquire a polarisation in the plane of the tissue in addition to apical-basal polarity. This polarisation is commonly known as planar cell polarity and has been found to be important in developmental processes, as planar polarity is required to define the in-plane tissue coordinate system at the cellular level. RESULTS We have built an in-silico functional model of cellular polarisation that includes cellular asymmetry, cell-cell signalling and a response to a global cue. The model has been validated and parameterised against domineering non-autonomous wing hair phenotypes in Drosophila. CONCLUSIONS We have carried out a systematic comparison of in-silico polarity phenotypes with patterns observed in vivo under different genetic manipulations in the wing. This has allowed us to classify the specific functional roles of proteins involved in generating cell polarity, providing new hypotheses about their specific functions, in particular for Pk and Dsh. The predictions from the model allow direct assignment of functional roles of genes from genetic mosaic analysis of Drosophila wings.
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Affiliation(s)
- Lee D Hazelwood
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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26
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Abstract
Motivation: The identification of nucleosomes along the chromatin is key to understanding their role in the regulation of gene expression and other DNA-related processes. However, current experimental methods (MNase-ChIP, MNase-Seq) sample nucleosome positions from a cell population and contain biases, making thus the precise identification of individual nucleosomes not straightforward. Recent works have only focused on the first point, where noise reduction approaches have been developed to identify nucleosome positions. Results: In this article, we propose a new approach, termed NucleoFinder, that addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a control sample. Despite the absence of validated dataset, we show that our approach (i) detects fewer false positives than two other nucleosome calling methods and (ii) identifies two important features of the nucleosome organization (the nucleosome spacing downstream of active promoters and the enrichment/depletion of GC/AT dinucleotides at the centre of in vitro nucleosomes) with equal or greater ability than the other two methods. Availability: The R code of NucleoFinder, an example datafile and instructions are available for download from https://sites.google.com/site/beckerjeremie/ Contact: cholmes@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeremie Becker
- Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
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Schofield PN, Hancock JM. Integration of global resources for human genetic variation and disease. Hum Mutat 2012; 33:813-6. [DOI: 10.1002/humu.22079] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 03/02/2012] [Indexed: 01/22/2023]
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Ainali C, Simon M, Freilich S, Espinosa O, Hazelwood L, Tsoka S, Ouzounis CA, Hancock JM. Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. BMC Evol Biol 2011; 11:142. [PMID: 21612628 PMCID: PMC3112093 DOI: 10.1186/1471-2148-11-142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 05/25/2011] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS) from the β-cells of pancreatic islets. We describe an analysis of the evolutionary processes affecting the core enzymes involved in glucose-stimulated insulin secretion in mammals. The proteins involved in this system belong to ancient enzymatic pathways: glycolysis, the TCA cycle and oxidative phosphorylation. RESULTS We identify two sets of proteins, or protein coalitions, in this group of 77 enzymes with distinct evolutionary patterns. Members of the glycolysis, TCA cycle, metabolite transport, pyruvate and NADH shuttles have low rates of protein sequence evolution, as inferred from a human-mouse comparison, and relatively high rates of evolutionary gene duplication. Respiratory chain and glutathione pathway proteins evolve faster, exhibiting lower rates of gene duplication. A small number of proteins in the system evolve significantly faster than co-pathway members and may serve as rapidly evolving adapters, linking groups of co-evolving genes. CONCLUSIONS Our results provide insights into the evolution of the involved proteins. We find evidence for two coalitions of proteins and the role of co-adaptation in protein evolution is identified and could be used in future research within a functional context.
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Affiliation(s)
- Chrysanthi Ainali
- Centre for Bioinformatics, Department of Informatics, School of Natural and Mathematical Sciences, King's College London, Strand, UK
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29
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Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) 2011; 2011:baq027. [PMID: 21205783 PMCID: PMC3017395 DOI: 10.1093/database/baq027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.
