1
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Fisher M, James-Zorn C, Ponferrada V, Bell AJ, Sundararaj N, Segerdell E, Chaturvedi P, Bayyari N, Chu S, Pells T, Lotay V, Agalakov S, Wang DZ, Arshinoff BI, Foley S, Karimi K, Vize PD, Zorn AM. Xenbase: Key Features and Resources of the Xenopus Model Organism Knowledgebase. Genetics 2023; 224:7031801. [PMID: 36755307 PMCID: PMC10158840 DOI: 10.1093/genetics/iyad018] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/10/2023] Open
Abstract
Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web accessible resource that integrates the diverse genomic and biological data from research on the laboratory frogs Xenopus laevis and Xenopus tropicalis. The goal of Xenbase is to accelerate discovery and empower Xenopus research, enhance the impact of Xenopus research data and to facilitate the dissemination of these data. Xenbase also enhances the value of Xenopus data through high quality curation, data integration, providing bioinformatics tools optimized for Xenopus experiments, and by linking Xenopus data to humans and other model organisms. Xenbase also plays an indispensable role in making Xenopus data interoperable and accessible to the broader biomedical community in accordance with FAIR principles. Xenbase provides annotated data updates to organizations such as NCBI, UniProtKB, Ensembl, the Gene Ontology consortium and mostly recently, the Alliance of Genomic Resources, a common clearing house for data from humans and model organisms. This article provides a brief overview of key and recently added features of Xenbase. New features include processing of Xenopus high throughput sequencing data from the NCBI Gene Expression Omnibus, curation of anatomical, physiological and expression phenotypes with the newly created Xenopus Phenotype Ontology, Xenopus Gene Ontology annotations, new anatomical drawings of the Normal Table of Xenopus development, and integration of the latest Xenopus laevis v10.1 genome annotations. Finally, we highlight areas for future development at Xenbase as we continue to support the Xenopus research community.
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Affiliation(s)
- Malcolm Fisher
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Christina James-Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Virgilio Ponferrada
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew J Bell
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nivitha Sundararaj
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erik Segerdell
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Praneet Chaturvedi
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nadia Bayyari
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Stanley Chu
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Troy Pells
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Vaneet Lotay
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sergei Agalakov
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Dong Zhuo Wang
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Bradley I Arshinoff
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kamran Karimi
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Peter D Vize
- Xenbase, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Aaron M Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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2
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Fisher ME, Segerdell E, Matentzoglu N, Nenni MJ, Fortriede JD, Chu S, Pells TJ, Osumi-Sutherland D, Chaturvedi P, James-Zorn C, Sundararaj N, Lotay VS, Ponferrada V, Wang DZ, Kim E, Agalakov S, Arshinoff BI, Karimi K, Vize PD, Zorn AM. The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. BMC Bioinformatics 2022; 23:99. [PMID: 35317743 PMCID: PMC8939077 DOI: 10.1186/s12859-022-04636-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease. Results Here we present the Xenopus phenotype ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated. Conclusions The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype–phenotype data that can be directly related to other uPheno compliant resources. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04636-8.
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Affiliation(s)
- Malcolm E Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Erik Segerdell
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nicolas Matentzoglu
- Monarch Initiative, London, UK.,Semanticly Ltd, London, UK.,European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Mardi J Nenni
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Joshua D Fortriede
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stanley Chu
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Troy J Pells
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | | | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nivitha Sundararaj
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vaneet S Lotay
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Virgilio Ponferrada
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dong Zhuo Wang
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Eugene Kim
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Sergei Agalakov
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Bradley I Arshinoff
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Kamran Karimi
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Peter D Vize
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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3
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Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res 2020; 48:D704-D715. [PMID: 31701156 PMCID: PMC7056945 DOI: 10.1093/nar/gkz997] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [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: 09/20/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022] Open
Abstract
In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.
