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1. The Human Phenotype Ontology in 2021

Author

Köhler, Sebastian, Gargano, Michael, Matentzoglu, Nicolas, Carmody, Leigh C, Lewis-Smith, David, Vasilevsky, Nicole A, Danis, Daniel, Balagura, Ganna, Baynam, Gareth, Brower, Amy M, Callahan, Tiffany J, Chute, Christopher G, Est, Johanna L, Galer, Peter D, Ganesan, Shiva, Griese, Matthias, Haimel, Matthias, Pazmandi, Julia, Hanauer, Marc, Harris, Nomi L, Hartnett, Michael J, Hastreiter, Maximilian, Hauck, Fabian, He, Yongqun, Jeske, Tim, Kearney, Hugh, Kindle, Gerhard, Klein, Christoph, Knoflach, Katrin, Krause, Roland, Lagorce, David, McMurry, Julie A, Miller, Jillian A, Munoz-Torres, Monica C, Peters, Rebecca L, Rapp, Christina K, Rath, Ana M, Rind, Shahmir A, Rosenberg, Avi Z, Segal, Michael M, Seidel, Markus G, Smedley, Damian, Talmy, Tomer, Thomas, Yarlalu, Wiafe, Samuel A, Xian, Julie, Yüksel, Zafer, Helbig, Ingo, Mungall, Christopher J, Haendel, Melissa A, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Neurosciences, Neurodegenerative, Networking and Information Technology R&D (NITRD), Animals, Biological Ontologies, Computational Biology, Databases, Factual, Disease, Disease Models, Animal, Genome, Genotype, Humans, Infant, Newborn, International Cooperation, Internet, Neonatal Screening, Pharmacogenetics, Phenotype, Software, Terminology as Topic, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

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 disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

Published
2021

2. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

Author

Shefchek, Kent A, Harris, Nomi L, Gargano, Michael, Matentzoglu, Nicolas, Unni, Deepak, Brush, Matthew, Keith, Daniel, Conlin, Tom, Vasilevsky, Nicole, Zhang, Xingmin Aaron, Balhoff, James P, Babb, Larry, Bello, Susan M, Blau, Hannah, Bradford, Yvonne, Carbon, Seth, Carmody, Leigh, Chan, Lauren E, Cipriani, Valentina, Cuzick, Alayne, Rocca, Maria D, Dunn, Nathan, Essaid, Shahim, Fey, Petra, Grove, Chris, Gourdine, Jean-Phillipe, Hamosh, Ada, Harris, Midori, Helbig, Ingo, Hoatlin, Maureen, Joachimiak, Marcin, Jupp, Simon, Lett, Kenneth B, Lewis, Suzanna E, McNamara, Craig, Pendlington, Zoë M, Pilgrim, Clare, Putman, Tim, Ravanmehr, Vida, Reese, Justin, Riggs, Erin, Robb, Sofia, Roncaglia, Paola, Seager, James, Segerdell, Erik, Similuk, Morgan, Storm, Andrea L, Thaxon, Courtney, Thessen, Anne, Jacobsen, Julius OB, McMurry, Julie A, Groza, Tudor, Köhler, Sebastian, Smedley, Damian, Robinson, Peter N, Mungall, Christopher J, Haendel, Melissa A, Munoz-Torres, Monica C, and Osumi-Sutherland, David

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Networking and Information Technology R&D (NITRD), 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Algorithms, Animals, Biological Ontologies, Computational Biology, Databases, Genetic, Exome, Genetic Association Studies, Genetic Variation, Genomics, Genotype, Humans, Internet, Phenotype, Software, Translational Research, Biomedical, User-Computer Interface, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
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.