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Affiliation(s)
- Pascale Gaudet
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- *Corresponding author: Tel: +41-22-379-5050; Fax: +41-22-379-5858;
| | - Amos Bairoch
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Dawn Field
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Susanna-Assunta Sansone
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chris Taylor
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Teresa K. Attwood
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alex Bateman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Judith A. Blake
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carol J. Bult
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - J. Michael Cherry
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rex L. Chisholm
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Guy Cochrane
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Charles E. Cook
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janan T. Eppig
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael Y. Galperin
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Gentleman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carole A. Goble
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Takashi Gojobori
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John M. Hancock
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Douglas G. Howe
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tadashi Imanishi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janet Kelso
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David Landsman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Suzanna E. Lewis
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ilene Karsch Mizrachi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sandra Orchard
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - B.F. Francis Ouellette
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shoba Ranganathan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Lorna Richardson
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Philippe Rocca-Serra
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul N. Schofield
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Damian Smedley
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Christopher Southan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tin W. Tan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tatiana Tatusova
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Patricia L. Whetzel
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Owen White
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chisato Yamasaki
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BFF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res 2010; 39:D7-10. [PMID: 21097465 PMCID: PMC3013734 DOI: 10.1093/nar/gkq1173] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.
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Affiliation(s)
- Pascale Gaudet
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- *To whom correspondence should be addressed. Tel: +41 22 379 5050; Fax: +41 22 379 5858;
| | - Amos Bairoch
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Dawn Field
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Susanna-Assunta Sansone
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chris Taylor
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Teresa K. Attwood
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alex Bateman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Judith A. Blake
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carol J. Bult
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - J. Michael Cherry
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rex L. Chisholm
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Guy Cochrane
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Charles E. Cook
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janan T. Eppig
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael Y. Galperin
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Gentleman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carole A. Goble
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Takashi Gojobori
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John M. Hancock
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Douglas G. Howe
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tadashi Imanishi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janet Kelso
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David Landsman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Suzanna E. Lewis
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ilene Karsch Mizrachi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sandra Orchard
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - B. F. Francis Ouellette
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shoba Ranganathan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Lorna Richardson
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Philippe Rocca-Serra
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul N. Schofield
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Damian Smedley
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Christopher Southan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tin Wee Tan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tatiana Tatusova
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Patricia L. Whetzel
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Owen White
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chisato Yamasaki
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Schofield PN, Eppig J, Huala E, de Angelis MH, Harvey M, Davidson D, Weaver T, Brown S, Smedley D, Rosenthal N, Schughart K, Aidinis V, Tocchini-Valentini G, Hancock JM. Research funding. Sustaining the data and bioresource commons. Science 2010; 330:592-3. [PMID: 21030633 DOI: 10.1126/science.1191506] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK.
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Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM. Phenotype ontologies for mouse and man: bridging the semantic gap. Dis Model Mech 2010; 3:281-9. [PMID: 20427557 DOI: 10.1242/dmm.002790] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A major challenge of the post-genomic era is coding phenotype data from humans and model organisms such as the mouse, to permit the meaningful translation of phenotype descriptions between species. This ability is essential if we are to facilitate phenotype-driven gene function discovery and empower comparative pathobiology. Here, we review the current state of the art for phenotype and disease description in mice and humans, and discuss ways in which the semantic gap between coding systems might be bridged to facilitate the discovery and exploitation of new mouse models of human diseases.
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Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R, Birney E, Blake A, Bongcam-Rudloff E, Brookes AJ, Cesareni G, Chandras C, Eppig J, Flicek P, Gkoutos G, Greenaway S, Gruenberger M, Hériché JK, Lyall A, Mallon AM, Muddyman D, Reisinger F, Ringwald M, Rosenthal N, Schughart K, Swertz M, Thorisson GA, Zouberakis M, Hancock JM. Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database (Oxford) 2010; 2010:baq014. [PMID: 20627863 PMCID: PMC2911849 DOI: 10.1093/database/baq014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 06/20/2010] [Indexed: 11/14/2022]
Abstract
The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them. Despite a rapid acceleration in uptake of syntactic and semantic standards for interoperability, it is still difficult for users to find which databases support the standards and interfaces that they need. To solve these problems, several groups are developing registries of databases that capture key metadata describing the biological scope, utility, accessibility, ease-of-use and existence of web services allowing interoperability between resources. Here, we describe some of these initiatives including a novel formalism, the Database Description Framework, for describing database operations and functionality and encouraging good database practise. We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf.
