Found: 59

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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

  • The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.

    Published in:
    Frontiers in Plant Science, 2019, p. N.PAG, doi. 10.3389/fpls.2019.00631
    By:
    • Walls, Ramona L.;
    • Cooper, Laurel;
    • Elser, Justin;
    • Gandolfo, Maria Alejandra;
    • Mungall, Christopher J.;
    • Smith, Barry;
    • Stevenson, Dennis W.;
    • Jaiswal, Pankaj
    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

  • Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

    Published in:
    Nucleic Acids Research, 2015, v. 43, n. D1, p. D1071, doi. 10.1093/nar/gku1011
    By:
    • Kibbe, Warren A.;
    • Arze, Cesar;
    • Felix, Victor;
    • Mitraka, Elvira;
    • Bolton, Evan;
    • Fu, Gang;
    • Mungall, Christopher J.;
    • Binder, Janos X.;
    • Malone, James;
    • Vasant, Drashtti;
    • Parkinson, Helen;
    • Schriml, Lynn M.
    Publication type:
    Article

  • The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

    Published in:
    Nucleic Acids Research, 2014, v. 42, n. D1, p. D966
    By:
    • 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.
    Publication type:
    Article

  • SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing.

    Published in:
    Genome Medicine, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13073-022-01046-6
    By:
    • 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;
    • Robinson, Peter N.
    Publication type:
    Article

  • Phenopacket-tools: Building and validating GA4GH Phenopackets.

    Published in:
    PLoS ONE, 2023, v. 17, n. 5, p. 1, doi. 10.1371/journal.pone.0285433
    By:
    • Danis, Daniel;
    • Jacobsen, Julius O. B.;
    • Wagner, Alex H.;
    • Groza, Tudor;
    • Beckwith, Martha A.;
    • Rekerle, Lauren;
    • Carmody, Leigh C.;
    • Reese, Justin;
    • Hegde, Harshad;
    • Ladewig, Markus S.;
    • Seitz, Berthold;
    • Munoz-Torres, Monica;
    • Harris, Nomi L.;
    • Rambla, Jordi;
    • Baudis, Michael;
    • Mungall, Christopher J.;
    • Haendel, Melissa A.;
    • Robinson, Peter N.
    Publication type:
    Article

  • The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

    Published in:
    Nature Biotechnology, 2007, v. 25, n. 11, p. 1251, doi. 10.1038/nbt1346
    By:
    • Smith, Barry;
    • Ashburner, Michael;
    • Rosse, Cornelius;
    • Bard, Jonathan;
    • Bug, William;
    • Ceusters, Werner;
    • Goldberg, Louis J.;
    • Eilbeck, Karen;
    • Ireland, Amelia;
    • Mungall, Christopher J.;
    • Leontis, Neocles;
    • Rocca-Serra, Philippe;
    • Ruttenberg, Alan;
    • Sansone, Susanna-Assunta;
    • Scheuermann, Richard H.;
    • Nigam Shah;
    • Whetzel, Patricia L.;
    • Lewis, Suzanna
    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

  • An expectation–maximization framework for comprehensive prediction of isoform-specific functions.

    Published in:
    Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad132
    By:
    • Karlebach, Guy;
    • Carmody, Leigh;
    • Sundaramurthi, Jagadish Chandrabose;
    • Casiraghi, Elena;
    • Hansen, Peter;
    • Reese, Justin;
    • Mungall, Christopher J;
    • Valentini, Giorgio;
    • Robinson, Peter N
    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

  • The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).

    Published in:
    Bioinformatics, 2020, v. 36, n. 24, p. 5712, doi. 10.1093/bioinformatics/btaa622
    By:
    • Touré, Vasundra;
    • Vercruysse, Steven;
    • Acencio, Marcio Luis;
    • Lovering, Ruth C;
    • Orchard, Sandra;
    • Bradley, Glyn;
    • Casals-Casas, Cristina;
    • Chaouiya, Claudine;
    • del-Toro, Noemi;
    • Flobak, Åsmund;
    • Gaudet, Pascale;
    • Hermjakob, Henning;
    • Hoyt, Charles Tapley;
    • Licata, Luana;
    • Lægreid, Astrid;
    • Mungall, Christopher J;
    • Niknejad, Anne;
    • Panni, Simona;
    • Perfetto, Livia;
    • Porras, Pablo
    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

  • The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

    Published in:
    Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0097-6
    By:
    • Buttigieg, Pier Luigi;
    • Pafilis, Evangelos;
    • Lewis, Suzanna E.;
    • Schildhauer, Mark P.;
    • Walls, Ramona L.;
    • Mungall, Christopher J.
    Publication type:
    Article

