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Yates T, Lain A, Campbell J, FitzPatrick DR, Simpson TI. Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders. Database (Oxford) 2022; 2022:baac038. [PMID: 35670729 PMCID: PMC9216525 DOI: 10.1093/database/baac038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/26/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
Abstract
There are >2500 different genetically determined developmental disorders (DD), which, as a group, show very high levels of both locus and allelic heterogeneity. This has led to the wide-spread use of evidence-based filtering of genome-wide sequence data as a diagnostic tool in DD. Determining whether the association of a filtered variant at a specific locus is a plausible explanation of the phenotype in the proband is crucial and commonly requires extensive manual literature review by both clinical scientists and clinicians. Access to a database of weighted clinical features extracted from rigorously curated literature would increase the efficiency of this process and facilitate the development of robust phenotypic similarity metrics. However, given the large and rapidly increasing volume of published information, conventional biocuration approaches are becoming impractical. Here, we present a scalable, automated method for the extraction of categorical phenotypic descriptors from the full-text literature. Papers identified through literature review were downloaded and parsed using the Cadmus custom retrieval package. Human Phenotype Ontology terms were extracted using MetaMap, with 76-84% precision and 65-73% recall. Mean terms per paper increased from 9 in title + abstract, to 68 using full text. We demonstrate that these literature-derived disease models plausibly reflect true disease expressivity more accurately than widely used manually curated models, through comparison with prospectively gathered data from the Deciphering Developmental Disorders study. The area under the curve for receiver operating characteristic (ROC) curves increased by 5-10% through the use of literature-derived models. This work shows that scalable automated literature curation increases performance and adds weight to the need for this strategy to be integrated into informatic variant analysis pipelines. Database URL: https://doi.org/10.1093/database/baac038.
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Affiliation(s)
- T.M Yates
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
- Transforming Genetic Medicine Initiative, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - A Lain
- Institute for Adaptive and Neural Computation, Informatics Forum, The University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - J Campbell
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XF, UK
| | - D R FitzPatrick
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
- Transforming Genetic Medicine Initiative, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XF, UK
| | - T I Simpson
- Institute for Adaptive and Neural Computation, Informatics Forum, The University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XF, UK
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3
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Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res 2020; 47:D1018-D1027. [PMID: 30476213 PMCID: PMC6324074 DOI: 10.1093/nar/gky1105] [Citation(s) in RCA: 409] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/24/2018] [Indexed: 12/12/2022] Open
Abstract
The Human Phenotype Ontology (HPO)—a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases—is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
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Affiliation(s)
- Sebastian Köhler
- Charité Centrum für Therapieforschung, Charité-Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.,Einstein Center Digital Future, Berlin 10117, Germany.,Monarch Initiative, monarchinitiative.org
| | - Leigh Carmody
- Monarch Initiative, monarchinitiative.org.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nicole Vasilevsky
- Monarch Initiative, monarchinitiative.org.,Oregon Health & Science University, Portland, OR 97217, USA
| | - Julius O B Jacobsen
- Monarch Initiative, monarchinitiative.org.,Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Daniel Danis
- Monarch Initiative, monarchinitiative.org.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jean-Philippe Gourdine
- Monarch Initiative, monarchinitiative.org.,Oregon Health & Science University, Portland, OR 97217, USA
| | - Michael Gargano
- Monarch Initiative, monarchinitiative.org.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nomi L Harris
- Monarch Initiative, monarchinitiative.org.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicolas Matentzoglu
- Monarch Initiative, monarchinitiative.org.,European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Julie A McMurry
- Monarch Initiative, monarchinitiative.org.,Linus Pauling institute, Oregon State University, Corvallis, OR, USA
| | - David Osumi-Sutherland
- Monarch Initiative, monarchinitiative.org.,European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Valentina Cipriani
