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152. Mondo: Unifying diseases for the world, by the world

Author

Vasilevsky, Nicole A, primary, Matentzoglu, Nicolas A, additional, Toro, Sabrina, additional, Flack, Joseph E, additional, Hegde, Harshad, additional, Unni, Deepak R, additional, Alyea, Gioconda F, additional, Amberger, Joanna S, additional, Babb, Larry, additional, Balhoff, James P, additional, Bingaman, Taylor I, additional, Burns, Gully A, additional, Buske, Orion J, additional, Callahan, Tiffany J, additional, Carmody, Leigh C, additional, Cordo, Paula Carrio, additional, Chan, Lauren E, additional, Chang, George S, additional, Christiaens, Sean L, additional, Dumontier, Michel, additional, Failla, Laura E, additional, Flowers, May J, additional, Garrett, H. Alpha, additional, Goldstein, Jennifer L, additional, Gration, Dylan, additional, Groza, Tudor, additional, Hanauer, Marc, additional, Harris, Nomi L, additional, Hilton, Jason A, additional, Himmelstein, Daniel S, additional, Hoyt, Charles Tapley, additional, Kane, Megan S, additional, Köhler, Sebastian, additional, Lagorce, David, additional, Lai, Abbe, additional, Larralde, Martin, additional, Lock, Antonia, additional, López Santiago, Irene, additional, Maglott, Donna R, additional, Malheiro, Adriana J, additional, Meldal, Birgit H M, additional, Munoz-Torres, Monica C, additional, Nelson, Tristan H, additional, Nicholas, Frank W, additional, Ochoa, David, additional, Olson, Daniel P, additional, Oprea, Tudor I, additional, Osumi-Sutherland, David, additional, Parkinson, Helen, additional, Pendlington, Zoë May, additional, Rath, Ana, additional, Rehm, Heidi L, additional, Remennik, Lyubov, additional, Riggs, Erin R, additional, Roncaglia, Paola, additional, Ross, Justyne E, additional, Shadbolt, Marion F, additional, Shefchek, Kent A, additional, Similuk, Morgan N, additional, Sioutos, Nicholas, additional, Smedley, Damian, additional, Sparks, Rachel, additional, Stefancsik, Ray, additional, Stephan, Ralf, additional, Storm, Andrea L, additional, Stupp, Doron, additional, Stupp, Gregory S, additional, Sundaramurthi, Jagadish Chandrabose, additional, Tammen, Imke, additional, Tay, Darin, additional, Thaxton, Courtney L, additional, Valasek, Eloise, additional, Valls-Margarit, Jordi, additional, Wagner, Alex H, additional, Welter, Danielle, additional, Whetzel, Patricia L, additional, Whiteman, Lori L, additional, Wood, Valerie, additional, Xu, Colleen H, additional, Zankl, Andreas, additional, Zhang, Xingmin Aaron, additional, Chute, Christopher G, additional, Robinson, Peter N, additional, Mungall, Christopher J, additional, Hamosh, Ada, additional, and Haendel, Melissa A, additional

Published
2022
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153. Guidelines for reporting cell types: the MIRACL standard

Author

Lubiana, Tiago, Roncaglia, Paola, Mungall, Christopher J., Quardokus, Ellen M., Fortriede, Joshua D., Osumi-Sutherland, David, and Diehl, Alexander D.

Subjects
FOS: Biological sciences, Other Quantitative Biology (q-bio.OT), Quantitative Biology - Other Quantitative Biology
Abstract

Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project. Surprisingly, there are no standards for reporting new cell types, leading to a gap between classes mentioned in biomedical literature and the Cell Ontology, the primary registry of cell types. Here we introduce the Minimal Information Reporting About a CelL (MIRACL) standard, a guideline for describing cell types alongside scientific articles. In a MIRACL sheet, authors organize a label, a diagnostic description, a taxon, an anatomical structure, and a parent cell class for each cell type of interest. The MIRACL standard bridges the gap between wet-lab researchers and ontologists, facilitating the integration of biomedical knowledge into ontologies and artificial intelligence systems., Comment: 8 pages, 1 figure, 1 table

Published
2022
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154. Additional file 1 of NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study

Author

Reese, Justin T., Coleman, Ben, Chan, Lauren, Blau, Hannah, Callahan, Tiffany J., Cappelletti, Luca, Fontana, Tommaso, Bradwell, Katie R., Harris, Nomi L., Casiraghi, Elena, Valentini, Giorgio, Karlebach, Guy, Deer, Rachel, McMurry, Julie A., Haendel, Melissa A., Chute, Christopher G., Pfaff, Emily, Moffitt, Richard, Spratt, Heidi, Singh, Jasvinder A., Mungall, Christopher J., Williams, Andrew E., and Robinson, Peter N.

Abstract

Additional file 1. Figures S1–S2, Tables S1–S4, and Supplemental Note 1.