  • The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

    Published in:
    Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0088-7
    By:
    • Diehl, Alexander D.;
    • Meehan, Terrence F.;
    • Bradford, Yvonne M.;
    • Brush, Matthew H.;
    • Dahdul, Wasila M.;
    • Dougall, David S.;
    • Yongqun He;
    • Osumi-Sutherland, David;
    • Ruttenberg, Alan;
    • Sarntivijai, Sirarat;
    • Van Slyke, Ceri E.;
    • Vasilevsky, Nicole A.;
    • Haendel, Melissa A.;
    • Blake, Judith A.;
    • Mungall, Christopher J.
    Publication type:
    Article

  • FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

    Published in:
    Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0067-z
    By:
    • Bolleman, Jerven T.;
    • Mungall, Christopher J.;
    • Strozzi, Francesco;
    • Baran, Joachim;
    • Dumontier, Michel;
    • Bonnal, Raoul J. P.;
    • Buels, Robert;
    • Hoehndorf, Robert;
    • Fujisawa, Takatomo;
    • Katayama, Toshiaki;
    • Cock, Peter J. A.
    Publication type:
    Article

  • TermGenie - a web-application for pattern-based ontology class generation.

    Published in:
    Journal of Biomedical Semantics, 2014, v. 5, n. 1, p. 1, doi. 10.1186/2041-1480-5-48
    By:
    • Dietze, Heiko;
    • Berardini, Tanya Z.;
    • Foulger, Rebecca E.;
    • Hill, David P.;
    • Lomax, Jane;
    • Osumi-Sutherland, David;
    • Roncaglia, Paola;
    • Mungall, Christopher J.
    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 environment ontology: contextualising biological and biomedical entities.

    Published in:
    Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 2, doi. 10.1186/2041-1480-4-43
    By:
    • Buttigieg, Pier Luigi;
    • Morrison, Norman;
    • Smith, Barry;
    • Mungall, Christopher J.;
    • Lewis, Suzanna E.
    Publication type:
    Article

  • Representing Kidney Development Using the Gene Ontology.

    Published in:
    PLoS ONE, 2014, v. 9, n. 6, p. 1, doi. 10.1371/journal.pone.0099864
    By:
    • Alam-Faruque, Yasmin;
    • Hill, David P.;
    • Dimmer, Emily C.;
    • Harris, Midori A.;
    • Foulger, Rebecca E.;
    • Tweedie, Susan;
    • Attrill, Helen;
    • Howe, Douglas G.;
    • Thomas, Stephen Randall;
    • Davidson, Duncan;
    • Woolf, Adrian S.;
    • Blake, Judith A.;
    • Mungall, Christopher J.;
    • O’Donovan, Claire;
    • Apweiler, Rolf;
    • Huntley, Rachael P.
    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

  • 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

  • An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.

    Published in:
    Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03069-7
    By:
    • Schadt, Christopher;
    • Martin, Stanton;
    • Carrell, Alyssa;
    • Fortner, Allison;
    • Hopp, Dan;
    • Jacobson, Dan;
    • Klingeman, Dawn;
    • Kristy, Brandon;
    • Phillips, Jana;
    • Piatkowski, Bryan;
    • Miller, Mark A.;
    • Smith, Montana;
    • Patil, Sujay;
    • Flynn, Mark;
    • Canon, Shane;
    • Clum, Alicia;
    • Mungall, Christopher J.;
    • Pennacchio, Christa;
    • Bowen, Benjamin;
    • Louie, Katherine
    Publication type:
    Article

  • FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bax105
    By:
    • Vita, Randi;
    • Overton, James A;
    • Mungall, Christopher J;
    • Sette, Alessandro;
    • Peters, Bjoern
    Publication type:
    Article

  • Modeling biochemical pathways in the gene ontology.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw126
    By:
    • Hill, David P.;
    • D'Eustachio, Peter;
    • Berardini, Tanya Z.;
    • Mungall, Christopher J.;
    • Renedo, Nikolai;
    • Blake, Judith A.
    Publication type:
    Article

  • Standardized description of scientific evidence using the Evidence Ontology (ECO).

    Published in:
    Database: The Journal of Biological Databases & Curation, 2014, v. 2014, p. 1, doi. 10.1093/database/bau075
    By:
    • Chibucos, Marcus C.;
    • Mungall, Christopher J.;
    • Balakrishnan, Rama;
    • Christie, Karen R.;
    • Huntley, Rachael P.;
    • White, Owen;
    • Blake, Judith A.;
    • Lewis, Suzanna E.;
    • Giglio, Michelle
    Publication type:
    Article

  • Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge.