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Affiliation(s)
- Damian Smedley
- European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA.
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Zouberakis M, Chandras C, Swertz M, Smedley D, Gruenberger M, Bard J, Schughart K, Rosenthal N, Hancock JM, Schofield PN, Kollias G, Aidinis V. Mouse Resource Browser--a database of mouse databases. Database (Oxford) 2010; 2010:baq010. [PMID: 20627861 PMCID: PMC2911845 DOI: 10.1093/database/baq010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The laboratory mouse has become the organism of choice for discovering gene function and unravelling pathogenetic mechanisms of human diseases through the application of various functional genomic approaches. The resulting deluge of data has led to the deployment of numerous online resources and the concomitant need for formalized experimental descriptions, data standardization, database interoperability and integration, a need that has yet to be met. We present here the Mouse Resource Browser (MRB), a database of mouse databases that indexes 217 publicly available mouse resources under 22 categories and uses a standardised database description framework (the CASIMIR DDF) to provide information on their controlled vocabularies (ontologies and minimum information standards), and technical information on programmatic access and data availability. Focusing on interoperability and integration, MRB offers automatic generation of downloadable and re-distributable SOAP application-programming interfaces for resources that provide direct database access. MRB aims to provide useful information to both bench scientists, who can easily navigate and find all mouse related resources in one place, and bioinformaticians, who will be provided with interoperable resources containing data which can be mined and integrated. Database URL: http://bioit.fleming.gr/mrb
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Affiliation(s)
- Michael Zouberakis
- Institute of Immunology, Biomedical Sciences Research Center Alexander Fleming, 34 Fleming Street, 16672 Athens, Greece
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Gkoutos GV, Green ECJ, Mallon AM, Blake A, Greenaway S, Hancock JM, Davidson D. Ontologies for the description of mouse phenotypes. Comp Funct Genomics 2010; 5:545-51. [PMID: 18629136 PMCID: PMC2447424 DOI: 10.1002/cfg.430] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Accepted: 10/18/2004] [Indexed: 11/12/2022] Open
Abstract
Ontologies are becoming increasingly important for the efficient storage, retrieval
and mining of biological data. The description of phenotypes using ontologies is a
particularly complex problem. We outline a schema that can be used to describe
phenotypes by combining orthologous axiomatic ontologies. We also describe tools for
storing, browsing and searching such complex ontologies. Central to this approach is
that assays (protocols for measuring phenotypic characters) describe what has been
measured as well as how this was done, allowing assays to link individual organisms to
ontologies describing phenotypes. We have evaluated this approach by automatically
annotating data on 600 000 mutant mice phenotypes using the SHIRPA protocol. We
believe this approach will enable the flexible, extensible and detailed description of
phenotypes from any organism.
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Affiliation(s)
- G V Gkoutos
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK.
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36
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Swertz MA, Velde KJVD, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, Jansen RC. XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biol 2010; 11:R27. [PMID: 20214801 PMCID: PMC2864567 DOI: 10.1186/gb-2010-11-3-r27] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 12/17/2009] [Accepted: 03/09/2010] [Indexed: 11/10/2022] Open
Abstract
XGAP, a software platform for the integration and analysis of genotype and phenotype data. We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.
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Affiliation(s)
- Morris A Swertz
- Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands.
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Abstract
The mouse is central to the goal of establishing a comprehensive functional annotation of the mammalian genome that will help elucidate various human disease genes and pathways. The mouse offers a unique combination of attributes, including an extensive genetic toolkit that underpins the creation and analysis of models of human disease. An international effort to generate mutations for every gene in the mouse genome is a first and essential step in this endeavor. However, the greater challenge will be the determination of the phenotype of every mutant. Large-scale phenotyping for genome-wide functional annotation presents numerous scientific, infrastructural, logistical, and informatics challenges. These include the use of standardized approaches to phenotyping procedures for the population of unified databases with comparable data sets. The ultimate goal is a comprehensive database of molecular interventions that allows us to create a framework for biological systems analysis in the mouse on which human biology and disease networks can be revealed.
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Affiliation(s)
- Steve D M Brown
- MRC Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom.
