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Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae).
Published in:
Biodiversity Data Journal, 2024, p. 1, doi. 10.3897/BDJ.12.e121562
By:
- Montanaro, Giulio;
- Balhoff, James P.;
- Girón, Jennifer C.;
- Söderholm, Max;
- Tarasov, Sergei
Publication type:
Article
Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.
Published in:
Biodiversity Data Journal, 2019, p. 1, doi. 10.3897/BDJ.7.e33303
By:
- Stucky, Brian J.;
- Balhoff, James P.;
- Barve, Narayani;
- Barve, Vijay;
- Brenskelle, Laura;
- Brush, Matthew H.;
- Dahlem, Gregory A.;
- Gilbert, James D. J.;
- Kawahara, Akito Y.;
- Keller, Oliver;
- Lucky, Andrea;
- Mayhew, Peter J.;
- Plotkin, David;
- Seltmann, Katja C.;
- Talamas, Elijah;
- Vaidya, Gaurav;
- Walls, Ramona;
- Yoder, Matt;
- Zhang, Guanyang;
- Guralnick, Rob
Publication type:
Article
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
Published in:
Nucleic Acids Research, 2019, v. 47, n. D1, p. D1018, doi. 10.1093/nar/gky1105
By:
- Köhler, Sebastian;
- Carmody, Leigh;
- Vasilevsky, Nicole;
- Jacobsen, Julius O B;
- 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
Publication type:
Article
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Published in:
Nucleic Acids Research, 2017, v. 45, n. D1, p. D712, doi. 10.1093/nar/gkw1128
By:
- Mungall, Christopher J.;
- McMurry, Julie A.;
- Köhler3, Sebastian;
- Balhoff, James P.;
- Borromeo, Charles;
- Brush, Matthew;
- Carbon, Seth;
- Conlin, Tom;
- Dunn, Nathan;
- Engelstad, Mark;
- Foster, Erin;
- Gourdine, J. P.;
- Jacobsen, Julius O. B.;
- Keith, Dan;
- Laraway, Bryan;
- Lewis, Suzanna E.;
- NguyenXuan, Jeremy;
- Shefchek, Kent;
- Vasilevsky, Nicole;
- Zhou Yuan
Publication type:
Article
Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.
Published in:
Genesis: The Journal of Genetics & Development, 2015, v. 53, n. 8, p. 561, doi. 10.1002/dvg.22878
By:
- Manda, Prashanti;
- Balhoff, James P.;
- Lapp, Hilmar;
- Mabee, Paula;
- Vision, Todd J.
Publication type:
Article
Reactome and the Gene Ontology: digital convergence of data resources.
Published in:
Bioinformatics, 2021, v. 37, n. 19, p. 3343, doi. 10.1093/bioinformatics/btab325
By:
- Good, Benjamin M;
- Auken, Kimberly Van;
- Hill, David P;
- Mi, Huaiyu;
- Carbon, Seth;
- Balhoff, James P;
- Albou, Laurent-Philippe;
- Thomas, Paul D;
- Mungall, Christopher J;
- Blake, Judith A;
- D'Eustachio, Peter
Publication type:
Article
Dead simple OWL design patterns.
Published in:
Journal of Biomedical Semantics, 2017, v. 8, p. 1, doi. 10.1186/s13326-017-0126-0
By:
- Osumi-Sutherland, David;
- Courtot, Melanie;
- Balhoff, James P.;
- Mungall, Christopher
Publication type:
Article
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
Published in:
Journal of Biomedical Semantics, 2014, v. 5, n. 1, p. 1, doi. 10.1186/2041-1480-5-21
By:
- Haendel, Melissa A.;
- Balhoff, James P.;
- Bastian, Frederic B.;
- Blackburn, David C.;
- Blake, Judith A.;
- Bradford, Yvonne;
- Comte, Aurelie;
- Dahdul, Wasila M.;
- Dececchi, Thomas A.;
- Druzinsky, Robert E.;
- Hayamizu, Terry F.;
- Ibrahim, Nizar;
- Lewis, Suzanna E.;
- Mabee, Paula M.;
- Niknejad, Anne;
- Robinson-Rechavi, Marc;
- Sereno, Paul C.;
- Mungall, Christopher J.