Published
2020

3. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Author

Köhler, Sebastian, Carmody, Leigh, Vasilevsky, Nicole, Jacobsen, Julius OB, Danis, Daniel, Gourdine, Jean-Philippe, Gargano, Michael, Harris, Nomi L, Matentzoglu, Nicolas, McMurry, Julie A, Osumi-Sutherland, David, Cipriani, Valentina, Balhoff, James P, Conlin, Tom, Blau, Hannah, Baynam, Gareth, Palmer, Richard, Gratian, Dylan, Dawkins, Hugh, Segal, Michael, Jansen, Anna C, Muaz, Ahmed, Chang, Willie H, Bergerson, Jenna, Laulederkind, Stanley JF, Yüksel, Zafer, Beltran, Sergi, Freeman, Alexandra F, Sergouniotis, Panagiotis I, Durkin, Daniel, Storm, Andrea L, Hanauer, Marc, Brudno, Michael, Bello, Susan M, Sincan, Murat, Rageth, Kayli, Wheeler, Matthew T, Oegema, Renske, Lourghi, Halima, Della Rocca, Maria G, Thompson, Rachel, Castellanos, Francisco, Priest, James, Cunningham-Rundles, Charlotte, Hegde, Ayushi, Lovering, Ruth C, Hajek, Catherine, Olry, Annie, Notarangelo, Luigi, Similuk, Morgan, Zhang, Xingmin A, Gómez-Andrés, David, Lochmüller, Hanns, Dollfus, Hélène, Rosenzweig, Sergio, Marwaha, Shruti, Rath, Ana, Sullivan, Kathleen, Smith, Cynthia, Milner, Joshua D, Leroux, Dorothée, Boerkoel, Cornelius F, Klion, Amy, Carter, Melody C, Groza, Tudor, Smedley, Damian, Haendel, Melissa A, Mungall, Chris, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Networking and Information Technology R&D (NITRD), Rare Diseases, Generic health relevance, Good Health and Well Being, Biological Ontologies, Computational Biology, Congenital Abnormalities, Databases, Genetic, Genetic Predisposition to Disease, Genetic Variation, Humans, Internet, Knowledge Bases, Phenotype, Whole Genome Sequencing, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
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.

Published
2019

4. The Human Phenotype Ontology in 2017

Author

Köhler, Sebastian, Vasilevsky, Nicole A, Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M, Boerkoel, Cornelius F, Boycott, Kym M, Brudno, Michael, Buske, Orion J, Chinnery, Patrick F, Cipriani, Valentina, Connell, Laureen E, Dawkins, Hugh JS, DeMare, Laura E, Devereau, Andrew D, de Vries, Bert BA, Firth, Helen V, Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A, James, Roger, Krause, Roland, Laulederkind, Stanley JF, Lochmüller, Hanns, Lyon, Gholson J, Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H, Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H, Segal, Michael, Sergouniotis, Panagiotis I, Sever, Richard, Smith, Cynthia L, Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke WM, Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius OB, Groza, Tudor, Smedley, Damian, Mungall, Christopher J, Haendel, Melissa, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Networking and Information Technology R&D (NITRD), Human Genome, Good Health and Well Being, Algorithms, Biological Ontologies, Computational Biology, Genetic Association Studies, Genomics, Humans, Phenotype, Precision Medicine, Rare Diseases, Software, Translational Research, Biomedical, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Published
2017

5. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Author

Mungall, Christopher J, McMurry, Julie A, Köhler, Sebastian, Balhoff, James P, Borromeo, Charles, Brush, Matthew, Carbon, Seth, Conlin, Tom, Dunn, Nathan, Engelstad, Mark, Foster, Erin, Gourdine, JP, Jacobsen, Julius OB, Keith, Dan, Laraway, Bryan, Lewis, Suzanna E, NguyenXuan, Jeremy, Shefchek, Kent, Vasilevsky, Nicole, Yuan, Zhou, Washington, Nicole, Hochheiser, Harry, Groza, Tudor, Smedley, Damian, Robinson, Peter N, and Haendel, Melissa A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Precision Medicine, Networking and Information Technology R&D (NITRD), Human Genome, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Animals, Biological Evolution, Computational Biology, Data Curation, Databases, Genetic, Genetic Association Studies, Genotype, Humans, Phenotype, Search Engine, Software, Species Specificity, User-Computer Interface, Web Browser, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype-phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.