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Affiliation(s)
- Kent A Shefchek
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Michael Gargano
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Nicolas Matentzoglu
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Deepak Unni
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Matthew Brush
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel Keith
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Tom Conlin
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Nicole Vasilevsky
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - James P Balhoff
- Renaissance Computing Institute at UNC, Chapel Hill, NC 27517, USA
| | - Larry Babb
- Broad Institute, Cambridge, MA 02142, USA
| | | | - Hannah Blau
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Yvonne Bradford
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Leigh Carmody
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Valentina Cipriani
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Maria Della Rocca
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Nathan Dunn
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Shahim Essaid
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Petra Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chris Grove
- California Institute of Technology, Pasadena, CA 91125, USA
| | - Jean-Phillipe Gourdine
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.,Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maureen Hoatlin
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marcin Joachimiak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Simon Jupp
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kenneth B Lett
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Suzanna E Lewis
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | | | - Zoë M Pendlington
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Tim Putman
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Vida Ravanmehr
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Erin Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA 17837, USA
| | - Sofia Robb
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Erik Segerdell
- Xenbase, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Morgan Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea L Storm
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Courtney Thaxon
- University of North Carolina Medical School, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Anne Thessen
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Julie A McMurry
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | | | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Peter N Robinson
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Melissa A Haendel
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.,Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Monica C Munoz-Torres
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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4
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Lie S, Rochet E, Segerdell E, Ma Y, Ashander LM, Shadforth AMA, Blenkinsop TA, Michael MZ, Appukuttan B, Wilmot B, Smith JR. Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection With Toxoplasma gondii. Front Immunol 2019; 10:708. [PMID: 31118929 PMCID: PMC6506780 DOI: 10.3389/fimmu.2019.00708] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/02/2018] [Accepted: 03/15/2019] [Indexed: 11/13/2022] Open
Abstract
Ocular toxoplasmosis is the commonest clinical manifestation of infection with obligate intracellular parasite, Toxoplasma gondii. Active ocular toxoplasmosis is characterized by replication of T. gondii tachyzoites in the retina, with reactive inflammation. The multifunctional retinal pigment epithelium is a key target cell population for T. gondii. Since the global gene expression profile is germane to understanding molecular involvements of retinal pigment epithelial cells in ocular toxoplasmosis, we performed RNA-Sequencing (RNA-Seq) of human cells following infection with T. gondii tachyzoites. Primary cell isolates from eyes of cadaveric donors (n = 3), and the ARPE-19 human retinal pigment epithelial cell line, were infected for 24 h with GT-1 strain T. gondii tachyzoites (multiplicity of infection = 5) or incubated uninfected as control. Total and small RNA were extracted from cells and sequenced on the Illumina NextSeq 500 platform; results were aligned to the human hg19 reference sequence. Multidimensional scaling showed good separation between transcriptomes of infected and uninfected primary cell isolates, which were compared in edgeR software. This differential expression analysis revealed a sizeable response in the total RNA transcriptome-with significantly differentially expressed genes totaling 7,234 (28.9% of assigned transcripts)-but very limited changes in the small RNA transcriptome-totaling 30 (0.35% of assigned transcripts) and including 8 microRNA. Gene ontology and pathway enrichment analyses of differentially expressed total RNA in CAMERA software, identified a strong immunologic transcriptomic signature. We conducted RT-qPCR for 26 immune response-related protein-coding and long non-coding transcripts in epithelial cell isolates from different cadaveric donors (n = 3), extracted by a different isolation protocol but similarly infected with T. gondii, to confirm immunological activity of infected cells. For microRNA, increases in miR-146b and miR-212 were detected by RT-qPCR in 2 and 3 of these independent cell isolates. Biological network analysis in the InnateDB platform, including 735 annotated differentially expressed genes plus 2,046 first-order interactors, identified 10 contextural hubs and 5 subnetworks in the transcriptomic immune response of cells to T. gondii. Our observations provide a solid base for future studies of molecular and cellular interactions between T. gondii and the human retinal pigment epithelium to illuminate mechanisms of ocular toxoplasmosis.
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Affiliation(s)
- Shervi Lie
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Elise Rochet
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Erik Segerdell
- Department of Biostatistics, Oregon Health and Sciences University, Portland, OR, United States
| | - Yuefang Ma
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Liam M. Ashander
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Audra M. A. Shadforth
- Queensland Eye Institute, Brisbane, QLD, Australia
- School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Timothy A. Blenkinsop
- Departments of Cell, Developmental and Regenerative Biology, and Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Michael Z. Michael
- Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Binoy Appukuttan
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
- Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Beth Wilmot
- Department of Biostatistics, Oregon Health and Sciences University, Portland, OR, United States
| | - Justine R. Smith
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
- Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
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5
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Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM. Xenbase: Facilitating the Use of Xenopus to Model Human Disease. Front Physiol 2019; 10:154. [PMID: 30863320 PMCID: PMC6399412 DOI: 10.3389/fphys.2019.00154] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 11/06/2018] [Accepted: 02/08/2019] [Indexed: 01/02/2023] Open
Abstract
At a fundamental level most genes, signaling pathways, biological functions and organ systems are highly conserved between man and all vertebrate species. Leveraging this conservation, researchers are increasingly using the experimental advantages of the amphibian Xenopus to model human disease. The online Xenopus resource, Xenbase, enables human disease modeling by curating the Xenopus literature published in PubMed and integrating these Xenopus data with orthologous human genes, anatomy, and more recently with links to the Online Mendelian Inheritance in Man resource (OMIM) and the Human Disease Ontology (DO). Here we review how Xenbase supports disease modeling and report on a meta-analysis of the published Xenopus research providing an overview of the different types of diseases being modeled in Xenopus and the variety of experimental approaches being used. Text mining of over 50,000 Xenopus research articles imported into Xenbase from PubMed identified approximately 1,000 putative disease- modeling articles. These articles were manually assessed and annotated with disease ontologies, which were then used to classify papers based on disease type. We found that Xenopus is being used to study a diverse array of disease with three main experimental approaches: cell-free egg extracts to study fundamental aspects of cellular and molecular biology, oocytes to study ion transport and channel physiology and embryo experiments focused on congenital diseases. We integrated these data into Xenbase Disease Pages to allow easy navigation to disease information on external databases. Results of this analysis will equip Xenopus researchers with a suite of experimental approaches available to model or dissect a pathological process. Ideally clinicians and basic researchers will use this information to foster collaborations necessary to interrogate the development and treatment of human diseases.