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Morgan H, Beck T, Blake A, Gates H, Adams N, Debouzy G, Leblanc S, Lengger C, Maier H, Melvin D, Meziane H, Richardson D, Wells S, White J, Wood J, de Angelis MH, Brown SDM, Hancock JM, Mallon AM. EuroPhenome: a repository for high-throughput mouse phenotyping data. Nucleic Acids Res 2009; 38:D577-85. [PMID: 19933761 PMCID: PMC2808931 DOI: 10.1093/nar/gkp1007] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.
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Affiliation(s)
- Hugh Morgan
- MRC Harwell, Mammalian Genetics Unit, MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
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Blake A, Pickford K, Greenaway S, Thomas S, Pickard A, Williamson CM, Adams NC, Walling A, Beck T, Fray M, Peters J, Weaver T, Brown SDM, Hancock JM, Mallon AM. MouseBook: an integrated portal of mouse resources. Nucleic Acids Res 2009; 38:D593-9. [PMID: 19854936 PMCID: PMC2808969 DOI: 10.1093/nar/gkp867] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The MouseBook (http://www.mousebook.org) databases and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. The MouseBook portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information above and beyond what is available through other routes such as International Mouse Stain Resource (IMSR). MouseBook can be searched either using an intuitive Google style free text search or using the Mammalian Phenotype (MP) ontology tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database. Results are returned in a tabbed format providing categorized results identified from each of the catalogs in MouseBook. Individual result lines from each catalog include information on gene, allele, chromosomal location and phenotype, and provide a simple click-through link to further information as well as ordering the strain. The infrastructure underlying MouseBook has been designed to be extensible, allowing additional data sources to be added and enabling other sites to make their data directly available through MouseBook.
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Affiliation(s)
- Andrew Blake
- MRC Harwell, Mammalian Genetics Unit and the Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
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40
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Chandras C, Weaver T, Zouberakis M, Smedley D, Schughart K, Rosenthal N, Hancock JM, Kollias G, Schofield PN, Aidinis V. Models for financial sustainability of biological databases and resources. Database (Oxford) 2009; 2009:bap017. [PMID: 20157490 PMCID: PMC2790311 DOI: 10.1093/database/bap017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/02/2009] [Accepted: 09/16/2009] [Indexed: 11/23/2022]
Abstract
Following the technological advances that have enabled genome-wide analysis in most model organisms over the last decade, there has been unprecedented growth in genomic and post-genomic science with concomitant generation of an exponentially increasing volume of data and material resources. As a result, numerous repositories have been created to store and archive data, organisms and material, which are of substantial value to the whole community. Sustained access, facilitating re-use of these resources, is essential, not only for validation, but for re-analysis, testing of new hypotheses and developing new technologies/platforms. A common challenge for most data resources and biological repositories today is finding financial support for maintenance and development to best serve the scientific community. In this study we examine the problems that currently confront the data and resource infrastructure underlying the biomedical sciences. We discuss the financial sustainability issues and potential business models that could be adopted by biological resources and consider long term preservation issues within the context of mouse functional genomics efforts in Europe.
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Affiliation(s)
- Christina Chandras
- Institute of Immunology, Biomedical Sciences Research Center Alexander Fleming, 34 Fleming Street, 16672 Athens, Greece, MRC Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, European Bioinformatics Institute, EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, Experimental Mouse Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine, Hannover, Inhoffenstrabe 7, D-38124 Braunschweig, Germany, EMBL-Monterotondo Outstation, Via Ramarini 32, 00015 Monterotondo-Scalo (RM), Italy, Bioinformatics Group, MRC Harwell, Harwell, Oxfordshire, OX11 0RD and Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
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Schofield PN, Bubela T, Weaver T, Portilla L, Brown SD, Hancock JM, Einhorn D, Tocchini-Valentini G, Hrabe de Angelis M, Rosenthal N. Post-publication sharing of data and tools. Nature 2009; 461:171-3. [PMID: 19741686 DOI: 10.1038/461171a] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Despite existing guidelines on access to data and bioresources, good practice is not widespread. A meeting of mouse researchers in Rome proposes ways to promote a culture of sharing.
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Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK.