Published
2022
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155. Additional file 1 of SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Author

Danis, Daniel, Jacobsen, Julius O. B., Balachandran, Parithi, Zhu, Qihui, Yilmaz, Feyza, Reese, Justin, Haimel, Matthias, Lyon, Gholson J., Helbig, Ingo, Mungall, Christopher J., Beck, Christine R., Lee, Charles, Smedley, Damian, and Robinson, Peter N.

Abstract

Additional file 1: Table S1. Summary of VCF fields used to report depth of coverage. Fig. S1. Distribution of lengths of the curated structural variants. Figs. S2-S9. Examples of graphical displays generated for different types of structural variants. Fig. S10. Mean variant rank depending on the number of phenotype terms. Fig. S11. Screenshot of tabular and graphical summary generated for structural variants.

Published
2022
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156. Harmonizing model organism data in the Alliance of Genome Resources

Author

Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A., Alexander, Micheal, Anagnostopoulos, Anna V., Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M., Blake, Judith A., Blodgett, Olin, Bradford, Yvonne M., Bult, Carol J., Cain, Scott, Calvi, Brian R., Carbon, Seth, Chan, Juancarlos, Chen, Wen J., Cherry, J. Michael, Cho, Jaehyoung, Christie, Karen R., Crosby, Madeline A., Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L., D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E., dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R., Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C., Gondwe, Felix, Goodman, Josh, Gramates, L. Sian, Grove, Christian A., Hale, Paul, Harris, Todd, Thomas Hayman, G., Hill, David P., Howe, Douglas G., Howe, Kevin L., Hu, Yanhui, Jha, Sagar, Kadin, James A., Kaufman, Thomas C., Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E., Laulederkind, Stanley J. F., Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A., Martin, Ryan, Marygold, Steven J., Matthews, Beverley, McAndrews, Monica S., Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Müller, Hans-Michael, Mungall, Christopher J., Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S., Nash, Robert S., Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E., Russo Gelbart, Susan, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R., Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M., Smith, Cynthia L., Smith, Jennifer R., Stein, Lincoln, Sternberg, Paul W., Tabone, Christopher J., Thomas, Paul D., Thorat, Ketaki, Thota, Jyothi, Toro, Sabrina, Tomczuk, Monika, Trovisco, Vitor, Tutaj, Marek A., Tutaj, Monika, Urbano, Jose-Maria, Van Auken, Kimberly, Van Slyke, Ceri E., Wang, Qinghua, Wang, Shur-Jen, Weng, Shuai, Westerfield, Monte, Williams, Gary, Wilming, Laurens G., Wong, Edith D., Wright, Adam, Yook, Karen, Zarowiecki, Magdalena, Zhou, Pinglei, and Zytkovicz, Mark

Subjects
Internet, Molecular Sequence Annotation, Rats, Mice, Gene Ontology, Databases, Genetic, Saccharomycetales, Genetics, Animals, Humans, Drosophila, Caenorhabditis elegans, Alleles, Zebrafish
Abstract

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Published
2021

159. Hematopoietic cell types: Prototype for a revised cell ontology

Author

Diehl, Alexander D., Augustine, Alison Deckhut, Blake, Judith A., Cowell, Lindsay G., Gold, Elizabeth S., Gondré-Lewis, Timothy A., Masci, Anna Maria, Meehan, Terrence F., Morel, Penelope A., Nijnik, Anastasia, Peters, Bjoern, Pulendran, Bali, Scheuermann, Richard H., Yao, Q. Alison, Zand, Martin S., and Mungall, Christopher J.

Published
2011
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161. A Simple Standard for Sharing Ontological Mappings (SSSOM)

Author

Matentzoglu, Nicolas, primary, Balhoff, James P, additional, Bello, Susan M, additional, Bizon, Chris, additional, Brush, Matthew, additional, Callahan, Tiffany J, additional, Chute, Christopher G, additional, Duncan, William D, additional, Evelo, Chris T, additional, Gabriel, Davera, additional, Graybeal, John, additional, Gray, Alasdair, additional, Gyori, Benjamin M, additional, Haendel, Melissa, additional, Harmse, Henriette, additional, Harris, Nomi L, additional, Harrow, Ian, additional, Hegde, Harshad B, additional, Hoyt, Amelia L, additional, Hoyt, Charles T, additional, Jiao, Dazhi, additional, Jiménez-Ruiz, Ernesto, additional, Jupp, Simon, additional, Kim, Hyeongsik, additional, Koehler, Sebastian, additional, Liener, Thomas, additional, Long, Qinqin, additional, Malone, James, additional, McLaughlin, James A, additional, McMurry, Julie A, additional, Moxon, Sierra, additional, Munoz-Torres, Monica C, additional, Osumi-Sutherland, David, additional, Overton, James A, additional, Peters, Bjoern, additional, Putman, Tim, additional, Queralt-Rosinach, Núria, additional, Shefchek, Kent, additional, Solbrig, Harold, additional, Thessen, Anne, additional, Tudorache, Tania, additional, Vasilevsky, Nicole, additional, Wagner, Alex H, additional, and Mungall, Christopher J, additional

Published
2022
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162. A roadmap for the functional annotation of protein families: a community perspective