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Affiliation(s)
- Mardi J Nenni
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Malcolm E Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Virgilio Ponferrada
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Stanley Chu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Joshua D Fortriede
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Kevin A Burns
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Ying Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Vaneet S Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Dong Zhou Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Erik Segerdell
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
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6
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Zhang H, Savage S, Schultz AR, Bottomly D, White L, Segerdell E, Wilmot B, McWeeney SK, Eide CA, Nechiporuk T, Carlos A, Henson R, Lin C, Searles R, Ho H, Lam YL, Sweat R, Follit C, Jain V, Lind E, Borthakur G, Garcia-Manero G, Ravandi F, Kantarjian HM, Cortes J, Collins R, Buelow DR, Baker SD, Druker BJ, Tyner JW. Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms. Nat Commun 2019; 10:244. [PMID: 30651561 PMCID: PMC6335421 DOI: 10.1038/s41467-018-08263-x] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [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: 03/01/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
FLT3 mutations are prevalent in AML patients and confer poor prognosis. Crenolanib, a potent type I pan-FLT3 inhibitor, is effective against both internal tandem duplications and resistance-conferring tyrosine kinase domain mutations. While crenolanib monotherapy has demonstrated clinical benefit in heavily pretreated relapsed/refractory AML patients, responses are transient and relapse eventually occurs. Here, to investigate the mechanisms of crenolanib resistance, we perform whole exome sequencing of AML patient samples before and after crenolanib treatment. Unlike other FLT3 inhibitors, crenolanib does not induce FLT3 secondary mutations, and mutations of the FLT3 gatekeeper residue are infrequent. Instead, mutations of NRAS and IDH2 arise, mostly as FLT3-independent subclones, while TET2 and IDH1 predominantly co-occur with FLT3-mutant clones and are enriched in crenolanib poor-responders. The remaining patients exhibit post-crenolanib expansion of mutations associated with epigenetic regulators, transcription factors, and cohesion factors, suggesting diverse genetic/epigenetic mechanisms of crenolanib resistance. Drug combinations in experimental models restore crenolanib sensitivity. FLT3 is commonly mutated in acute myeloid leukaemia and treatment with FLT3 inhibitors often ends with relapse. Here, the authors perform exome sequencing of samples from patients treated with the FLT3 inhibitor, crenolanib, to show that resistance occurs due to diverse molecular mechanisms, not primarily due to secondary FLT3 mutations.
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Affiliation(s)
- Haijiao Zhang
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA.,Division of Hematology and Medical Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Samantha Savage
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA.,Division of Hematology and Medical Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Anna Reister Schultz
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA.,Division of Hematology and Medical Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Daniel Bottomly
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Libbey White
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Erik Segerdell
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Beth Wilmot
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Christopher A Eide
- Division of Hematology and Medical Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA.,Howard Hughes Medical Institute, Portland, 97239, OR, USA
| | - Tamilla Nechiporuk
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA.,Division of Hematology and Medical Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Amy Carlos
- Integrated Genomics, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Rachel Henson
- Integrated Genomics, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Chenwei Lin
- Integrated Genomics, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Robert Searles
- Integrated Genomics, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Hoang Ho
- AROG Pharmaceuticals, Dallas, 75240, TX, USA
| | | | | | | | - Vinay Jain
- AROG Pharmaceuticals, Dallas, 75240, TX, USA
| | - Evan Lind
- Molecular Microbiology & Immunology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA
| | - Gautam Borthakur
- The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | | | - Farhad Ravandi
- The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Hagop M Kantarjian
- The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Jorge Cortes
- The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Robert Collins
- University of Texas Southwestern Medical Center, Dallas, 75390, TX, USA
| | - Daelynn R Buelow
- The Ohio State University College of Pharmacy and Comprehensive Cancer Center, Columbus, 43210, OH, USA
| | - Sharyn D Baker
- The Ohio State University College of Pharmacy and Comprehensive Cancer Center, Columbus, 43210, OH, USA
| | - Brian J Druker
- Division of Hematology and Medical Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA.,Howard Hughes Medical Institute, Portland, 97239, OR, USA
| | - Jeffrey W Tyner
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA. .,Division of Hematology and Medical Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, 97239, OR, USA.