    Published in:
    PLoS ONE, 2021, v. 16, n. 3, p. 1, doi. 10.1371/journal.pone.0231916
    By:
    • Hannestad, Lance M.;
    • Dančík, Vlado;
    • Godden, Meera;
    • Suen, Imelda W.;
    • Huellas-Bruskiewicz, Kenneth C.;
    • Good, Benjamin M.;
    • Mungall, Christopher J.;
    • Bruskiewich, Richard M.
    Publication type:
    Article

  • A method for increasing expressivity of Gene Ontology annotations using a compositional approach.

    Published in:
    BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-155
    By:
    • Huntley, Rachael P.;
    • Harris, Midori A.;
    • Alam-Faruque, Yasmin;
    • Blake, Judith A.;
    • Carbon, Seth;
    • Dietze, Heiko;
    • Dimmer, Emily C.;
    • Foulger, Rebecca E.;
    • Hil, David P.;
    • Khodiyar, Varsha K.;
    • Lock, Antonia;
    • Lomax, Jane;
    • Lovering, Ruth C.;
    • Mutowo-Meullenet, Prudence;
    • Sawford, Tony;
    • Auken, Kimberly Van;
    • Wood, Valerie;
    • Mungall, Christopher J.
    Publication type:
    Article

  • Ontology based molecular signatures for immune cell types via gene expression analysis.

    Published in:
    BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-263
    By:
    • Meehan, Terrence F.;
    • Vasilevsky, Nicole A.;
    • Mungall, Christopher J.;
    • Dougall, David S.;
    • Haendel, Melissa A.;
    • Blake, Judith A.;
    • Diehl, Alexander D.
    Publication type:
    Article

  • Logical Development of the Cell Ontology.

    Published in:
    BMC Bioinformatics, 2011, v. 12, n. 1, p. 1, doi. 10.1186/1471-2105-12-6
    By:
    • Meehan, Terrence F.;
    • Masci, Anna Maria;
    • Abdulla, Amina;
    • Cowell, Lindsay G.;
    • Blake, Judith A.;
    • Mungall, Christopher J.;
    • Diehl, Alexander D.
    Publication type:
    Article

  • Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development.

    Published in:
    BMC Bioinformatics, 2010, v. 11, p. 530, doi. 10.1186/1471-2105-11-530
    By:
    • Deegan (née Clark), Jennifer I.;
    • Dimmer, Emily C.;
    • Mungall, Christopher J.
    Publication type:
    Article

  • GA4GH Phenopackets: A Practical Introduction.

    Published in:
    Advanced Genetics, 2023, v. 4, n. 1, p. 1, doi. 10.1002/ggn2.202200016
    By:
    • Ladewig, Markus S.;
    • Jacobsen, Julius O. B.;
    • Wagner, Alex H.;
    • Danis, Daniel;
    • El Kassaby, Baha;
    • Gargano, Michael;
    • Groza, Tudor;
    • Baudis, Michael;
    • Steinhaus, Robin;
    • Seelow, Dominik;
    • Bechrakis, Nikolaos E.;
    • Mungall, Christopher J.;
    • Schofield, Paul N.;
    • Elemento, Olivier;
    • Smith, Lindsay;
    • McMurry, Julie A.;
    • Munoz‐Torres, Monica;
    • Haendel, Melissa A.;
    • Robinson, Peter N.
    Publication type:
    Article

  • ONTOLOGIES AS INTEGRATIVE TOOLS FOR PLANT SCIENCE.

    Published in:
    American Journal of Botany, 2012, v. 99, n. 8, p. 1263, doi. 10.3732/ajb.1200222
    By:
    • Walls, Ramona L.;
    • Athreya, Balaji;
    • Cooper, Laurel;
    • Elser, Justin;
    • Gandolfo, Maria A.;
    • Jaiswal, Pankaj;
    • Mungall, Christopher J.;
    • Preece, Justin;
    • Rensing, Stefan;
    • Smith, Barry;
    • Stevenson, Dennis W.
    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

  • On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

    Published in:
    PLoS Computational Biology, 2012, v. 8, n. 2, p. 1, doi. 10.1371/journal.pcbi.1002386
    By:
    • Thomas, Paul D.;
    • Wood, Valerie;
    • Mungall, Christopher J.;
    • Lewis, Suzanna E.;
    • Blake, Judith A.
    Publication type:
    Article

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

    Published in:
    Plant & Cell Physiology, 2013, v. 54, n. 2, p. e1, doi. 10.1093/pcp/pcs163
    By:
    • 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
    Publication type:
    Article

  • Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery.