- Monarch Initiative, monarchinitiative.org.,William Harvey Research Institute, Queen Mary University College of London.,UCL Genetics Institute, University College of London.,UCL Institute of Ophthalmology, University College of London
| | - James P Balhoff
- Monarch Initiative, monarchinitiative.org.,Renaissance Computing Institute, University of North Carolina at Chapel Hill
| | - Tom Conlin
- Monarch Initiative, monarchinitiative.org.,Linus Pauling institute, Oregon State University, Corvallis, OR, USA
| | - Hannah Blau
- Monarch Initiative, monarchinitiative.org.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Department of Health, Government of Western Australia, WA, Australia.,School of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Spatial Sciences, Department of Science and Engineering, Curtin University, Perth, WA, Australia.,The Office of Population Health Genomics, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Richard Palmer
- Spatial Sciences, Department of Science and Engineering, Curtin University, Perth, WA, Australia
| | - Dylan Gratian
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Department of Health, Government of Western Australia, WA, Australia
| | - Hugh Dawkins
- The Office of Population Health Genomics, Department of Health, Government of Western Australia, Perth, WA, Australia
| | | | - Anna C Jansen
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium.,Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | - Ahmed Muaz
- Monarch Initiative, monarchinitiative.org.,Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Willie H Chang
- Centre for Computational Medicine, Hospital for Sick Children and Department of Computer Science, University of Toronto, Toronto, Canada
| | - Jenna Bergerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Stanley J F Laulederkind
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, 8701 Watertown Plank Road Milwaukee, WI 53226, USA
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandra F Freeman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Daniel Durkin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Andrea L Storm
- ICF, Rockville, MD, USA.,National Center for Advancing Translational Sciences, Office of Rare Diseases Research, National Institutes of Health, Bethesda, MD, USA
| | - Marc Hanauer
- INSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Michael Brudno
- Centre for Computational Medicine, Hospital for Sick Children and Department of Computer Science, University of Toronto, Toronto, Canada
| | | | - Murat Sincan
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, USA
| | - Kayli Rageth
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, USA
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, the Netherlands
| | - Halima Lourghi
- INSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Maria G Della Rocca
- ICF, Rockville, MD, USA.,National Center for Advancing Translational Sciences, Office of Rare Diseases Research, National Institutes of Health, Bethesda, MD, USA
| | - Rachel Thompson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - James Priest
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Ayushi Hegde
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ruth C Lovering
- Institute of Cardiovascular Science, University College London, UK
| | | | - Annie Olry
- INSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Luigi Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Morgan Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xingmin A Zhang
- Monarch Initiative, monarchinitiative.org.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - David Gómez-Andrés
- Child Neurology Unit. Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Hanns Lochmüller
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.,Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Hélène Dollfus
- Centre for Rare Eye Diseases CARGO, SENSGENE FSMR Network, Strasbourg University Hospital, Strasbourg, France
| | - Sergio Rosenzweig
- Immunology Service, Department of Laboratory Medicine, NIH Clinical Center, Bethesda, MD, USA
| | - Shruti Marwaha
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Ana Rath
- INSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Kathleen Sullivan
- Department of Pediatrics, Division of Allergy Immunology, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | | | - Joshua D Milner
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dorothée Leroux
- Centre for Rare Eye Diseases CARGO, SENSGENE FSMR Network, Strasbourg University Hospital, Strasbourg, France
| | | | - Amy Klion
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Melody C Carter
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tudor Groza
- Monarch Initiative, monarchinitiative.org.,Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Damian Smedley
- Monarch Initiative, monarchinitiative.org.,Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Melissa A Haendel
- Monarch Initiative, monarchinitiative.org.,Oregon Health & Science University, Portland, OR 97217, USA.,Linus Pauling institute, Oregon State University, Corvallis, OR, USA
| | - Chris Mungall
- Monarch Initiative, monarchinitiative.org.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter N Robinson
- Monarch Initiative, monarchinitiative.org.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
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