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7
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Tyner JW, Tognon CE, Bottomly D, Wilmot B, Kurtz SE, Savage SL, Long N, Schultz AR, Traer E, Abel M, Agarwal A, Blucher A, Borate U, Bryant J, Burke R, Carlos A, Carpenter R, Carroll J, Chang BH, Coblentz C, d'Almeida A, Cook R, Danilov A, Dao KHT, Degnin M, Devine D, Dibb J, Edwards DK, Eide CA, English I, Glover J, Henson R, Ho H, Jemal A, Johnson K, Johnson R, Junio B, Kaempf A, Leonard J, Lin C, Liu SQ, Lo P, Loriaux MM, Luty S, Macey T, MacManiman J, Martinez J, Mori M, Nelson D, Nichols C, Peters J, Ramsdill J, Rofelty A, Schuff R, Searles R, Segerdell E, Smith RL, Spurgeon SE, Sweeney T, Thapa A, Visser C, Wagner J, Watanabe-Smith K, Werth K, Wolf J, White L, Yates A, Zhang H, Cogle CR, Collins RH, Connolly DC, Deininger MW, Drusbosky L, Hourigan CS, Jordan CT, Kropf P, Lin TL, Martinez ME, Medeiros BC, Pallapati RR, Pollyea DA, Swords RT, Watts JM, Weir SJ, Wiest DL, Winters RM, McWeeney SK, Druker BJ. Functional genomic landscape of acute myeloid leukaemia. Nature 2018; 562:526-531. [PMID: 30333627 PMCID: PMC6280667 DOI: 10.1038/s41586-018-0623-z] [Citation(s) in RCA: 731] [Impact Index Per Article: 121.8] [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: 04/04/2018] [Accepted: 08/14/2018] [Indexed: 01/08/2023]
Abstract
The implementation of targeted therapies for acute myeloid leukaemia (AML) has been challenging because of the complex mutational patterns within and across patients as well as a dearth of pharmacologic agents for most mutational events. Here we report initial findings from the Beat AML programme on a cohort of 672 tumour specimens collected from 562 patients. We assessed these specimens using whole-exome sequencing, RNA sequencing and analyses of ex vivo drug sensitivity. Our data reveal mutational events that have not previously been detected in AML. We show that the response to drugs is associated with mutational status, including instances of drug sensitivity that are specific to combinatorial mutational events. Integration with RNA sequencing also revealed gene expression signatures, which predict a role for specific gene networks in the drug response. Collectively, we have generated a dataset-accessible through the Beat AML data viewer (Vizome)-that can be leveraged to address clinical, genomic, transcriptomic and functional analyses of the biology of AML.
