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The Human Phenotype Ontology in 2021

Sebastian Köhler, Michael Gargano, Nicolas Matentzoglu, Leigh C Carmody, David Lewis-Smith, Nicole A Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M Brower, Tiffany J Callahan, Christopher G Chute (+39 others)
2020 Nucleic Acids Research  
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human  ...  We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease.  ...  INTRODUCTION The Human Phenotype Ontology (HPO) is a comprehensive resource that systematically defines and logically organizes human phenotypes.  ... 
doi:10.1093/nar/gkaa1043 pmid:33264411 pmcid:PMC7778952 fatcat:2lnshw3e7fcknncihgiqtfnc5y

Modeling seizures in the Human Phenotype Ontology according to contemporary ILAE concepts makes big phenotypic data tractable

David Lewis-Smith, Peter D Galer, Ganna Balagura, Hugh Kearney, Shiva Ganesan, Mahgenn Cosico, Margaret O'Brien, Priya Vaidiswaran, Roland Krause, Colin A Ellis, Rhys H Thomas, Peter N Robinson (+1 others)
2021 Epilepsia  
The Human Phenotype Ontology (HPO) is used widely in clinical and research genetics for concise communication and modeling of clinical features, allowing extracted data to be harmonized using logical inference  ...  This will help to overcome the phenotypic bottleneck in genomics, facilitate reuse of valuable data, and ultimately improve diagnostics and precision treatment of the epilepsies.  ...  ACKNOWLEDGEMENTS We thank the attendees who contributed to early discussions at the EMBO workshop on Phenotyping neurological syndromes for systems genetics, in Luxembourg, October 4-10, 2018; HPO users  ... 
doi:10.1111/epi.16908 pmid:33949685 pmcid:PMC8272408 fatcat:6yw5k7tv7ndp3g2lzq62lv22ye

How much do model organism phenotypes contribute to the computational identification of human disease genes? [article]

Sarah M Alghamdi, Paul N Schofield, Robert Hoehndorf
2021 bioRxiv   pre-print
Our work has implications for the future development of integrated phenotype ontologies, as well as for the use of model organism phenotypes in human genetic variant interpretation.  ...  We use methods based on phenotype ontologies to semantically relate phenotypes resulting from loss-of-function mutations in different model organisms to disease-associated phenotypes in humans.  ...  Acknowledgements We acknowledge use of resources from the KAUST Supercomputing Laboratory. PNS acknowledges the support of The Alan Turing Institute.  ... 
doi:10.1101/2021.12.24.474099 fatcat:mpm3uuspynfctezrgfdajezipe

Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function

Tomasz Konopka, Letizia Vestito, Damian Smedley
2021 Bioinformatics Advances  
We also summarize some of the difficulties in producing and interpreting embeddings of sparse phenotypic data.  ...  to study human diseases.  ...  Acknowledgments This work was supported by a grant from the National Institutes of Health [Grant 5-UM1-HG006370 to D.S.].  ... 
doi:10.1093/bioadv/vbab026 pmid:34870209 pmcid:PMC8633315 fatcat:apzx2ocaqvhxriujklurhovjp4

Mouse Genome Informatics (MGI): latest news from MGD and GXD

Martin Ringwald, Joel E. Richardson, Richard M. Baldarelli, Judith A. Blake, James A. Kadin, Cynthia Smith, Carol J. Bult
2021 Mammalian Genome  
MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of the Gene Ontology and Disease Ontology and uses these ontologies as standard terminologies for annotation.  ...  MGI's mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease.  ...  Acknowledgements We thank all the MGI curators and developers for their dedication and their many contributions to MGI. We are grateful to Dr. Hagit Shatkay (University of Delaware) and Dr.  ... 
doi:10.1007/s00335-021-09921-0 pmid:34698891 pmcid:PMC8913530 fatcat:zwlwn4gb5vhwzfnkx5qszjn7ii

Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function [article]

Tomasz Konopka, Letizia Vestito, Damian Smedley
2021 bioRxiv   pre-print
We also summarize some of the difficulties in producing and interpreting embeddings of sparse phenotypic data.  ...  to study human diseases.  ...  Projections of human diseases into embeddings of mouse models Human diseases with phenotype annotations from the HP ontology were translated to the MP ontology by replacing their HP terms with best-matching  ... 
doi:10.1101/2021.06.10.447851 fatcat:56jthopkrrf3dktd7qiwrn6jjy

Zebrafish Information Network, the knowledgebase for Danio rerio research

Yvonne M Bradford, Ceri E Van Slyke, Leyla Ruzicka, Amy Singer, Anne Eagle, David Fashena, Douglas G Howe, Ken Frazer, Ryan Martin, Holly Paddock, Christian Pich, Sridhar Ramachandran (+1 others)
2022 Genetics  
Key data types available at ZFIN include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function.  ...  diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.  ...  compartment ontology (GO-CC, Ashburner et al. 2000, Carbon et al. 2021), and Spatial ontology (BSPO, Dahdul et al. 2014).  ... 
doi:10.1093/genetics/iyac016 pmid:35166825 pmcid:PMC8982015 fatcat:v737talhbvbqdn4edyablydogi

The Landscape of Disease and Phenotype Ontologies [article]