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42
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Hancock JM, Mallon AM, Beck T, Gkoutos GV, Mungall C, Schofield PN. Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mamm Genome 2009; 20:457-61. [PMID: 19649761 PMCID: PMC2759022 DOI: 10.1007/s00335-009-9208-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 07/10/2009] [Indexed: 12/16/2022]
Abstract
Now that the laboratory mouse genome is sequenced and the annotation of its gene content is improving, the next major challenge is the annotation of the phenotypic associations of mouse genes. This requires the development of systematic phenotyping pipelines that use standardized phenotyping procedures which allow comparison across laboratories. It also requires the development of a sophisticated informatics infrastructure for the description and interchange of phenotype data. Here we focus on the current state of the art in the description of data produced by systematic phenotyping approaches using ontologies, in particular, the EQ (Entity-Quality) approach, and what developments are required to facilitate the linking of phenotypic descriptions of mutant mice to human diseases.
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Affiliation(s)
- John M Hancock
- Bioinformatics Group, MRC Harwell, Harwell, Oxfordshire, OX11 0RD, UK.
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43
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Abstract
BACKGROUND Amino acid repeats (AARs) are common features of protein sequences. They often evolve rapidly and are involved in a number of human diseases. They also show significant associations with particular Gene Ontology (GO) functional categories, particularly transcription, suggesting they play some role in protein function. It has been suggested recently that AARs play a significant role in the evolution of intrinsically unstructured regions (IURs) of proteins. We investigate the relationship between AAR frequency and evolution and their localization within proteins based on a set of 5,815 orthologous proteins from four mammalian (human, chimpanzee, mouse and rat) and a bird (chicken) genome. We consider two classes of AAR (tandem repeats and cryptic repeats: regions of proteins containing overrepresentations of short amino acid repeats). RESULTS Mammals show very similar repeat frequencies but chicken shows lower frequencies of many of the cryptic repeats common in mammals. Regions flanking tandem AARs evolve more rapidly than the rest of the protein containing the repeat and this phenomenon is more pronounced for non-conserved repeats than for conserved ones. GO associations are similar to those previously described for the mammals, but chicken cryptic repeats show fewer significant associations. Comparing the overlaps of AARs with IURs and protein domains showed that up to 96% of some AAR types are associated preferentially with IURs. However, no more than 15% of IURs contained an AAR. CONCLUSIONS Their location within IURs explains many of the evolutionary properties of AARs. Further study is needed on the types of IURs containing AARs.
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Affiliation(s)
- Michelle Simon
- Bioinformatics Group, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxfordshire, OX11 0RD, UK
| | - John M Hancock
- Bioinformatics Group, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxfordshire, OX11 0RD, UK
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Beck T, Morgan H, Blake A, Wells S, Hancock JM, Mallon AM. Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. BMC Bioinformatics 2009; 10 Suppl 5:S2. [PMID: 19426459 PMCID: PMC2679402 DOI: 10.1186/1471-2105-10-s5-s2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Large-scale international projects are underway to generate collections of knockout mouse mutants and subsequently to perform high throughput phenotype assessments, raising new challenges for computational researchers due to the complexity and scale of the phenotype data. Phenotypes can be described using ontologies in two differing methodologies. Traditionally an individual phenotypic character has either been defined using a single compound term, originating from a species-specific dedicated phenotype ontology, or alternatively by a combinatorial annotation, using concepts from a range of disparate ontologies, to define a phenotypic character as an entity with an associated quality (EQ). Both methods have their merits, which include the dedicated approach allowing use of community standard terminology, and the combinatorial approach facilitating cross-species phenotypic statement comparisons. Previously databases have favoured one approach over another. The EUMODIC project will generate large amounts of mouse phenotype data, generated as a result of the execution of a set of Standard Operating Procedures (SOPs) and will implement both ontological approaches to capture the phenotype data generated. Results For all SOPs a four-tier annotation is made: a high-level description of the SOP, to broadly define the type of data generated by the SOP; individual parameter annotation using the EQ model; annotation of the qualitative data generated for each mouse; and the annotation of mutant lines after statistical analysis. The qualitative assessments of phenodeviance are made at the point of data entry, using child PATO qualities to the parameter quality. To facilitate data querying by scientists more familiar with single compound terms to describe phenotypes, the mappings between the Mammalian Phenotype (MP) ontology and the EQ PATO model are exploited to allow querying via MP terms. Conclusion Well-annotated and comparable phenotype databases can be achieved through the use of ontologically derived comparable phenotypic statements and have been implemented here by means of OBO compatible EQ annotations. The implementation we describe also sees scientists working seamlessly with ontologies through the assessment of qualitative phenotypes in terms of PATO qualities and the ability to query the database using community-accepted compound MP terms. This work represents the first time the combinatorial and single-dedicated approaches have both been implemented to annotate a phenotypic dataset.