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Affiliation(s)
- Jeffrey W Tyner
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Portland, OR, USA
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Beth Wilmot
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Stephen E Kurtz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Samantha L Savage
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Anna Reister Schultz
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Melissa Abel
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Aurora Blucher
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Uma Borate
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jade Bryant
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Russell Burke
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Amy Carlos
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Richie Carpenter
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Joseph Carroll
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Technology Transfer & Business Development, Oregon Health & Science University, Portland, OR, USA
| | - Bill H Chang
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Cody Coblentz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Amanda d'Almeida
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Rachel Cook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Alexey Danilov
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kim-Hien T Dao
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Michie Degnin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Deirdre Devine
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - James Dibb
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - David K Edwards
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Christopher A Eide
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Portland, OR, USA
| | - Isabel English
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jason Glover
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Rachel Henson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Hibery Ho
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Abdusebur Jemal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Kara Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Ryan Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian Junio
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Andy Kaempf
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Biostatistics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Jessica Leonard
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Chenwei Lin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Selina Qiuying Liu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Pierrette Lo
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Marc M Loriaux
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Dapartment of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Samuel Luty
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Tara Macey
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jason MacManiman
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jacqueline Martinez
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Motomi Mori
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Biostatistics Shared Resource, Oregon Health & Science University, Portland, OR, USA
- Oregon Health & Science University-Portland State University School of Public Health, Portland, OR, USA
| | - Dylan Nelson
- High-Throughput Screening Services Laboratory, Oregon State University, Corvalis, OR, USA
| | - Ceilidh Nichols
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jill Peters
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Justin Ramsdill
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Angela Rofelty
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Robert Schuff
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Robert Searles
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Erik Segerdell
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Rebecca L Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Stephen E Spurgeon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Tyler Sweeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Aashis Thapa
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Corinne Visser
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jake Wagner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kevin Watanabe-Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kristen Werth
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Joelle Wolf
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Libbey White
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Amy Yates
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Haijiao Zhang
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Christopher R Cogle
- Department of Medicine, Division of Hematology and Oncology, University of Florida, Gainesville, FL, USA
| | - Robert H Collins
- Department of Internal Medicine/Hematology Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Fox Chase Cancer Center Biosample Repository Facility, Philadelphia, PA, USA
| | - Michael W Deininger
- Division of Hematology & Hematologic Malignancies, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Leylah Drusbosky
- Department of Medicine, Division of Hematology and Oncology, University of Florida, Gainesville, FL, USA
| | - Christopher S Hourigan
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado, Denver, CO, USA
| | - Patricia Kropf
- Bone Marrow Transplant Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Tara L Lin
- Division of Hematologic Malignancies & Cellular Therapeutics, University of Kansas, Kansas City, KS, USA
| | - Micaela E Martinez
- Clinical Research Services, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Bruno C Medeiros
- Department of Medicine-Hematology, Stanford University, Stanford, CA, USA
| | - Rachel R Pallapati
- Clinical Research Services, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | | | - Ronan T Swords
- Department of Hematology, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Justin M Watts
- Department of Hematology, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Scott J Weir
- Department of Toxicology, Pharmacology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ryan M Winters
- Fox Chase Cancer Center Biosample Repository Facility, Philadelphia, PA, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA.
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA.
- Howard Hughes Medical Institute, Portland, OR, USA.
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8
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Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. Finding our way through phenotypes. PLoS Biol 2015; 13:e1002033. [PMID: 25562316 PMCID: PMC4285398 DOI: 10.1371/journal.pbio.1002033] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [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: 01/04/2023] Open
Abstract
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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Affiliation(s)
- Andrew R. Deans
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Suzanna E. Lewis
- Genome Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Eva Huala
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
- Phoenix Bioinformatics, Palo Alto, California, United States of America
| | - Salvatore S. Anzaldo
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - James P. Balhoff
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
| | - David C. Blackburn
- Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California, United States of America
| | - Judith A. Blake
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - J. Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Bruno Chanet
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Laurel D. Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mélanie Courtot
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sándor Csösz
- MTA-ELTE-MTM, Ecology Research Group, Pázmány Péter sétány 1C, Budapest, Hungary
| | - Hong Cui
- School of Information Resources and Library Science, University of Arizona, Tucson, Arizona, United States of America
| | - Wasila Dahdul
