Found: 22

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  • Unifying the identification of biomedical entities with the Bioregistry.

    Published in:
    Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01807-3
    By:
    • 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;
    • Gyori, Benjamin M.
    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

  • Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

    Published in:
    Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae104
    By:
    • Caufield, J Harry;
    • Hegde, Harshad;
    • Emonet, Vincent;
    • Harris, Nomi L;
    • Joachimiak, Marcin P;
    • Matentzoglu, Nicolas;
    • Kim, HyeongSik;
    • Moxon, Sierra;
    • Reese, Justin T;
    • Haendel, Melissa A;
    • Robinson, Peter N;
    • Mungall, Christopher J
    Publication type:
    Article

  • KG-Hub—building and exchanging biological knowledge graphs.

    Published in:
    Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad418
    By:
    • Caufield, J Harry;
    • Putman, Tim;
    • Schaper, Kevin;
    • Unni, Deepak R;
    • Hegde, Harshad;
    • Callahan, Tiffany J;
    • Cappelletti, Luca;
    • Moxon, Sierra A T;
    • Ravanmehr, Vida;
    • Carbon, Seth;
    • Chan, Lauren E;
    • Cortes, Katherina;
    • Shefchek, Kent A;
    • Elsarboukh, Glass;
    • Balhoff, Jim;
    • Fontana, Tommaso;
    • Matentzoglu, Nicolas;
    • Bruskiewich, Richard M;
    • Thessen, Anne E;
    • Harris, Nomi L
    Publication type:
    Article

  • The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond.

    Published in:
    Journal of Biomedical Semantics, 2023, v. 14, n. 1, p. 1, doi. 10.1186/s13326-023-00283-x
    By:
    • Chan, Lauren E.;
    • Thessen, Anne E.;
    • Duncan, William D.;
    • Matentzoglu, Nicolas;
    • Schmitt, Charles;
    • Grondin, Cynthia J.;
    • Vasilevsky, Nicole;
    • McMurry, Julie A.;
    • Robinson, Peter N.;
    • Mungall, Christopher J.;
    • Haendel, Melissa A.
    Publication type:
    Article

  • MIRO: guidelines for minimum information for the reporting of an ontology.

    Published in:
    Journal of Biomedical Semantics, 2018, v. 9, p. 1, doi. 10.1186/s13326-017-0172-7
    By:
    • Matentzoglu, Nicolas;
    • Malone, James;
    • Mungall, Chris;
    • Stevens, Robert
    Publication type:
    Article

  • An open source knowledge graph ecosystem for the life sciences.

    Published in:
    Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03171-w
    By:
    • Callahan, Tiffany J.;
    • Tripodi, Ignacio J.;
    • Stefanski, Adrianne L.;
    • Cappelletti, Luca;
    • Taneja, Sanya B.;
    • Wyrwa, Jordan M.;
    • Casiraghi, Elena;
    • Matentzoglu, Nicolas A.;
    • Reese, Justin;
    • Silverstein, Jonathan C.;
    • Hoyt, Charles Tapley;
    • Boyce, Richard D.;
    • Malec, Scott A.;
    • Unni, Deepak R.;
    • Joachimiak, Marcin P.;
    • Robinson, Peter N.;
    • Mungall, Christopher J.;
    • Cavalleri, Emanuele;
    • Fontana, Tommaso;
    • Valentini, Giorgio
    Publication type:
    Article

  • Virtual Fly Brain--An interactive atlas of the Drosophila nervous system.

    Published in:
    Frontiers in Physiology, 2023, v. 14, p. 1, doi. 10.3389/fphys.2023.1076533
    By:
    • Court, Robert;
    • Costa, Marta;
    • Pilgrim, Clare;
    • Millburn, Gillian;
    • Holmes, Alex;
    • McLachlan, Alex;
    • Larkin, Aoife;
    • Matentzoglu, Nicolas;
    • Kir, Huseyin;
    • Parkinson, Helen;
    • Brown, Nicolas H.;
    • O'Kane, Cahir J.;
    • Armstrong, J. Douglas;
    • Jefferis, Gregory S. X. E.;
    • Osumi-Sutherland, David
    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

  • Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/baz114
    By:
    • Gourdine, Jean-Philippe F;
    • Brush, Matthew H;
    • Vasilevsky, Nicole A;
    • Shefchek, Kent;
    • Köhler, Sebastian;
    • Matentzoglu, Nicolas;
    • Munoz-Torres, Monica C;
    • McMurry, Julie A;
    • Zhang, Xingmin Aaron;
    • Robinson, Peter N;
    • Haendel, Melissa A
    Publication type:
    Article

  • Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop.