Published
2017

6. The Human Phenotype Ontology in 2024: phenotypes around the world

Author

Gargano, Michael A, primary, Matentzoglu, Nicolas, additional, Coleman, Ben, additional, Addo-Lartey, Eunice B, additional, Anagnostopoulos, Anna V, additional, Anderton, Joel, additional, Avillach, Paul, additional, Bagley, Anita M, additional, Bakštein, Eduard, additional, Balhoff, James P, additional, Baynam, Gareth, additional, Bello, Susan M, additional, Berk, Michael, additional, Bertram, Holli, additional, Bishop, Somer, additional, Blau, Hannah, additional, Bodenstein, David F, additional, Botas, Pablo, additional, Boztug, Kaan, additional, Čady, Jolana, additional, Callahan, Tiffany J, additional, Cameron, Rhiannon, additional, Carbon, Seth J, additional, Castellanos, Francisco, additional, Caufield, J Harry, additional, Chan, Lauren E, additional, Chute, Christopher G, additional, Cruz-Rojo, Jaime, additional, Dahan-Oliel, Noémi, additional, Davids, Jon R, additional, de Dieuleveult, Maud, additional, de Souza, Vinicius, additional, de Vries, Bert B A, additional, de Vries, Esther, additional, DePaulo, J Raymond, additional, Derfalvi, Beata, additional, Dhombres, Ferdinand, additional, Diaz-Byrd, Claudia, additional, Dingemans, Alexander J M, additional, Donadille, Bruno, additional, Duyzend, Michael, additional, Elfeky, Reem, additional, Essaid, Shahim, additional, Fabrizzi, Carolina, additional, Fico, Giovanna, additional, Firth, Helen V, additional, Freudenberg-Hua, Yun, additional, Fullerton, Janice M, additional, Gabriel, Davera L, additional, Gilmour, Kimberly, additional, Giordano, Jessica, additional, Goes, Fernando S, additional, Moses, Rachel Gore, additional, Green, Ian, additional, Griese, Matthias, additional, Groza, Tudor, additional, Gu, Weihong, additional, Guthrie, Julia, additional, Gyori, Benjamin, additional, Hamosh, Ada, additional, Hanauer, Marc, additional, Hanušová, Kateřina, additional, He, Yongqun (Oliver), additional, Hegde, Harshad, additional, Helbig, Ingo, additional, Holasová, Kateřina, additional, Hoyt, Charles Tapley, additional, Huang, Shangzhi, additional, Hurwitz, Eric, additional, Jacobsen, Julius O B, additional, Jiang, Xiaofeng, additional, Joseph, Lisa, additional, Keramatian, Kamyar, additional, King, Bryan, additional, Knoflach, Katrin, additional, Koolen, David A, additional, Kraus, Megan L, additional, Kroll, Carlo, additional, Kusters, Maaike, additional, Ladewig, Markus S, additional, Lagorce, David, additional, Lai, Meng-Chuan, additional, Lapunzina, Pablo, additional, Laraway, Bryan, additional, Lewis-Smith, David, additional, Li, Xiarong, additional, Lucano, Caterina, additional, Majd, Marzieh, additional, Marazita, Mary L, additional, Martinez-Glez, Victor, additional, McHenry, Toby H, additional, McInnis, Melvin G, additional, McMurry, Julie A, additional, Mihulová, Michaela, additional, Millett, Caitlin E, additional, Mitchell, Philip B, additional, Moslerová, Veronika, additional, Narutomi, Kenji, additional, Nematollahi, Shahrzad, additional, Nevado, Julian, additional, Nierenberg, Andrew A, additional, Čajbiková, Nikola Novák, additional, Nurnberger, John I, additional, Ogishima, Soichi, additional, Olson, Daniel, additional, Ortiz, Abigail, additional, Pachajoa, Harry, additional, Perez de Nanclares, Guiomar, additional, Peters, Amy, additional, Putman, Tim, additional, Rapp, Christina K, additional, Rath, Ana, additional, Reese, Justin, additional, Rekerle, Lauren, additional, Roberts, Angharad M, additional, Roy, Suzy, additional, Sanders, Stephan J, additional, Schuetz, Catharina, additional, Schulte, Eva C, additional, Schulze, Thomas G, additional, Schwarz, Martin, additional, Scott, Katie, additional, Seelow, Dominik, additional, Seitz, Berthold, additional, Shen, Yiping, additional, Similuk, Morgan N, additional, Simon, Eric S, additional, Singh, Balwinder, additional, Smedley, Damian, additional, Smith, Cynthia L, additional, Smolinsky, Jake T, additional, Sperry, Sarah, additional, Stafford, Elizabeth, additional, Stefancsik, Ray, additional, Steinhaus, Robin, additional, Strawbridge, Rebecca, additional, Sundaramurthi, Jagadish Chandrabose, additional, Talapova, Polina, additional, Tenorio Castano, Jair A, additional, Tesner, Pavel, additional, Thomas, Rhys H, additional, Thurm, Audrey, additional, Turnovec, Marek, additional, van Gijn, Marielle E, additional, Vasilevsky, Nicole A, additional, Vlčková, Markéta, additional, Walden, Anita, additional, Wang, Kai, additional, Wapner, Ron, additional, Ware, James S, additional, Wiafe, Addo A, additional, Wiafe, Samuel A, additional, Wiggins, Lisa D, additional, Williams, Andrew E, additional, Wu, Chen, additional, Wyrwoll, Margot J, additional, Xiong, Hui, additional, Yalin, Nefize, additional, Yamamoto, Yasunori, additional, Yatham, Lakshmi N, additional, Yocum, Anastasia K, additional, Young, Allan H, additional, Yüksel, Zafer, additional, Zandi, Peter P, additional, Zankl, Andreas, additional, Zarante, Ignacio, additional, Zvolský, Miroslav, additional, Toro, Sabrina, additional, Carmody, Leigh C, additional, Harris, Nomi L, additional, Munoz-Torres, Monica C, additional, Danis, Daniel, additional, Mungall, Christopher J, additional, Köhler, Sebastian, additional, Haendel, Melissa A, additional, and Robinson, Peter N, additional