Author

de Crécy-lagard, Valérie, primary, Amorin de Hegedus, Rocio, additional, Arighi, Cecilia, additional, Babor, Jill, additional, Bateman, Alex, additional, Blaby, Ian, additional, Blaby-Haas, Crysten, additional, Bridge, Alan J, additional, Burley, Stephen K, additional, Cleveland, Stacey, additional, Colwell, Lucy J, additional, Conesa, Ana, additional, Dallago, Christian, additional, Danchin, Antoine, additional, de Waard, Anita, additional, Deutschbauer, Adam, additional, Dias, Raquel, additional, Ding, Yousong, additional, Fang, Gang, additional, Friedberg, Iddo, additional, Gerlt, John, additional, Goldford, Joshua, additional, Gorelik, Mark, additional, Gyori, Benjamin M, additional, Henry, Christopher, additional, Hutinet, Geoffrey, additional, Jaroch, Marshall, additional, Karp, Peter D, additional, Kondratova, Liudmyla, additional, Lu, Zhiyong, additional, Marchler-Bauer, Aron, additional, Martin, Maria-Jesus, additional, McWhite, Claire, additional, Moghe, Gaurav D, additional, Monaghan, Paul, additional, Morgat, Anne, additional, Mungall, Christopher J, additional, Natale, Darren A, additional, Nelson, William C, additional, O’Donoghue, Seán, additional, Orengo, Christine, additional, O’Toole, Katherine H, additional, Radivojac, Predrag, additional, Reed, Colbie, additional, Roberts, Richard J, additional, Rodionov, Dmitri, additional, Rodionova, Irina A, additional, Rudolf, Jeffrey D, additional, Saleh, Lana, additional, Sheynkman, Gloria, additional, Thibaud-Nissen, Francoise, additional, Thomas, Paul D, additional, Uetz, Peter, additional, Vallenet, David, additional, Carter, Erica Watson, additional, Weigele, Peter R, additional, Wood, Valerie, additional, Wood-Charlson, Elisha M, additional, and Xu, Jin, additional

Published
2022
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163. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies

Author

Matentzoglu, Nicolas, primary, Goutte-Gattat, Damien, additional, Tan, Shawn Zheng Kai, additional, Balhoff, James P, additional, Carbon, Seth, additional, Caron, Anita R, additional, Duncan, William D, additional, Flack, Joe E, additional, Haendel, Melissa, additional, Harris, Nomi L, additional, Hogan, William R, additional, Hoyt, Charles Tapley, additional, Jackson, Rebecca C, additional, Kim, HyeongSik, additional, Kir, Huseyin, additional, Larralde, Martin, additional, McMurry, Julie A, additional, Overton, James A, additional, Peters, Bjoern, additional, Pilgrim, Clare, additional, Stefancsik, Ray, additional, Robb, Sofia MC, additional, Toro, Sabrina, additional, Vasilevsky, Nicole A, additional, Walls, Ramona, additional, Mungall, Christopher J, additional, and Osumi-Sutherland, David, additional

Published
2022
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164. The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Author

Jacobsen, Julius O. B., primary, Baudis, Michael, additional, Baynam, Gareth S., additional, Beckmann, Jacques S., additional, Beltran, Sergi, additional, Callahan, Tiffany J., additional, Chute, Christopher G., additional, Courtot, Mélanie, additional, Danis, Daniel, additional, Elemento, Olivier, additional, Freimuth, Robert R., additional, Gargano, Michael A., additional, Groza, Tudor, additional, Hamosh, Ada, additional, Harris, Nomi L., additional, Kaliyaperumal, Rajaram, additional, Khalifa, Aly, additional, Krawitz, Peter M., additional, Köhler, Sebastian, additional, Laraway, Brian J., additional, Lehväslaiho, Heikki, additional, Lloyd, Kent C., additional, Matalonga, Leslie, additional, McMurry, Julie A., additional, Metke-Jimenez, Alejandro, additional, Mungall, Christopher J., additional, Munoz-Torres, Monica C., additional, Ogishima, Soichi, additional, Papakonstantinou, Anastasios, additional, Piscia, Davide, additional, Pontikos, Nikolas, additional, Queralt-Rosinach, Núria, additional, Roos, Marco, additional, Schofield, Paul N., additional, Siapos, Anastasios, additional, Smedley, Damian, additional, Smith, Lindsay D., additional, Steinhaus, Robin, additional, Sundaramurthi, Jagadish Chandrabose, additional, Swietlik, Emilia M., additional, Thun, Sylvia, additional, Vasilevsky, Nicole A., additional, Wagner, Alex H., additional, Warner, Jeremy L., additional, Weiland, Claus, additional, Haendel, Melissa A., additional, and Robinson, Peter N., additional

Published
2021
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165. ECO: the Evidence and Conclusion Ontology, an update for 2022

Author

Nadendla, Suvarna, primary, Jackson, Rebecca, additional, Munro, James, additional, Quaglia, Federica, additional, Mészáros, Bálint, additional, Olley, Dustin, additional, Hobbs, Elizabeth T, additional, Goralski, Stephen M, additional, Chibucos, Marcus, additional, Mungall, Christopher John, additional, Tosatto, Silvio C E, additional, Erill, Ivan, additional, and Giglio, Michelle G, additional

Published
2021
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166. Brain Data Standards - A method for building data-driven cell-type ontologies.