    Published in:
    Research Ideas & Outcome Journal, 2017, v. 3, p. 1, doi. 10.3897/rio.3.e13236
    By:
    • Jay, Caroline;
    • Haines, Robert;
    • Vigo, Markel;
    • Matentzoglu, Nicolas;
    • Stevens, Robert;
    • Boyle, Jonathan;
    • Davies, Alan;
    • Del Vescovo, Chiara;
    • Gruel, Nicolas;
    • Le Blanc, Anja;
    • Mawdsley, David;
    • Mellor, Dale;
    • Mikroyannidi, Eleni;
    • Rollins, Richard Peter;
    • Rowley, Andrew;
    • Vega, Julio
    Publication type:
    Article

  • Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies.

    Published in:
    2023
    By:
    • 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.;
    • Osumi-Sutherland, David
    Publication type:
    Correction Notice

  • Brain Data Standards - A method for building data-driven cell-type ontologies.

    Published in:
    Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-022-01886-2
    By:
    • 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.;
    • Osumi-Sutherland, David
    Publication type:
    Article

  • Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.

    Published in:
    Systematic Biology, 2023, v. 72, n. 5, p. 1084, doi. 10.1093/sysbio/syad025
    By:
    • Girón, Jennifer C;
    • Tarasov, Sergei;
    • Montaña, Luis Antonio González;
    • Matentzoglu, Nicolas;
    • Smith, Aaron D;
    • Koch, Markus;
    • Boudinot, Brendon E;
    • Bouchard, Patrice;
    • Burks, Roger;
    • Vogt, Lars;
    • Yoder, Matthew;
    • Osumi-Sutherland, David;
    • Friedrich, Frank;
    • Beutel, Rolf G;
    • Mikó, István
    Publication type:
    Article

  • 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

  • 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 2024: an analytic platform integrating phenotypes, genes and diseases across species.

    Published in:
    Nucleic Acids Research, 2024, v. 52, n. D1, p. D938, doi. 10.1093/nar/gkad1082
    By:
    • Putman, Tim E;
    • Schaper, Kevin;
    • Matentzoglu, Nicolas;
    • Rubinetti, Vincent P;
    • Alquaddoomi, Faisal S;
    • Cox, Corey;
    • Caufield, J Harry;
    • Elsarboukh, Glass;
    • Gehrke, Sarah;
    • Hegde, Harshad;
    • Reese, Justin T;
    • Braun, Ian;
    • Bruskiewich, Richard M;
    • Cappelletti, Luca;
    • Carbon, Seth;
    • Caron, Anita R;
    • Chan, Lauren E;
    • Chute, Christopher G;
    • Cortes, Katherina G;
    • De Souza, Vinícius
    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

  • Ontologizing health systems data at scale: making translational discovery a reality.

    Published in:
    NPJ Digital Medicine, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s41746-023-00830-x
    By:
    • Callahan, Tiffany J.;
    • Stefanski, Adrianne L.;
    • Wyrwa, Jordan M.;
    • Zeng, Chenjie;
    • Ostropolets, Anna;
    • Banda, Juan M.;
    • Baumgartner Jr., William A.;
    • Boyce, Richard D.;
    • Casiraghi, Elena;
    • Coleman, Ben D.;
    • Collins, Janine H.;
    • Deakyne Davies, Sara J.;
    • Feinstein, James A.;
    • Lin, Asiyah Y.;
    • Martin, Blake;
    • Matentzoglu, Nicolas A.;
    • Meeker, Daniella;
    • Reese, Justin;
    • Sinclair, Jessica;
    • Taneja, Sanya B.
    Publication type:
    Article

  • The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.

    Published in:
    BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04636-8
    By:
    • Fisher, Malcolm E.;
    • Segerdell, Erik;
    • Matentzoglu, Nicolas;
    • Nenni, Mardi J.;
    • Fortriede, Joshua D.;
    • Chu, Stanley;
    • Pells, Troy J.;
    • Osumi-Sutherland, David;
    • Chaturvedi, Praneet;
    • James-Zorn, Christina;
    • Sundararaj, Nivitha;
    • Lotay, Vaneet S.;
    • Ponferrada, Virgilio;
    • Wang, Dong Zhuo;
    • Kim, Eugene;
    • Agalakov, Sergei;
    • Arshinoff, Bradley I.;
    • Karimi, Kamran;
    • Vize, Peter D.;
    • Zorn, Aaron M.
    Publication type:
    Article