Nicole Vasilevsky
2022 Zenodo  
A compliation of disease and phenotype terminologies and ontologies. Last updated 2021-10-22.  ...  Developed by the Disease Ontology (DO) team and used for describing symptoms of human diseases in the DO.  ...  Still under development (last verssion released in BioPortal was in 2021) but there is little information about its usage online.  ... 
doi:10.5281/zenodo.6299897 fatcat:ryvbudptq5gtno2b7ntlhbnbcm

A Comparative Analysis of Phenotypes Derived from Genes or Biomedical Literature in COVID-19 [chapter]

Sophie Steenson, Christopher Hawthorne, Guillermo Lopez-Campos
2022 Studies in Health Technology and Informatics  
Using an "in-house" developed script we retrieved gene annotations and identified phenotype enrichments. Human Phenotype Ontology terms were retrieved from the literature using the Onassis R package.  ...  Since the emergence of SARS-CoV-2 in November 2019, there has been an exponential production of literature due to worldwide efforts to understand the interactions between the virus and the human body.  ...  GAPAL analyses ultimately generated a list of genes and "gene-derived" phenotypes based on the Human Phenotype Ontology enrichments.  ... 
doi:10.3233/shti220283 pmid:35673221 fatcat:6qdripuhrra7xaujo7a62gjr44

DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes

Wang Liu-Wei, Şenay Kafkas, Jun Chen, Nicholas J Dimonaco, Jesper Tegnér, Robert Hoehndorf
2021 Bioinformatics  
Motivated by the potential utility of infectious disease phenotypes, we first embedded human proteins and viruses in a shared space using their associated phenotypes and functions, supported by formalized  ...  background knowledge from biomedical ontologies.  ...  We also thank Jeffery Law for making public the mappings of the SARS-CoV-2 proteins. We acknowledge the use of computational resources from the KAUST Supercomputing Core Laboratory.  ... 
doi:10.1093/bioinformatics/btab147 pmid:33682875 fatcat:3wcpswlc35hl5osif2sgxclpbi

The Human Disease Ontology 2022 update

Lynn M Schriml, James B Munro, Mike Schor, Dustin Olley, Carrie McCracken, Victor Felix, J Allen Baron, Rebecca Jackson, Susan M Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi (+3 others)
2021 Nucleic Acids Research  
The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO's 2018 Nucleic Acids Research DATABASE  ...  Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years.  ...  We acknowledge the creators of images from the noun project (https://thenounproject.com), purchased for use in the graphical abstract: Léa Lortal (DNA), Alzam (DNA), iconixar (environment), Adrien Coquet  ... 
doi:10.1093/nar/gkab1063 pmid:34755882 pmcid:PMC8728220 fatcat:hpj2qrshtbdzdki5rdzciv36pe

Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology [article]

Midori A Harris, Kim Matthew Rutherford, Jacqueline Hayles, Antonia Lock, Jürg Bähler, Stephen G Oliver, Juan Mata, Valerie Wood
2021 biorxiv/medrxiv   pre-print
With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.  ...  PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic  ...  We are grateful to Pascale Gaudet for acting on our recommendations for improving GO annotations and ontology content.  ... 
doi:10.1101/2021.09.07.459264 fatcat:scsw42oaancxnccwy5dtudgxoi

ONTOLOGIES MOST USED IN AGRICULTURE: Make your data interpretable and interoperable with ontologies [article]

Céline Aubert, Elizabeth Arnaud, Marie Angélique Laporte, Erick Antezana
2021 Zenodo  
This webpage, published in the site of the CGIAR Platform for big data in agriculture (https://bigdata.cgiar.org/ontologies-for-agriculture/), provides a visual thematic access to the most used ontologies  ...  in agrifood research including the ontologies developed by the Ontologies Community of Practice and its partners. .  ...  Trait Ontology Phenotypic traits in plants. 9 Livestock phenotype Animal Trait Ontology for Livestock Phenotypes of livestock in their environment.  ... 
doi:10.5281/zenodo.6609665 fatcat:zmvzelw63faalbsxn3cjcoob6y

The Aliment to Bodily Condition knowledgebase (ABCkb): A database connecting plants and human health [article]

Aaron Trautman, Richard Linchangco, Rachel Walstead, Jeremy J Jay, Cory Brouwer
2021 bioRxiv   pre-print
integrate between the domains of human health and agriculture.  ...  Results: We created the Aliment to Bodily Condition Knowledgebase (ABCkb) to connect plants to human health by creating a stepwise path from plant → plant product → human gene → pathways → indication.  ...  Acknowledgements Steven Blanchard, P2EP program, and the many interns that aided the development of this resource  ... 
doi:10.1101/2021.03.20.436160 fatcat:udat3qrivvbx7f3qd4kshyimhu

Best Paper Selection

2021 IMIA Yearbook of Medical Informatics  
A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System. https://pubmed.ncbi.nlm.nih.gov/32918476/  ...  Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-020-01336-2 Zheng F, Shi  ...  Phenotypic abnormalities are represented by Human Phenotype Ontology (HPO) terms and the LHR calculations are derived from the subsumption hierarchies in the HPO.  ... 
doi:10.1055/s-0041-1726509 fatcat:rjh3xjccoreahnma3g33xb43uq
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