Publication type:
Article
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.
Published in:
Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 3, doi. 10.1186/2041-1480-4-34
By:
- Midford, Peter E.;
- Dececchi, Thomas Alex;
- Balhoff, James P.;
- Dahdul, Wasila M.;
- Ibrahim, Nizar;
- Lapp, Hilmar;
- Lundberg, John G.;
- Mabee, Paula M.;
- Sereno, Paul C.;
- Westerfield, Monte;
- Vision, Todd J.;
- Blackburn, David C.
Publication type:
Article
Folding Wings like a Cockroach: A Review of Transverse Wing Folding Ensign Wasps (Hymenoptera: Evaniidae: <i>Afrevania</i> and <i>Trissevania</i>).
Published in:
PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0094056
By:
- Mikó, István;
- Copeland, Robert S.;
- Balhoff, James P.;
- Yoder, Matthew J.;
- Deans, Andrew R.
Publication type:
Article
A Unified Anatomy Ontology of the Vertebrate Skeletal System.
Published in:
PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0051070
By:
- Dahdul, Wasila M.;
- Balhoff, James P.;
- Blackburn, David C.;
- Diehl, Alexander D.;
- Haendel, Melissa A.;
- Hall, Brian K.;
- Lapp, Hilmar;
- Lundberg, John G.;
- Mungall, Christopher J.;
- Ringwald, Martin;
- Segerdell, Erik;
- Van Slyke, Ceri E.;
- Vickaryous, Matthew K.;
- Westerfield, Monte;
- Mabee, Paula M.
Publication type:
Article
Evolutionary Characters, Phenotypes and Ontologies : Curating Data from the Systematic Biology Literature.
Published in:
PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010708
By:
- Dahdul, Wasila M.;
- Balhoff, James P.;
- Engeman, Jeffrey;
- Grande, Terry;
- Hilton, Eric J.;
- Kothari, Cartik;
- Lapp, Hilmar;
- Lundberg, John G.;
- Midford, Peter E.;
- Vision, Todd J.;
- Westerfield, Monte;
- Mabee, Paula M.
Publication type:
Article
Phenex: Ontological Annotation of Phenotypic Diversity.
Published in:
PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010500
By:
- Balhoff, James P.;
- Dahdul, Wasila M.;
- Kothari, Cartik R.;
- Lapp, Hilmar;
- Lundberg, John G.;
- Mabee, Paula;
- Midford, Peter E.;
- Westerfield, Monte;
- Vision, Todd J.
Publication type:
Article
A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions.
Published in:
Journal of Hymenoptera Research, 2012, n. 27, p. 67, doi. 10.3897/JHR.27.2961
By:
- Seltmann, Katja C.;
- Yoder, Matthew J.;
- Mikó, István;
- Forshage, Mattias;
- Bertone, Matthew A.;
- Agosti, Donat;
- Austin, Andrew D.;
- Balhoff, James P.;
- Borowiec, Marek L.;
- Brady, Seán G.;
- Broad, Gavin R.;
- Brothers, Denis J.;
- Burks, Roger A.;
- Buffington, Matthew L.;
- Campbell, Heather M.;
- Dew, Kelly J.;
- Ernst, Andrew F.;
- Fernández-Triana, José L.;
- Gates, Michael W.;
- Gibson, Gary A.P.
Publication type:
Article
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits.
Published in:
Methods in Ecology & Evolution, 2023, v. 14, n. 10, p. 2531, doi. 10.1111/2041-210X.14210
By:
- Porto, Diego S.;
- Tarasov, Sergei;
- Charpentier, Caleb;
- Lapp, Hilmar;
- Balhoff, James P.;
- Vision, Todd J.;
- Dahdul, Wasila M.;
- Mabee, Paula M.;
- Uyeda, Josef
Publication type:
Article
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.
Published in:
Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac087
By:
- Matentzoglu, Nicolas;
- Goutte-Gattat, Damien;
- Tan, Shawn Zheng Kai;
- Balhoff, James P;
- Carbon, Seth;
- Caron, Anita R;
- Duncan, William D;
- Flack, Joe E;
- Haendel, Melissa;
- Harris, Nomi L;
- Hogan, William R;
- Hoyt, Charles Tapley;
- Jackson, Rebecca C;
- Kim, HyeongSik;
- Kir, Huseyin;
- Larralde, Martin;
- McMurry, Julie A;
- Overton, James A;
- Peters, Bjoern;
- Pilgrim, Clare
Publication type:
Article
Simple Standard for Sharing Ontological Mappings (SSSOM).