Author

Tan, Shawn Zheng Kai, Kir, Huseyin, Aevermann, Brian D., Gillespie, Tom, Harris, Nomi, Hawrylycz, Michael J., Jorstad, Nikolas L., Lein, Ed S., Matentzoglu, Nicolas, Miller, Jeremy A., Mollenkopf, Tyler S., Mungall, Christopher J., Ray, Patrick L., Sanchez, Raymond E. A., Staats, Brian, Vermillion, Jim, Yadav, Ambika, Zhang, Yun, Scheuermann, Richard H., and Osumi-Sutherland, David

Subjects
MOTOR cortex, ONTOLOGY, BUILDING additions, MARMOSETS, PROBLEM solving
Abstract

Large-scale single-cell 'omics profiling is being used to define a complete catalogue of brain cell types, something that traditional methods struggle with due to the diversity and complexity of the brain. But this poses a problem: How do we organise such a catalogue - providing a standard way to refer to the cell types discovered, linking their classification and properties to supporting data? Cell ontologies provide a partial solution to these problems, but no existing ontology schemas support the definition of cell types by direct reference to supporting data, classification of cell types using classifications derived directly from data, or links from cell types to marker sets along with confidence scores. Here we describe a generally applicable schema that solves these problems and its application in a semi-automated pipeline to build a data-linked extension to the Cell Ontology representing cell types in the Primary Motor Cortex of humans, mice and marmosets. The methods and resulting ontology are designed to be scalable and applicable to similar whole-brain atlases currently in preparation. [ABSTRACT FROM AUTHOR]

Published
2023
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167. Unifying the identification of biomedical entities with the Bioregistry.

Author

Hoyt, Charles Tapley, Balk, Meghan, Callahan, Tiffany J., Domingo-Fernández, Daniel, Haendel, Melissa A., Hegde, Harshad B., Himmelstein, Daniel S., Karis, Klas, Kunze, John, Lubiana, Tiago, Matentzoglu, Nicolas, McMurry, Julie, Moxon, Sierra, Mungall, Christopher J., Rutz, Adriano, Unni, Deepak R., Willighagen, Egon, Winston, Donald, and Gyori, Benjamin M.

Subjects
SCIENTIFIC literature, SMALL molecules, LIFE sciences, SOURCE code, INFRASTRUCTURE (Economics), NETWORK governance, METADATA
Abstract

The standardized identification of biomedical entities is a cornerstone of interoperability, reuse, and data integration in the life sciences. Several registries have been developed to catalog resources maintaining identifiers for biomedical entities such as small molecules, proteins, cell lines, and clinical trials. However, existing registries have struggled to provide sufficient coverage and metadata standards that meet the evolving needs of modern life sciences researchers. Here, we introduce the Bioregistry, an integrative, open, community-driven metaregistry that synthesizes and substantially expands upon 23 existing registries. The Bioregistry addresses the need for a sustainable registry by leveraging public infrastructure and automation, and employing a progressive governance model centered around open code and open data to foster community contribution. The Bioregistry can be used to support the standardized annotation of data, models, ontologies, and scientific literature, thereby promoting their interoperability and reuse. The Bioregistry can be accessed through https://bioregistry.io and its source code and data are available under the MIT and CC0 Licenses at https://github.com/biopragmatics/bioregistry. [ABSTRACT FROM AUTHOR]

Published
2022
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168. Systematic curation of disease concept mappings in Mondo

Author

Mungall, Christopher J

Subjects
PistoiaAlliance, invited, OBO, mapping, mondo, monarch-initiative, OWL, bio-ontologies, diseases
Abstract

Numerous sources for disease definitions and data models currently exist, which include HPO, OMIM, SNOMED CT, ICD, PhenoDB, MedDRA, MedGen, ORDO, DO, GARD, etc; however, these sources partially overlap and sometimes conflict, making it difficult to know definitively how they relate to each other. This has resulted in a proliferation of mappings between disease entries in different resources; however mappings are problematic: collectively, they are expensive to create and maintain. Most importantly, the mappings lack completeness, accuracy, and precision; as a result, mapping calls are often inconsistent between resources. The UMLS provides intermediate concepts through which other resources can be mapped, but these mappings suffer from the same challenges: they are not guaranteed to be one-to-one, especially in areas with evolving disease concepts such as rare disease. In order to address the lack of a unified disease terminology that provides precise equivalences between disease concepts, we created Mondo, which provides a logic-based structure for unifying multiple disease resources. Mondo utilizes human curation assisted by a combination of logical, probabilistic and lexical methods to assist in curation and hone curation on difficult areas, together with fostering a broader community of disease resources committed to working together. &nbsp