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, India
| | - T. Alexander Dececchi
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Agnes Dettai
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Rui Diogo
- Department of Anatomy, Howard University College of Medicine, Washington D.C., United States of America
| | - Robert E. Druzinsky
- Department of Oral Biology, College of Dentistry, University of Illinois, Chicago, Illinois, United States of America
| | - Michel Dumontier
- Stanford Center for Biomedical Informatics Research, Stanford, California, United States of America
| | - Nico M. Franz
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Frank Friedrich
- Biocenter Grindel and Zoological Museum, Hamburg University, Hamburg, Germany
| | - George V. Gkoutos
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - Melissa Haendel
- Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Luke J. Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Terry F. Hayamizu
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Yongqun He
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Heather M. Hines
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Nizar Ibrahim
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Laura M. Jackson
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Christina James-Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, Cincinnati, Ohio, United States of America
| | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Guillaume Lecointre
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Hilmar Lapp
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
| | - Carolyn J. Lawrence
- Department of Genetics, Development and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | | | - John G. Lundberg
- Department of Ichthyology, The Academy of Natural Sciences, Philadelphia, Pennsylvania, United States of America
| | - James Macklin
- Eastern Cereal and Oilseed Research Centre, Ottawa, Ontario, Canada
| | - Austin R. Mast
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | | | - István Mikó
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Christopher J. Mungall
- Genome Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Anika Oellrich
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Helen Parkinson
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Martín J. Ramírez
- Division of Arachnology, Museo Argentino de Ciencias Naturales - CONICET, Buenos Aires, Argentina
| | - Stefan Richter
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, Rostock, Germany
| | - Peter N. Robinson
- Institut für Medizinische Genetik und Humangenetik Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Alan Ruttenberg
- School of Dental Medicine, University at Buffalo, Buffalo, New York, United States of America
| | - Katja S. Schulz
- Smithsonian Institution, National Museum of Natural History, Washington, D.C., United States of America
| | - Erik Segerdell
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Katja C. Seltmann
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Michael J. Sharkey
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Aaron D. Smith
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, New York, United States of America
| | - Chelsea D. Specht
- Department of Plant and Microbial Biology, Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California, United States of America
| | - R. Burke Squires
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert W. Thacker
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Anne Thessen
- The Data Detektiv, 1412 Stearns Hill Road, Waltham, Massachusetts, United States of America
| | | | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Peter D. Vize
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Lars Vogt
- Universität Bonn, Institut für Evolutionsbiologie und Ökologie, Bonn, Germany
| | - Christine E. Wall
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Ramona L. Walls
- iPlant Collaborative University of Arizona, Thomas J. Keating Bioresearch Building, Tucson, Arizona, United States of America
| | - Monte Westerfeld
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Robert A. Wharton
- Department of Entomology, Texas A & M University, College, Station, Texas, United States of America
| | - Christian S. Wirkner
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, Rostock, Germany
| | - James B. Woolley
- Department of Entomology, Texas A & M University, College, Station, Texas, United States of America
| | - Matthew J. Yoder
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Aaron M. Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, Cincinnati, Ohio, United States of America
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
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9
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Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J Biomed Semantics 2014; 5:39. [PMID: 25276334 PMCID: PMC4177528 DOI: 10.1186/2041-1480-5-39] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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: 07/01/2013] [Accepted: 07/22/2014] [Indexed: 12/31/2022] Open
Abstract
Background Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. Results The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/. Conclusions By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.
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Affiliation(s)
- Robert W Thacker
- Department of Biology, University of Alabama at Birmingham, Birmingham, USA
| | | | - Adeline Kerner
- CR2P, UMR 7207 CNRS-MNHN-UPMC, Département Histoire de la Terre, Muséum National d'Histoire Naturelle, Bâtiment de Géologie, CP48, 57 rue Cuvier, 75005 Paris, France
| | - Régine Vignes-Lebbe
- CR2P, UMR 7207 CNRS-MNHN-UPMC, Département Histoire de la Terre, Muséum National d'Histoire Naturelle, Bâtiment de Géologie, CP48, 57 rue Cuvier, 75005 Paris, France
| | - Erik Segerdell
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, USA
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, USA
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10
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Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, Vize PD, Zorn AM. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. J Biomed Semantics 2013; 4:31. [PMID: 24139024 PMCID: PMC3816597 DOI: 10.1186/2041-1480-4-31] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/11/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying human disease. The Xenopus Anatomy Ontology (XAO) reflects the anatomy and embryological development of Xenopus. The XAO provides consistent terminology that can be applied to anatomical feature descriptions along with a set of relationships that indicate how each anatomical entity is related to others in the embryo, tadpole, or adult frog. The XAO is integral to the functionality of Xenbase (http://www.xenbase.org), the Xenopus model organism database. RESULTS We significantly expanded the XAO in the last five years by adding 612 anatomical terms, 2934 relationships between them, 640 synonyms, and 547 ontology cross-references. Each term now has a definition, so database users and curators can be certain they are selecting the correct term when specifying an anatomical entity. With developmental timing information now asserted for every anatomical term, the ontology provides internal checks that ensure high-quality gene expression and phenotype data annotation. The XAO, now with 1313 defined anatomical and developmental stage terms, has been integrated with Xenbase expression and anatomy term searches and it enables links between various data types including images, clones, and publications. Improvements to the XAO structure and anatomical definitions have also enhanced cross-references to anatomy ontologies of other model organisms and humans, providing a bridge between Xenopus data and other vertebrates. The ontology is free and open to all users. CONCLUSIONS The expanded and improved XAO allows enhanced capture of Xenopus research data and aids mechanisms for performing complex retrieval and analysis of gene expression, phenotypes, and antibodies through text-matching and manual curation. Its comprehensive references to ontologies across taxa help integrate these data for human disease modeling.