    Published in:
    NPJ Digital Medicine, 2019, v. 2, p. N.PAG, doi. 10.1038/s41746-019-0110-4
    By:
    • Zhang, Xingmin Aaron;
    • Yates, Amy;
    • Vasilevsky, Nicole;
    • Gourdine, J. P.;
    • Callahan, Tiffany J.;
    • Carmody, Leigh C.;
    • Danis, Daniel;
    • Joachimiak, Marcin P.;
    • Ravanmehr, Vida;
    • Pfaff, Emily R.;
    • Champion, James;
    • Robasky, Kimberly;
    • Xu, Hao;
    • Fecho, Karamarie;
    • Walton, Nephi A.;
    • Zhu, Richard L.;
    • Ramsdill, Justin;
    • Mungall, Christopher J.;
    • Köhler, Sebastian;
    • Haendel, Melissa A.
    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
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    Published in:
    Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0953-9
    By:
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    • Afrasiabi, Cyrus;
    • Tsueng, Ginger;
    • Juchler, Moritz;
    • Gopal, Nikhil;
    • Stupp, Gregory S.;
    • Putman, Timothy E.;
    • Ainscough, Benjamin J.;
    • Griffith, Obi L.;
    • Torkamani, Ali;
    • Whetzel, Patricia L.;
    • Mungall, Christopher J.;
    • Mooney, Sean D.;
    • Su, Andrew I.;
    • Chunlei Wu
    Publication type:
    Article

  • Gateways to the FANTOM5 promoter level mammalian expression atlas.

    Published in:
    Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-014-0560-6
    By:
    • Lizio, Marina;
    • Harshbarger, Jayson;
    • Hisashi Shimoji;
    • Severin, Jessica;
    • Takeya Kasukawa;
    • Sahin, Serkan;
    • Abugessaisa, Imad;
    • Shiro Fukuda;
    • Fumi Hori;
    • Sachi Ishikawa-Kato;
    • Mungall, Christopher J.;
    • Arner, Erik;
    • Baillie, J. Kenneth;
    • Bertin, Nicolas;
    • Hidemasa Bono;
    • de Hoon, Michiel;
    • Diehl, Alexander D.;
    • Dimont, Emmanuel;
    • Freeman, Tom C.;
    • Kaori Fujieda
    Publication type:
    Article

  • Deletions of chromosomal regulatory boundaries are associated with congenital disease.

    Published in:
    Genome Biology, 2014, v. 15, n. 7, p. 423, doi. 10.1186/s13059-014-0423-1
    By:
    • Ibn-Salem, Jonas;
    • Köhler, Sebastian;
    • Love, Michael I.;
    • Ho-Ryun Chung;
    • Ni Huang;
    • Hurles, Matthew E.;
    • Haendel, Melissa;
    • Washington, Nicole L.;
    • Smedley, Damian;
    • Mungall, Christopher J.;
    • Lewis, Suzanna E.;
    • Ott, Claus-Eric;
    • Bauer, Sebastian;
    • Schofield, Paul N.;
    • Mundlos, Stefan;
    • Spielmann, Malte;
    • Robinson, Peter N.
    Publication type:
    Article

  • Uberon, an integrative multi-species anatomy ontology.

    Published in:
    Genome Biology, 2012, v. 13, n. 1, p. 1, doi. 10.1186/gb-2012-13-1-r5
    By:
    • Mungall, Christopher J.;
    • Torniai, Carlo;
    • Gkoutos, Georgios V.;
    • Lewis, Suzanna E.;
    • Haendel, Melissa A.
    Publication type:
    Article

  • An evaluation of GPT models for phenotype concept recognition.

    Published in:
    BMC Medical Informatics & Decision Making, 2024, v. 24, n. 1, p. 1, doi. 10.1186/s12911-024-02439-w
    By:
    • Groza, Tudor;
    • Caufield, Harry;
    • Gration, Dylan;
    • Baynam, Gareth;
    • Haendel, Melissa A.;
    • Robinson, Peter N.;
    • Mungall, Christopher J.;
    • Reese, Justin T.
    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

  • 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:
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  • 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:
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  • Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation.

    Published in:
    PLoS Biology, 2009, v. 7, n. 11, p. 1, doi. 10.1371/journal.pbio.1000247
    By:
    • Washington, Nicole L.;
    • Haendel, Melissa A.;
    • Mungall, Christopher J.;
    • Ashburner, Michael;
    • Westerfield, Monte;
    • Lewis, Suzanna E.
    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:
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  • A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

    Published in:
    Bioinformatics, 2007, v. 23, n. 13, p. i337
    By:
    • Christopher J. Mungall;
    • David B. Emmert;
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    Publication type:
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