Published
2021
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169. Semantic Annotations and Data Integration in Ecology

Author

Thessen, Anne E, Schildhauer, Mark, Balk, Meghan A, and Mungall, Christopher J

Subjects
data, knowledge graph, ontology, ecology
Abstract

In order to address society’s most pressing challenges, extremely heterogeneous ecological and organismal data must be integrated. Semantic technology, using terms and design patterns from ontologies and knowledge graphs, provides a more scalable approach than database and spreadsheet technology. In this talk, we will discuss the use of semantic technology for ecological data integration in the context of three projects: FuTRES, the Arctic Data Center, and the National Microbiome Data Collaborative. Semantic technology holds great promise for large-scale data integration in ecology, but more work is needed to create a machine-actionable view across data resources., This talk was created for the Ecological Society of America 2021 meeting in an INSPIRE session. These talks are only 5 min long.

Published
2021
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170. Brain Data Standards - A method for building data-driven cell-type ontologies

Author

Tan, Shawn Zheng Kai, primary, Kir, Huseyin, additional, Aevermann, Brian D., additional, Gillespie, Tom, additional, Harris, Nomi, additional, Hawrylycz, Michael, additional, Jorstad, Nik, additional, Lein, Ed, additional, Matentzoglu, Nicolas, additional, Miller, Jeremy A., additional, Mollenkopf, Tyler S., additional, Mungall, Christopher J., additional, Ray, Patrick L., additional, Sanchez, Raymond E. A., additional, Staats, Brian, additional, Vermillion, Jim, additional, Yadav, Ambika, additional, Zhang, Yun, additional, Scheuermann, Richard H., additional, and Osumi-Sutherland, David, additional

Published
2021
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171. Sequence Ontology terminology for gene regulation

Author

Sant, David W., primary, Sinclair, Michael, additional, Mungall, Christopher J., additional, Schulz, Stefan, additional, Zerbino, Daniel, additional, Lovering, Ruth C., additional, Logie, Colin, additional, and Eilbeck, Karen, additional

Published
2021
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172. OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

Author

Jackson, Rebecca, primary, Matentzoglu, Nicolas, additional, Overton, James A, additional, Vita, Randi, additional, Balhoff, James P, additional, Buttigieg, Pier Luigi, additional, Carbon, Seth, additional, Courtot, Melanie, additional, Diehl, Alexander D, additional, Dooley, Damion M, additional, Duncan, William D, additional, Harris, Nomi L, additional, Haendel, Melissa A, additional, Lewis, Suzanna E, additional, Natale, Darren A, additional, Osumi-Sutherland, David, additional, Ruttenberg, Alan, additional, Schriml, Lynn M, additional, Smith, Barry, additional, Stoeckert Jr., Christian J, additional, Vasilevsky, Nicole A, additional, Walls, Ramona L, additional, Zheng, Jie, additional, Mungall, Christopher J, additional, and Peters, Bjoern, additional

Published
2021
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174. GENE REGULATION: Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Author

Arner, Erik, Daub, Carsten O., Vitting-Seerup, Kristoffer, Andersson, Robin, Lilje, Berit, Drabløs, Finn, Lennartsson, Andreas, Rönnerblad, Michelle, Hrydziuszko, Olga, Vitezic, Morana, Freeman, Tom C., Alhendi, Ahmad M. N., Arner, Peter, Axton, Richard, Baillie, Kenneth J., Beckhouse, Anthony, Bodega, Beatrice, Briggs, James, Brombacher, Frank, Davis, Margaret, Detmar, Michael, Ehrlund, Anna, Endoh, Mitsuhiro, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E., Forrester, Lesley, Goldowitz, Daniel, Guler, Reto, Ha, Thomas, Hara, Mitsuko, Herlyn, Meenhard, Ikawa, Tomokatsu, Kai, Chieko, Kawamoto, Hiroshi, Khachigian, Levon M., Klinken, Peter S., Kojima, Soichi, Koseki, Haruhiko, Klein, Sarah, Mejhert, Niklas, Miyaguchi, Ken, Mizuno, Yosuke, Morimoto, Mitsuru, Morris, Kelly J., Mummery, Christine, Nakachi, Yutaka, Ogishima, Soichi, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry, Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Qin, Xian-Yang, Roy, Sugata, Sato, Hiroki, Savvi, Suzana, Saxena, Alka, Schwegmann, Anita, Sugiyama, Daisuke, Swoboda, Rolf, Tanaka, Hiroshi, Tomoiu, Andru, Winteringham, Louise N., Wolvetang, Ernst, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Zabierowski, Susan, Zhang, Peter, Abugessaisa, Imad, Bertin, Nicolas, Diehl, Alexander D., Fukuda, Shiro, Furuno, Masaaki, Harshbarger, Jayson, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Ishizu, Yuri, Itoh, Masayoshi, Kawashima, Tsugumi, Kojima, Miki, Kondo, Naoto, Lizio, Marina, Meehan, Terrence F., Mungall, Christopher J., Murata, Mitsuyoshi, Nishiyori-Sueki, Hiromi, Sahin, Serkan, Nagao-Sato, Sayaka, Severin, Jessica, de Hoon, Michiel J. L., Kawai, Jun, Kasukawa, Takeya, Lassmann, Timo, Suzuki, Harukazu, Kawaji, Hideya, Summers, Kim M., Wells, Christine, Hume, David A., Forrest, Alistair R. R., Sandelin, Albin, Carninci, Piero, and Hayashizaki, Yoshihide