Published in:
Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac035
By:
- Matentzoglu, Nicolas;
- Balhoff, James P;
- Bello, Susan M;
- Bizon, Chris;
- Brush, Matthew;
- Callahan, Tiffany J;
- Chute, Christopher G;
- Duncan, William D;
- Evelo, Chris T;
- Gabriel, Davera;
- Graybeal, John;
- Gray, Alasdair;
- Gyori, Benjamin M;
- Haendel, Melissa;
- Harmse, Henriette;
- Harris, Nomi L;
- Harrow, Ian;
- Hegde, Harshad B;
- Hoyt, Amelia L;
- Hoyt, Charles T
Publication type:
Article
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
Published in:
Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab069
By:
- Jackson, Rebecca;
- Matentzoglu, Nicolas;
- Overton, James A;
- Vita, Randi;
- Balhoff, James P;
- Buttigieg, Pier Luigi;
- Carbon, Seth;
- Courtot, Melanie;
- Diehl, Alexander D;
- Dooley, Damion M;
- Duncan, William D;
- Harris, Nomi L;
- Haendel, Melissa A;
- Lewis, Suzanna E;
- Natale, Darren A;
- Osumi-Sutherland, David;
- Ruttenberg, Alan;
- Schriml, Lynn M;
- Smith, Barry;
- Stoeckert Jr., Christian J
Publication type:
Article
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.
Published in:
Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay110
By:
- Dahdul, Wasila;
- Manda, Prashanti;
- Cui, Hong;
- Balhoff, James P;
- Dececchi, T Alexander;
- Ibrahim, Nizar;
- Lapp, Hilmar;
- Vision, Todd;
- Mabee, Paula M
Publication type:
Article
Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.
Published in:
Database: The Journal of Biological Databases & Curation, 2013, v. 2013, p. 1, doi. 10.1093/database/bas057
By:
- Bertone, Matthew A.;
- Mikó, István;
- Yoder, Matthew J.;
- Seltmann, Katja C.;
- Balhoff, James P.;
- Deans, Andrew R.
Publication type:
Article
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.
Published in:
BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-158
By:
- Stoltzfus, Arlin;
- Lapp, Hilmar;
- Matasci, Naim;
- Deus, Helena;
- Sidlauskas, Brian;
- Zmasek, Christian M.;
- Vaidya, Gaurav;
- Pontelli, Enrico;
- Cranston, Karen;
- Vos, Rutger;
- Webb, Campbell O.;
- Harmon, Luke J.;
- Pirrung, Megan;
- O'Meara, Brian;
- Pennell, Matthew W.;
- Mirarab, Siavash;
- Rosenberg, Michael S;
- Balhoff, James P.;
- Bik, Holly M.;
- Heath, Tracy A.
Publication type:
Article
Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.
Published in:
Molecular Biology & Evolution, 2016, v. 33, n. 1, p. 13, doi. 10.1093/molbev/msv223
By:
- Edmunds, Richard C.;
- Baofeng Su;
- Balhoff, James P.;
- Eames, B. Frank;
- Dahdul, Wasila M.;
- Lapp, Hilmar;
- Lundberg, John G.;
- Vision, Todd J.;
- Dunham, Rex A.;
- Mabee, Paula M.;
- Westerfield, Monte
Publication type:
Article
ROBOT: A Tool for Automating Ontology Workflows.
Published in:
BMC Bioinformatics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12859-019-3002-3
By:
- Jackson, Rebecca C.;
- Balhoff, James P.;
- Douglass, Eric;
- Harris, Nomi L.;
- Mungall, Christopher J.;
- Overton, James A.
Publication type:
Article
Transforming the study of organisms: Phenomic data models and knowledge bases.