Published
2023
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7. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

Author

Köhler, Sebastian, Doelken, Sandra C., Mungall, Christopher J., Bauer, Sebastian, Firth, Helen V., Bailleul-Forestier, Isabelle, Black, Graeme C. M., Brown, Danielle L., Brudno, Michael, Campbell, Jennifer, FitzPatrick, David R., Eppig, Janan T., Jackson, Andrew P., Freson, Kathleen, Girdea, Marta, Helbig, Ingo, Hurst, Jane A., Jähn, Johanna, Jackson, Laird G., Kelly, Anne M., Ledbetter, David H., Mansour, Sahar, Martin, Christa L., Moss, Celia, Mumford, Andrew, Ouwehand, Willem H., Park, Soo-Mi, Riggs, Erin Rooney, Scott, Richard H., Sisodiya, Sanjay, Van Vooren, Steven, Wapner, Ronald J., Wilkie, Andrew O. M., Wright, Caroline F., Vulto-van Silfhout, Anneke T., de Leeuw, Nicole, de Vries, Bert B. A., Washingthon, Nicole L., Smith, Cynthia L., Westerfield, Monte, Schofield, Paul, Ruef, Barbara J., Gkoutos, Georgios V., Haendel, Melissa, Smedley, Damian, Lewis, Suzanna E., and Robinson, Peter N.

Published
2014
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8. The Human Phenotype Ontology in 2021

Author

Köhler, Sebastian, primary, Gargano, Michael, additional, Matentzoglu, Nicolas, additional, Carmody, Leigh C, additional, Lewis-Smith, David, additional, Vasilevsky, Nicole A, additional, Danis, Daniel, additional, Balagura, Ganna, additional, Baynam, Gareth, additional, Brower, Amy M, additional, Callahan, Tiffany J, additional, Chute, Christopher G, additional, Est, Johanna L, additional, Galer, Peter D, additional, Ganesan, Shiva, additional, Griese, Matthias, additional, Haimel, Matthias, additional, Pazmandi, Julia, additional, Hanauer, Marc, additional, Harris, Nomi L, additional, Hartnett, Michael J, additional, Hastreiter, Maximilian, additional, Hauck, Fabian, additional, He, Yongqun, additional, Jeske, Tim, additional, Kearney, Hugh, additional, Kindle, Gerhard, additional, Klein, Christoph, additional, Knoflach, Katrin, additional, Krause, Roland, additional, Lagorce, David, additional, McMurry, Julie A, additional, Miller, Jillian A, additional, Munoz-Torres, Monica C, additional, Peters, Rebecca L, additional, Rapp, Christina K, additional, Rath, Ana M, additional, Rind, Shahmir A, additional, Rosenberg, Avi Z, additional, Segal, Michael M, additional, Seidel, Markus G, additional, Smedley, Damian, additional, Talmy, Tomer, additional, Thomas, Yarlalu, additional, Wiafe, Samuel A, additional, Xian, Julie, additional, Yüksel, Zafer, additional, Helbig, Ingo, additional, Mungall, Christopher J, additional, Haendel, Melissa A, additional, and Robinson, Peter N, additional

Published
2020
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10. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