Published
2015
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176. Yosemite Project Webinar: LinkML - A Linked Open Data Modeling Language

Author

Mungall, Christopher J and Solbrig, Harold

Subjects
semantic-web, YosemiteSummit, healthcare, keynote, linked-data, linkml, RDF
Abstract

LinkMLis a modeling language and collection of tools that joins the data processing world with the semantic, making it possible for developers to continue to employ tools such as JSON, YAML, SQL, spreadsheets, etc., while _directly_ working with RDF and ontology based semantics.LinkMLleverages and integrates technologies such as JSON-LD, Knowledge Graphs, RDF and Shape Expressions (ShEx), and provides an environment where semantics and data are seamlessly integrated and structural and representational transformations between communities can be based on the combination of RDF and ontology. WhyLinkML? Twenty years ago, Tim Berners-Lee coined the term "The Semantic Web" in a seminal article in Scientific American. While it is heartening to see how much of his vision has been realized, gaps still remain. Berners-Lee's vision included the notion that the "Semantic Web is not a separate Web but an _extension_ of the current one, in which information is given well-defined meaning...". While progress has been made in some areas (e.g.schema.org), the world of data and the world of semantics still exist in separate spaces. While tools and techniques exist to _transform_ (lift) data into the RDF space, to date these environments have been separate.LinkMLhelps to bridge this gap. This webinar provides a short introduction to theLinkMLmodeling language and tools: how it came to be, what it can be used for today, how it is being used in biomedical research, and where the developers intend to take it in the future. ABOUT THE SPEAKERS Harold Solbrig is an active contributor to healthcare information modeling, semantics and standards-based information exchange for 40+ years. He has served in multiple roles in the ISO, W3C, HL7 and other standards communities. He has a master's degree in Software Engineering from Oxford University and is an assistant professor at Johns Hopkins University. Chris Mungall is Department Head of Biosystems Data Science at Lawrence Berkeley National Laboratory, working on the application of computational techniques to problems life sciences of relevance to the health of humans and the health of the planet. His main interest is the application of artificial intelligence, knowledge-based methods, and bio-curation to advance our understanding of the interconnected role of genes and genetic mechanisms in key biological processes.

Published
2021
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178. SvAnna: efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

Author

Danis, Daniel, primary, Jacobsen, Julius O.B., additional, Balachandran, Parithi, additional, Zhu, Qihui, additional, Yilmaz, Feyza, additional, Reese, Justin, additional, Haimel, Matthias, additional, Lyon, Gholson J., additional, Helbig, Ingo, additional, Mungall, Christopher J, additional, Beck, Christine, additional, Lee, Charles, additional, Smedley, Damian, additional, and Robinson, Peter N, additional

Published
2021
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179. OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

Author

Jackson, Rebecca C., primary, Matentzoglu, Nicolas, additional, Overton, James A., additional, Vita, Randi, additional, Balhoff, James P., additional, Buttigieg, Pier Luigi, additional, Carbon, Seth, additional, Courtot, Melanie, additional, Diehl, Alexander D., additional, Dooley, Damion, additional, Duncan, William, additional, Harris, Nomi L., additional, Haendel, Melissa A., additional, Lewis, Suzanna E., additional, Natale, Darren A., additional, Osumi-Sutherland, David, additional, Ruttenberg, Alan, additional, Schriml, Lynn M., additional, Smith, Barry, additional, Stoeckert, Christian J., additional, Vasilevsky, Nicole A., additional, Walls, Ramona L., additional, Zheng, Jie, additional, Mungall, Christopher J., additional, and Peters, Bjoern, additional

Published
2021
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180. ICBO_Poster_Mondo_Vasilevsky_2021-09-17.pdf

Author

Vasilevsky, Nicole, Toro, Sabrina, Matentzoglu, Nicolas, Jiao, Dahi, Haendel, Melissa, N Robinson, Peter, and Mungall, Christopher

Subjects
ComputingMethodologies_GENERAL, ComputingMilieux_MISCELLANEOUS
Abstract

Poster presentation at International Conference for Biomedical Ontologies (ICBO), Virtual, September 15, 2021.