Published in:
PLoS Computational Biology, 2020, v. 16, n. 11, p. 1, doi. 10.1371/journal.pcbi.1008376
By:
- Thessen, Anne E.;
- Walls, Ramona L.;
- Vogt, Lars;
- Singer, Jessica;
- Warren, Robert;
- Buttigieg, Pier Luigi;
- Balhoff, James P.;
- Mungall, Christopher J.;
- McGuinness, Deborah L.;
- Stucky, Brian J.;
- Yoder, Matthew J.;
- Haendel, Melissa A.
Publication type:
Article
The Evolution of Transcriptional Regulation in Eukaryotes.
Published in:
Molecular Biology & Evolution, 2003, v. 20, n. 9, p. 1377, doi. 10.1093/molbev/msg140
By:
- Wray, Gregory A.;
- Hahn, Matthew W.;
- Abouheif, Ehab;
- Balhoff, James P.;
- Pizer, Margaret;
- Rockman, Matthew V.;
- Romano, Laura A.
Publication type:
Article
Corrigenda: Mullins PL, Kawada R, Balhoff JP, Deans AR (2012) A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223: 1-38, doi: 10.3897/zookeys.223.3572.
Published in:
2013
By:
- Mullins, Patricia L.;
- Kawada, Rico;
- Balhoff, James P.;
- Deans, Andrew R.
Publication type:
Correction Notice
Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.
Published in:
PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0149102
By:
- Druzinsky, Robert E.;
- Balhoff, James P.;
- Crompton, Alfred W.;
- Done, James;
- German, Rebecca Z.;
- Haendel, Melissa A.;
- Herrel, Anthony;
- Herring, Susan W.;
- Lapp, Hilmar;
- Mabee, Paula M.;
- Muller, Hans-Michael;
- Mungall, Christopher J.;
- Sternberg, Paul W.;
- Van Auken, Kimberly;
- Vinyard, Christopher J.;
- Williams, Susan H.;
- Wall, Christine E.
Publication type:
Article
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.
Published in:
Systematic Biology, 2022, v. 71, n. 6, p. 1290, doi. 10.1093/sysbio/syac022
By:
- Porto, Diego S;
- Dahdul, Wasila M;
- Lapp, Hilmar;
- Balhoff, James P;
- Vision, Todd J;
- Mabee, Paula M;
- Uyeda, Josef
Publication type:
Article
A Logical Model of Homology for Comparative Biology.
Published in:
Systematic Biology, 2020, v. 69, n. 2, p. 345, doi. 10.1093/sysbio/syz067
By:
- Mabee, Paula M;
- Balhoff, James P;
- Dahdul, Wasila M;
- Lapp, Hilmar;
- Mungall, Christopher J;
- Vision, Todd J
Publication type:
Article
Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes.
Published in:
Systematic Biology, 2018, v. 67, n. 4, p. 559, doi. 10.1093/sysbio/syx098
By:
- JACKSON, LAURA M.;
- FERNANDO, PASAN C.;
- HANSCOM, JOSH S.;
- BALHOFF, JAMES P.;
- MABEE, PAULA M.
Publication type:
Article
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.
Published in:
Systematic Biology, 2015, v. 64, n. 6, p. 936, doi. 10.1093/sysbio/syv031
By:
- DECECCHI, T. ALEXANDER;
- MABEE, PAULA M.;
- BALHOFF, JAMES P.;
- LAPP, HILMAR
Publication type:
Article
A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia.
Published in:
Systematic Biology, 2013, v. 62, n. 5, p. 639, doi. 10.1093/sysbio/syt028
By:
- Balhoff, James P.;
- Mikó, István;
- Yoder, Matthew J.;
- Mullins, Patricia L.;
- Deans, Andrew R.
Publication type:
Article
NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata.
Published in:
Systematic Biology, 2012, v. 61, n. 4, p. 675, doi. 10.1093/sysbio/sys025
By:
- Vos, Rutger A.;
- Balhoff, James P.;
- Caravas, Jason A.;
- Holder, Mark T.;
- Lapp, Hilmar;
- Maddison, Wayne P.;
- Midford, Peter E.;
- Priyam, Anurag;
- Sukumaran, Jeet;
- Xia, Xuhua;
- Stoltzfus, Arlin
Publication type:
Article
The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age.