Author

Shefchek, Kent A, primary, Harris, Nomi L, primary, Gargano, Michael, primary, Matentzoglu, Nicolas, primary, Unni, Deepak, primary, Brush, Matthew, primary, Keith, Daniel, primary, Conlin, Tom, primary, Vasilevsky, Nicole, primary, Zhang, Xingmin Aaron, primary, Balhoff, James P, primary, Babb, Larry, primary, Bello, Susan M, primary, Blau, Hannah, primary, Bradford, Yvonne, primary, Carbon, Seth, primary, Carmody, Leigh, primary, Chan, Lauren E, primary, Cipriani, Valentina, primary, Cuzick, Alayne, primary, Della Rocca, Maria, primary, Dunn, Nathan, primary, Essaid, Shahim, primary, Fey, Petra, primary, Grove, Chris, primary, Gourdine, Jean-Phillipe, primary, Hamosh, Ada, primary, Harris, Midori, primary, Helbig, Ingo, primary, Hoatlin, Maureen, primary, Joachimiak, Marcin, primary, Jupp, Simon, primary, Lett, Kenneth B, primary, Lewis, Suzanna E, primary, McNamara, Craig, primary, Pendlington, Zoë M, primary, Pilgrim, Clare, primary, Putman, Tim, primary, Ravanmehr, Vida, primary, Reese, Justin, primary, Riggs, Erin, primary, Robb, Sofia, primary, Roncaglia, Paola, primary, Seager, James, primary, Segerdell, Erik, primary, Similuk, Morgan, primary, Storm, Andrea L, primary, Thaxon, Courtney, primary, Thessen, Anne, primary, Jacobsen, Julius O B, primary, McMurry, Julie A, primary, Groza, Tudor, primary, Köhler, Sebastian, primary, Smedley, Damian, primary, Robinson, Peter N, primary, Mungall, Christopher J, primary, Haendel, Melissa A, primary, Munoz-Torres, Monica C, primary, and Osumi-Sutherland, David, primary

Published
2019
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12. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Author

Köhler, Sebastian, primary, Carmody, Leigh, additional, Vasilevsky, Nicole, additional, Jacobsen, Julius O B, additional, Danis, Daniel, additional, Gourdine, Jean-Philippe, additional, Gargano, Michael, additional, Harris, Nomi L, additional, Matentzoglu, Nicolas, additional, McMurry, Julie A, additional, Osumi-Sutherland, David, additional, Cipriani, Valentina, additional, Balhoff, James P, additional, Conlin, Tom, additional, Blau, Hannah, additional, Baynam, Gareth, additional, Palmer, Richard, additional, Gratian, Dylan, additional, Dawkins, Hugh, additional, Segal, Michael, additional, Jansen, Anna C, additional, Muaz, Ahmed, additional, Chang, Willie H, additional, Bergerson, Jenna, additional, Laulederkind, Stanley J F, additional, Yüksel, Zafer, additional, Beltran, Sergi, additional, Freeman, Alexandra F, additional, Sergouniotis, Panagiotis I, additional, Durkin, Daniel, additional, Storm, Andrea L, additional, Hanauer, Marc, additional, Brudno, Michael, additional, Bello, Susan M, additional, Sincan, Murat, additional, Rageth, Kayli, additional, Wheeler, Matthew T, additional, Oegema, Renske, additional, Lourghi, Halima, additional, Della Rocca, Maria G, additional, Thompson, Rachel, additional, Castellanos, Francisco, additional, Priest, James, additional, Cunningham-Rundles, Charlotte, additional, Hegde, Ayushi, additional, Lovering, Ruth C, additional, Hajek, Catherine, additional, Olry, Annie, additional, Notarangelo, Luigi, additional, Similuk, Morgan, additional, Zhang, Xingmin A, additional, Gómez-Andrés, David, additional, Lochmüller, Hanns, additional, Dollfus, Hélène, additional, Rosenzweig, Sergio, additional, Marwaha, Shruti, additional, Rath, Ana, additional, Sullivan, Kathleen, additional, Smith, Cynthia, additional, Milner, Joshua D, additional, Leroux, Dorothée, additional, Boerkoel, Cornelius F, additional, Klion, Amy, additional, Carter, Melody C, additional, Groza, Tudor, additional, Smedley, Damian, additional, Haendel, Melissa A, additional, Mungall, Chris, additional, and Robinson, Peter N, additional

Published
2018
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13. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Author

Mungall, Christopher J., primary, McMurry, Julie A., additional, Köhler, Sebastian, additional, Balhoff, James P., additional, Borromeo, Charles, additional, Brush, Matthew, additional, Carbon, Seth, additional, Conlin, Tom, additional, Dunn, Nathan, additional, Engelstad, Mark, additional, Foster, Erin, additional, Gourdine, J.P., additional, Jacobsen, Julius O.B., additional, Keith, Dan, additional, Laraway, Bryan, additional, Lewis, Suzanna E., additional, NguyenXuan, Jeremy, additional, Shefchek, Kent, additional, Vasilevsky, Nicole, additional, Yuan, Zhou, additional, Washington, Nicole, additional, Hochheiser, Harry, additional, Groza, Tudor, additional, Smedley, Damian, additional, Robinson, Peter N., additional, and Haendel, Melissa A., additional