Published
2021
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181. Sequence Ontology terminology for gene regulation

Author

Sant, David W., Sinclair, Michael, Mungall, Christopher J., Schulz, Stefan, Zerbino, Daniel, Lovering, Ruth C., Logie, C., Eilbeck, Karen, Sant, David W., Sinclair, Michael, Mungall, Christopher J., Schulz, Stefan, Zerbino, Daniel, Lovering, Ruth C., Logie, C., and Eilbeck, Karen

Abstract

Contains fulltext : 237100.pdf (Publisher’s version ) (Closed access)

Published
2021

182. OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

Author

Jackson, R.C., Matentzoglu, N., Overton, J.A., Vita, R., Balhoff, J.P., Buttigieg, Pier Luigi, Carbon, S., Courtot, M., Diehl, A.D., Dooley, Damion M, Duncan, W., Harris, N.L., Haendel, M.A., Lewis, Suzanna E., Natale, D.A., Osumi-Sutherland, David, Ruttenberg, A., Schriml, Lynn M, Smith, Barry, Stoeckert, C.J., Vasilevsky, N.A., Walls, R.L., Zheng, Jie, Mungall, Christopher J, Peters, Björn, Jackson, R.C., Matentzoglu, N., Overton, J.A., Vita, R., Balhoff, J.P., Buttigieg, Pier Luigi, Carbon, S., Courtot, M., Diehl, A.D., Dooley, Damion M, Duncan, W., Harris, N.L., Haendel, M.A., Lewis, Suzanna E., Natale, D.A., Osumi-Sutherland, David, Ruttenberg, A., Schriml, Lynn M, Smith, Barry, Stoeckert, C.J., Vasilevsky, N.A., Walls, R.L., Zheng, Jie, Mungall, Christopher J, and Peters, Björn

Published
2021

183. Aligning Design Patterns across Multiple Ontologies in the Life Sciences

Author

Mungall, Christopher J

Subjects
semantic-web, design-patterns, DOSDPs, keynote, WorkshopOntologyPatterns, ontology-design-patterns, OWL
Abstract

https://douroucouli.wordpress.com/2020/11/02/aligning-design-patterns-across-multiple-ontologies-in-the-life-sciences/ https://docs.google.com/presentation/d/1M6zxYQPwy3fgyQRstaFYCZ3uscTg4J5OwooYQkNCQ8E/edit#slide=id.p

Published
2020
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184. A promoter-level mammalian expression atlas

Author

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., ’t Hoen, Peter A. C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Published
2014
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185. An atlas of active enhancers across human cell types and tissues

Author

Andersson, Robin, Gebhard, Claudia, Miguel-Escalada, Irene, Hoof, Ilka, Bornholdt, Jette, Boyd, Mette, Chen, Yun, Zhao, Xiaobei, Schmidl, Christian, Suzuki, Takahiro, Ntini, Evgenia, Arner, Erik, Valen, Eivind, Li, Kang, Schwarzfischer, Lucia, Glatz, Dagmar, Raithel, Johanna, Lilje, Berit, Rapin, Nicolas, Bagger, Frederik Otzen, Jørgensen, Mette, Andersen, Peter Refsing, Bertin, Nicolas, Rackham, Owen, Burroughs, Maxwell A., Baillie, Kenneth J., Ishizu, Yuri, Shimizu, Yuri, Furuhata, Erina, Maeda, Shiori, Negishi, Yutaka, Mungall, Christopher J., Meehan, Terrence F., Lassmann, Timo, Itoh, Masayoshi, Kawaji, Hideya, Kondo, Naoto, Kawai, Jun, Lennartsson, Andreas, Daub, Carsten O., Heutink, Peter, Hume, David A., Jensen, Torben Heick, Suzuki, Harukazu, Hayashizaki, Yoshihide, Müller, Ferenc, Consortium, The FANTOM, Forrest, Alistair R. R., Carninci, Piero, Rehli, Michael, and Sandelin, Albin

Published
2014
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186. 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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187. NSAID use and clinical outcomes in COVID-19 patients: A 38-center retrospective cohort study

Author

Reese, Justin T., primary, Coleman, Ben, additional, Chan, Lauren, additional, Blau, Hannah, additional, Callahan, Tiffany J., additional, Cappelletti, Luca, additional, Fontana, Tommaso, additional, Bradwell, Katie Rebecca, additional, Harris, Nomi L., additional, Casiraghi, Elena, additional, Valentini, Giorgio, additional, Karlebach, Guy, additional, Deer, Rachel, additional, McMurry, Julie A., additional, Haendel, Melissa A., additional, Chute, Christopher G., additional, Pfaff, Emily, additional, Moffitt, Richard, additional, Spratt, Heidi, additional, Singh, Jasvinder, additional, Mungall, Christopher J., additional, Williams, Andrew E., additional, and Robinson, Peter N., additional

Published
2021
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188. Semantic models for environmental exposures: Linking geo and bio via the toxicology community

Author

Thessen, Anne E, Chan, Lauren E, Boyles, Rebecca, Mungall, Christopher J, and Haendel, Melissa A

Subjects
knowledge graph, exposure, fungi, ontology, semantics, environment, toxicology
Abstract

Semantic technology has the potential to advance research by acting as a bridge across bespoke standards. This has already been demonstrated through projects like the Monarch Initiative (Shefchek et al., 2020) and Phenoscape (Edmunds et al., 2015). Both of these projects are biologically-focused repositories for relating genes and phenotypes, but the environment plays an important role in the observable traits of organisms. To represent environmental exposures in the Monarch knowledge graph we created the Environmental Conditions, Treatments, and Exposures Ontology (ECTO) and proposed a model for linking environments to diseases and phenotypes. Development of the ontology and the model was guided by biomedicine and toxicology, two user communities that have a keen interest in understanding the effect of elements of the environment on gene expression, observable phenotypes, and disease progression. This talk will present the semantic model and review the process for its development within the toxicology and biomedical communities.