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Affiliation(s)
- Tim Beck
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK.
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Kaput J, Cotton RGH, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MRN, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SGE, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AMO, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS. Planning the human variome project: the Spain report. Hum Mutat 2009; 30:496-510. [PMID: 19306394 PMCID: PMC5879779 DOI: 10.1002/humu.20972] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.
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Affiliation(s)
- Jim Kaput
- Division of Personalised Nutrition and Medicine, FDA/National Center for Toxicological Research, Jefferson, Arkansas 72079, USA.
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Smedley D, Swertz MA, Wolstencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P. Solutions for data integration in functional genomics: a critical assessment and case study. Brief Bioinform 2009; 9:532-44. [PMID: 19112082 DOI: 10.1093/bib/bbn040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.
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Affiliation(s)
- Damian Smedley
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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47
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Abstract
MOTIVATION Conventional phylogenetic analysis for characterizing the relatedness between taxa typically assumes that a single relationship exists between species at every site along the genome. This assumption fails to take into account recombination which is a fundamental process for generating diversity and can lead to spurious results. Recombination induces a localized phylogenetic structure which may vary along the genome. Here, we generalize a hidden Markov model (HMM) to infer changes in phylogeny along multiple sequence alignments while accounting for rate heterogeneity; the hidden states refer to the unobserved phylogenic topology underlying the relatedness at a genomic location. The dimensionality of the number of hidden states (topologies) and their structure are random (not known a priori) and are sampled using Markov chain Monte Carlo algorithms. The HMM structure allows us to analytically integrate out over all possible changepoints in topologies as well as all the unknown branch lengths. RESULTS We demonstrate our approach on simulated data and also to the genome of a suspected HIV recombinant strain as well as to an investigation of recombination in the sequences of 15 laboratory mouse strains sequenced by Perlegen Sciences. Our findings indicate that our method allows us to distinguish between rate heterogeneity and variation in phylogeny caused by recombination without being restricted to 4-taxa data.
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Affiliation(s)
- Alex Webb
- Department of Statistics, Oxford, UK
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Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008; 26:889-96. [PMID: 18688244 PMCID: PMC2771753 DOI: 10.1038/nbt.1411] [Citation(s) in RCA: 356] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated development of such checklists.
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Affiliation(s)
- Chris F Taylor
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. ,
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Abstract
An essential aspect to understanding the functional significance of individual genes in the mouse genome is an understanding of the phenotypic consequences of gene mutations. A wide variety of online sites exist that provide different types of phenotypic information on the laboratory mouse. In this review, we describe the major resources that are currently available and discuss some of the bioinformatics requirements that will be necessary to make more seamless searching, comparison and analysis of these various data types possible.
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Affiliation(s)
- John M Hancock
- Bioinformatics Group, MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK.
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Abstract
EuroPhenome (http://www.europhenome.org) and EMPReSS (http://empress.har.mrc.ac.uk/) form an integrated resource to provide access to data and procedures for mouse phenotyping. EMPReSS describes 96 Standard Operating Procedures for mouse phenotyping. EuroPhenome contains data resulting from carrying out EMPReSS protocols on four inbred laboratory mouse strains. As well as web interfaces, both resources support web services to enable integration with other mouse phenotyping and functional genetics resources, and are committed to initiatives to improve integration of mouse phenotype databases. EuroPhenome will be the repository for a recently initiated effort to carry out large-scale phenotyping on a large number of knockout mouse lines (EUMODIC).
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Affiliation(s)
- Ann-Marie Mallon
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, OX11 0RD, UK.
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