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Affiliation(s)
- Erik Segerdell
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Virgilio G Ponferrada
- Division of Developmental Biology, Cincinnati Children’s Research Foundation, Cincinnati, OH, USA
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children’s Research Foundation, Cincinnati, OH, USA
| | - Kevin A Burns
- Division of Developmental Biology, Cincinnati Children’s Research Foundation, Cincinnati, OH, USA
| | - Joshua D Fortriede
- Division of Developmental Biology, Cincinnati Children’s Research Foundation, Cincinnati, OH, USA
| | - Wasila M Dahdul
- Department of Biology, University of South Dakota, Vermillion, SD, USA
- National Evolutionary Synthesis Center, Durham, NC, USA
| | - Peter D Vize
- Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children’s Research Foundation, Cincinnati, OH, USA
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11
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Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. A unified anatomy ontology of the vertebrate skeletal system. PLoS One 2012; 7:e51070. [PMID: 23251424 PMCID: PMC3519498 DOI: 10.1371/journal.pone.0051070] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [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: 05/23/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
Abstract
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.
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Affiliation(s)
- Wasila M Dahdul
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
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12
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Vasilevsky N, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, Wilson M, Shaffer C, Robinson D, Haendel M. Research resources: curating the new eagle-i discovery system. Database (Oxford) 2012; 2012:bar067. [PMID: 22434835 PMCID: PMC3308157 DOI: 10.1093/database/bar067] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Development of biocuration processes and guidelines for new data types or projects is a challenging task. Each project finds its way toward defining annotation standards and ensuring data consistency with varying degrees of planning and different tools to support and/or report on consistency. Further, this process may be data type specific even within the context of a single project. This article describes our experiences with eagle-i, a 2-year pilot project to develop a federated network of data repositories in which unpublished, unshared or otherwise ‘invisible’ scientific resources could be inventoried and made accessible to the scientific community. During the course of eagle-i development, the main challenges we experienced related to the difficulty of collecting and curating data while the system and the data model were simultaneously built, and a deficiency and diversity of data management strategies in the laboratories from which the source data was obtained. We discuss our approach to biocuration and the importance of improving information management strategies to the research process, specifically with regard to the inventorying and usage of research resources. Finally, we highlight the commonalities and differences between eagle-i and similar efforts with the hope that our lessons learned will assist other biocuration endeavors. Database URL:www.eagle-i.net
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Affiliation(s)
- Nicole Vasilevsky
- Oregon Health & Science University, Library, LIB, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239-3098, USA
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13
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Abstract
Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information for Xenopus research. Recent improvements include the addition of the literature and interaction tabs to gene catalog pages. New content has been added including a section on gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. Gene expression data are integrated into the gene catalog via an expression tab and is also searchable by multiple criteria using an expression search interface. The gene catalog has grown to contain over 15 000 genes. Collaboration with the European Xenopus Research Center (EXRC) has resulted in a stock center section with data on frog lines supplied by the EXRC. Numerous improvements have also been made to search and navigation. Xenbase is also the source of the Xenopus Anatomical Ontology and the clearinghouse for Xenopus gene nomenclature.
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Affiliation(s)
- Jeff B Bowes
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada.
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14
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Abstract
Background The frogs Xenopus laevis and Xenopus (Silurana) tropicalis are model systems that have produced a wealth of genetic, genomic, and developmental information. Xenbase is a model organism database that provides centralized access to this information, including gene function data from high-throughput screens and the scientific literature. A controlled, structured vocabulary for Xenopus anatomy and development is essential for organizing these data. Results We have constructed a Xenopus anatomical ontology that represents the lineage of tissues and the timing of their development. We have classified many anatomical features in a common framework that has been adopted by several model organism database communities. The ontology is available for download at the Open Biomedical Ontologies Foundry . Conclusion The Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. We encourage community recommendations for updates and improvements to the ontology.
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Affiliation(s)
- Erik Segerdell
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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15
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Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SAT, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 2007; 36:D768-72. [PMID: 17991680 PMCID: PMC2238839 DOI: 10.1093/nar/gkm956] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [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: 11/26/2022] Open
Abstract
The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map positions, publications and community resources facilitates the use of the zebrafish as a model for studying gene function, development, behavior and disease. Access to ZFIN data is provided via web-based query forms and through bulk data files. ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations. ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO). Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources.
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Affiliation(s)
- Judy Sprague
- The Zebrafish Information Network, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
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16
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Abstract
Xenbase (www.xenbase.org) is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis. Data is collected from other databases, high-throughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and genomic analysis. Gene pages are automatically assembled from data piped from the Entrez Gene, Gurdon Institute, JGI, Metazome, MGI, OMIM, PubMed, Unigene, Zfin, commercial suppliers and others. These data are then supplemented with in-house annotation. Xenbase has implemented the Gbrowse genome browser and also provides a BLAST service that allows users to specifically search either laevis or tropicalis DNA or protein targets. A table of Xenopus gene synonyms has been implemented and allows the genome, genes, publications and high-throughput gene expression data to be seamlessly integrated with other Xenopus data and to external database resources, making the wealth of developmental and functional data from the frog available to the broader research community.