Published
2020
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190. 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
endocrine system, Genotype, International Cooperation, Neurodegenerative, Databases, Neonatal Screening, Terminology as Topic, Information and Computing Sciences, Animals, Humans, Disease, Factual, Internet, Genome, Animal, fungi, Computational Biology, Infant, Biological Sciences, Newborn, equipment and supplies, body regions, Phenotype, Networking and Information Technology R&D, Networking and Information Technology R&D (NITRD), Biological Ontologies, Pharmacogenetics, Disease Models, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Software, Environmental Sciences, Developmental Biology
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
2020

191. The ontologies community of practice: a CGIAR initiative for big data in agrifood systems

Author

Arnaud, E., Laporte, M.A., Kim, S., Aubert, C., Leonelli, S., Miro, B., Cooper, L., Jaiswal, P., Kruseman, G., Shrestha, R., Buttigieg, Pier Luigi, Mungall, Christopher J, Pietragalla, J., Agbona, A., Muliro, J., Detras, J., Hualla, V., Rathore, A., Das, R.R., Dieng, I., Bauchet, G.J., Menda, N., Pommier, C., Shaw, F., Lyon, D., Mwanzia, L., Juarez, H., Bonaiuti, E., Chiputwa, B., Obileye, O., Auzoux, S., Yeumo, E.D., Mueller, L., Silverstein, K., Lafargue, A., Antezana, E., Devare, M., King, B., Arnaud, E., Laporte, M.A., Kim, S., Aubert, C., Leonelli, S., Miro, B., Cooper, L., Jaiswal, P., Kruseman, G., Shrestha, R., Buttigieg, Pier Luigi, Mungall, Christopher J, Pietragalla, J., Agbona, A., Muliro, J., Detras, J., Hualla, V., Rathore, A., Das, R.R., Dieng, I., Bauchet, G.J., Menda, N., Pommier, C., Shaw, F., Lyon, D., Mwanzia, L., Juarez, H., Bonaiuti, E., Chiputwa, B., Obileye, O., Auzoux, S., Yeumo, E.D., Mueller, L., Silverstein, K., Lafargue, A., Antezana, E., Devare, M., and King, B.

Published
2020

192. 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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193. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Author

Cooper, Laurel, Walls, Ramona L., Elser, Justin, Gandolfo, Maria A., Stevenson, Dennis W., Smith, Barry, Preece, Justin, Athreya, Balaji, Mungall, Christopher J., Rensing, Stefan, Hiss, Manuel, Lang, Daniel, Reski, Ralf, Berardini, Tanya Z., Li, Donghui, Huala, Eva, Schaeffer, Mary, Menda, Naama, Arnaud, Elizabeth, Shrestha, Rosemary, Yamazaki, Yukiko, and Jaiswal, Pankaj

Published
2013
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196. KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

Author

Reese, Justin, primary, Unni, Deepak, additional, Callahan, Tiffany J., additional, Cappelletti, Luca, additional, Ravanmehr, Vida, additional, Carbon, Seth, additional, Fontana, Tommaso, additional, Blau, Hannah, additional, Matentzoglu, Nicolas, additional, Harris, Nomi L., additional, Munoz-Torres, Monica C., additional, Robinson, Peter N., additional, Joachimiak, Marcin P., additional, and Mungall, Christopher J., additional

Published
2020
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197. The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

Author

Touré, Vasundra, primary, Vercruysse, Steven, additional, Acencio, Marcio Luis, additional, Lovering, Ruth C, additional, Orchard, Sandra, additional, Bradley, Glyn, additional, Casals-Casas, Cristina, additional, Chaouiya, Claudine, additional, del-Toro, Noemi, additional, Flobak, Åsmund, additional, Gaudet, Pascale, additional, Hermjakob, Henning, additional, Hoyt, Charles Tapley, additional, Licata, Luana, additional, Lægreid, Astrid, additional, Mungall, Christopher J, additional, Niknejad, Anne, additional, Panni, Simona, additional, Perfetto, Livia, additional, Porras, Pablo, additional, Pratt, Dexter, additional, Saez-Rodriguez, Julio, additional, Thieffry, Denis, additional, Thomas, Paul D, additional, Türei, Dénes, additional, and Kuiper, Martin, additional

Published
2020
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198. Extension of Roles in the ChEBI Ontology

Author

Hoyt, Charles Tapley, primary, Mungall, Christopher, additional, Vasilevsky, Nicole, additional, Domingo-Fernández, Daniel, additional, Healy, Matthew, additional, and Colluru, Viswa, additional

Published
2020
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