Published in:
Systematic Biology, 2010, v. 59, n. 4, p. 369, doi. 10.1093/sysbio/syq013
By:
- DAHDUL, WASILA M.;
- LUNDBERG, JOHN G.;
- MIDFORD, PETER E.;
- BALHOFF, JAMES P.;
- LAPP, HILMAR;
- VISION, TODD J.;
- HAENDEL, MELISSA A.;
- WESTERFIELD, MONTE;
- MABEE, PAULA M.
Publication type:
Article
Finding Our Way through Phenotypes.
Published in:
2015
By:
- Deans, Andrew R.;
- Lewis, Suzanna E.;
- Huala, Eva;
- Anzaldo, Salvatore S.;
- Ashburner, Michael;
- Balhoff, James P.;
- Blackburn, David C.;
- Blake, Judith A.;
- Burleigh, J. Gordon;
- Chanet, Bruno;
- Cooper, Laurel D.;
- Courtot, Mélanie;
- Csösz, Sándor;
- Cui, Hong;
- Dahdul, Wasila;
- Das, Sandip;
- Dececchi, T. Alexander;
- Dettai, Agnes;
- Diogo, Rui;
- Druzinsky, Robert E.
Publication type:
Opinion
The Ontology of Biological Attributes (OBA)—computational traits for the life sciences.
Published in:
Mammalian Genome, 2023, v. 34, n. 3, p. 364, doi. 10.1007/s00335-023-09992-1
By:
- Stefancsik, Ray;
- Balhoff, James P.;
- Balk, Meghan A.;
- Ball, Robyn L.;
- Bello, Susan M.;
- Caron, Anita R.;
- Chesler, Elissa J.;
- de Souza, Vinicius;
- Gehrke, Sarah;
- Haendel, Melissa;
- Harris, Laura W.;
- Harris, Nomi L.;
- Ibrahim, Arwa;
- Koehler, Sebastian;
- Matentzoglu, Nicolas;
- McMurry, Julie A.;
- Mungall, Christopher J.;
- Munoz-Torres, Monica C.;
- Putman, Tim;
- Robinson, Peter
Publication type:
Article
Navigating the Phenotype Frontier: The Monarch Initiative.
Published in:
Genetics, 2016, v. 203, n. 4, p. 1491, doi. 10.1534/genetics.116.188870
By:
- McMurry, Julie A.;
- Köhler, Sebastian;
- Washington, Nicole L.;
- Balhoff, James P.;
- Borromeo, Charles;
- Brush, Matthew;
- Carbon, Seth;
- Conlin, Tom;
- Dunn, Nathan;
- Engelstad, Mark;
- Foster, Erin;
- Gourdine, Jean-Philippe;
- Jacobsen, Julius O. B.;
- Keith, Daniel;
- Laraway, Bryan;
- Nguyen Xuan, Jeremy;
- Shefchek, Kent;
- Vasilevsky, Nicole A.;
- Zhou Yuan;
- Lewis, Suzanna E.
Publication type:
Article
The Human Phenotype Ontology in 2024: phenotypes around the world.
Published in:
Nucleic Acids Research, 2024, v. 52, n. D1, p. D1333, doi. 10.1093/nar/gkad1005
By:
- Gargano, Michael A;
- Matentzoglu, Nicolas;
- Coleman, Ben;
- Addo-Lartey, Eunice B;
- Anagnostopoulos, Anna V;
- Anderton, Joel;
- Avillach, Paul;
- Bagley, Anita M;
- Bakštein, Eduard;
- Balhoff, James P;
- Baynam, Gareth;
- Bello, Susan M;
- Berk, Michael;
- Bertram, Holli;
- Bishop, Somer;
- Blau, Hannah;
- Bodenstein, David F;
- Botas, Pablo;
- Boztug, Kaan;
- Čady, Jolana
Publication type:
Article
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Published in:
Nucleic Acids Research, 2020, v. 48, n. D1, p. D704, doi. 10.1093/nar/gkz997
By:
- 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
Publication type:
Article
A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation.
Published in:
ZooKeys, 2012, v. 223, p. 1, doi. 10.3897/zookeys.223.3572
By:
- Mullins, Patricia L.;
- Kawada, Ricardo;
- Balhoff, James P.;
- Deans, Andrew R.
Publication type:
Article

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