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Affiliation(s)
- Jeff B Bowes
- Department of Computer Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
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17
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Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol 2007; 22:345-50. [PMID: 17416439 DOI: 10.1016/j.tree.2007.03.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [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: 11/20/2006] [Revised: 03/08/2007] [Accepted: 03/26/2007] [Indexed: 11/23/2022]
Abstract
Understanding the developmental and genetic underpinnings of particular evolutionary changes has been hindered by inadequate databases of evolutionary anatomy and by the lack of a computational approach to identify underlying candidate genes and regulators. By contrast, model organism studies have been enhanced by ontologies shared among genomic databases. Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies. This would facilitate computing on evolutionary questions pertaining to the genetic basis of evolutionary change, the genetic and developmental bases of correlated characters and independent evolution, biomedical parallels to evolutionary change, and the ecological and paleontological correlates of particular types of change in genes, gene networks and developmental pathways.
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Affiliation(s)
- Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
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18
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Sprague J, Bayraktaroglu L, Clements D, Conlin T, Fashena D, Frazer K, Haendel M, Howe DG, Mani P, Ramachandran S, Schaper K, Segerdell E, Song P, Sprunger B, Taylor S, Van Slyke CE, Westerfield M. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res 2006; 34:D581-5. [PMID: 16381936 PMCID: PMC1347449 DOI: 10.1093/nar/gkj086] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [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: 11/25/2022] Open
Abstract
The Zebrafish Information Network (ZFIN; ) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community resources such as meeting announcements and contact information. Recent enhancements to ZFIN include (i) comprehensive curation of gene expression data from the literature and from directly submitted data, (ii) increased support and annotation of the genome sequence, (iii) expanded use of ontologies to support curation and query forms, (iv) curation of morpholino data from the literature, and (v) increased versatility of gene pages, with new data types, links and analysis tools.
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Affiliation(s)
- Judy Sprague
- The Zebrafish Information Network, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
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19
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Henrich T, Ramialison M, Segerdell E, Westerfield M, Furutani-Seiki M, Wittbrodt J, Kondoh H. GSD: a genetic screen database. Mech Dev 2005; 121:959-63. [PMID: 15210199 DOI: 10.1016/j.mod.2004.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 12/22/2003] [Revised: 02/23/2004] [Accepted: 02/25/2004] [Indexed: 10/26/2022]
Abstract
The systematic assignment of gene function to a sequenced genome is one of the outstanding challenges in the post-genomic era. Large-scale systematic mutagenesis screens are important tools for reaching this goal. Here we describe GSD, a software package that allows storage and integration of data from genetic screens. GSD was initially developed for a large-scale F3 mutagenesis screen for developmental mutants of medaka (Oryzias latipes). The version presented here supports a wide range of different screens (mutagenesis, RNAi, morpholinos, transgenesis and others) using different organisms. Data are stored in a relational database and can be made accessible through web interfaces. Researchers can enter data describing their screened embryos: They can track statistics, submit images and describe the resulting phenotypes using a phenotype classification ontology. We developed a fish phenotype classification ontology of medaka and zebrafish for this software package and made it available to the public. In addition, a list of genetic lines resulting from each screen can be generated. These lines (mutant alleles, transgenic lines) can be described and categorized in the same ways as the screened individuals. Raw data from the screen can be integrated to describe these lines. A query module that searches this list can be used to publish the screen results on the Internet. A test version is available at and the software can be downloaded from this site.
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Affiliation(s)
- Thorsten Henrich
- European Molecular Biology Laboratory-Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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20
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Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res 2003; 31:241-3. [PMID: 12519991 PMCID: PMC165474 DOI: 10.1093/nar/gkg027] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [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: 11/14/2022] Open
Abstract
The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data. ZFIN is publicly accessible at http://zfin.org. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community contact data. Recent enhancements to ZFIN include: (i) an anatomical dictionary that provides a controlled vocabulary of anatomical terms, grouped by developmental stages, that may be used to annotate and query gene expression data; (ii) gene expression data; (iii) expanded support for genome sequence; (iv) gene annotation using the standardized vocabulary of Gene Ontology (GO) terms that can be used to elucidate relationships between gene products in zebrafish and other organisms; and (v) collaborations with other databases (NCBI, Sanger Institute and SWISS-PROT) to provide standardization and interconnections based on shared curation.
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Affiliation(s)
- Judy Sprague
- The Zebrafish International Resource Center, University of Oregon, Eugene, OR 97403-5274, USA.
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