Published
2016
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14. The Human Phenotype Ontology in 2017

Author

Köhler, Sebastian, primary, Vasilevsky, Nicole A., additional, Engelstad, Mark, additional, Foster, Erin, additional, McMurry, Julie, additional, Aymé, Ségolène, additional, Baynam, Gareth, additional, Bello, Susan M., additional, Boerkoel, Cornelius F., additional, Boycott, Kym M., additional, Brudno, Michael, additional, Buske, Orion J., additional, Chinnery, Patrick F., additional, Cipriani, Valentina, additional, Connell, Laureen E., additional, Dawkins, Hugh J.S., additional, DeMare, Laura E., additional, Devereau, Andrew D., additional, de Vries, Bert B.A., additional, Firth, Helen V., additional, Freson, Kathleen, additional, Greene, Daniel, additional, Hamosh, Ada, additional, Helbig, Ingo, additional, Hum, Courtney, additional, Jähn, Johanna A., additional, James, Roger, additional, Krause, Roland, additional, F. Laulederkind, Stanley J., additional, Lochmüller, Hanns, additional, Lyon, Gholson J., additional, Ogishima, Soichi, additional, Olry, Annie, additional, Ouwehand, Willem H., additional, Pontikos, Nikolas, additional, Rath, Ana, additional, Schaefer, Franz, additional, Scott, Richard H., additional, Segal, Michael, additional, Sergouniotis, Panagiotis I., additional, Sever, Richard, additional, Smith, Cynthia L., additional, Straub, Volker, additional, Thompson, Rachel, additional, Turner, Catherine, additional, Turro, Ernest, additional, Veltman, Marijcke W.M., additional, Vulliamy, Tom, additional, Yu, Jing, additional, von Ziegenweidt, Julie, additional, Zankl, Andreas, additional, Züchner, Stephan, additional, Zemojtel, Tomasz, additional, Jacobsen, Julius O.B., additional, Groza, Tudor, additional, Smedley, Damian, additional, Mungall, Christopher J., additional, Haendel, Melissa, additional, and Robinson, Peter N., additional

Published
2016
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15. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

Author

Köhler, Sebastian, primary, Doelken, Sandra C., additional, Mungall, Christopher J., additional, Bauer, Sebastian, additional, Firth, Helen V., additional, Bailleul-Forestier, Isabelle, additional, Black, Graeme C. M., additional, Brown, Danielle L., additional, Brudno, Michael, additional, Campbell, Jennifer, additional, FitzPatrick, David R., additional, Eppig, Janan T., additional, Jackson, Andrew P., additional, Freson, Kathleen, additional, Girdea, Marta, additional, Helbig, Ingo, additional, Hurst, Jane A., additional, Jähn, Johanna, additional, Jackson, Laird G., additional, Kelly, Anne M., additional, Ledbetter, David H., additional, Mansour, Sahar, additional, Martin, Christa L., additional, Moss, Celia, additional, Mumford, Andrew, additional, Ouwehand, Willem H., additional, Park, Soo-Mi, additional, Riggs, Erin Rooney, additional, Scott, Richard H., additional, Sisodiya, Sanjay, additional, Vooren, Steven Van, additional, Wapner, Ronald J., additional, Wilkie, Andrew O. M., additional, Wright, Caroline F., additional, Vulto-van Silfhout, Anneke T., additional, Leeuw, Nicole de, additional, de Vries, Bert B. A., additional, Washingthon, Nicole L., additional, Smith, Cynthia L., additional, Westerfield, Monte, additional, Schofield, Paul, additional, Ruef, Barbara J., additional, Gkoutos, Georgios V., additional, Haendel, Melissa, additional, Smedley, Damian, additional, Lewis, Suzanna E., additional, and Robinson, Peter N., additional

Published
2013
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17. The Human Phenotype Ontology in 2024: phenotypes around the world.

Author

Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He YO, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI Jr, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts AM, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, and Robinson PN

Subjects
Humans, Phenotype, Genomics, Algorithms, Rare Diseases, Biological Ontologies
Abstract

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2024
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