Works by Harris, Nomi L

Results: 24

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. W1, p. W84, doi. 10.1093/nar/gkaf402

By:

Vendetti, Jennifer;
Harris, Nomi L;
Dorf, Michael V;
Skrenchuk, Alex;
Caufield, J Harry;
Gonçalves, Rafael S;
Graybeal, John B;
Hegde, Harshad;
Redmond, Timothy;
Mungall, Christopher J;
Musen, Mark A

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

NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study.

Published in:

Virology Journal, 2022, v. 19, n. 1, p. 1, doi. 10.1186/s12985-022-01813-2

By:

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.

Publication type:

Article

Empirical evaluation of prior beliefs about frequencies: Methodology and a case study in congenital heart disease.

Published in:

Journal of the American Statistical Association, 1994, v. 89, n. 426, p. 435, doi. 10.1080/01621459.1994.10476765

By:

Spiegelhalter, David J.;
Harris, Nomi L.;
Bull, Kate;
Franklin, Rodney C. G.

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

The Bioinformatics Open Source Conference (BOSC) 2013.

Published in:

2015

By:

Harris, Nomi L.;
Cock, Peter J. A.;
Chapman, Brad A.;
Goecks, Jeremy;
Hotz, Hans-Rudolf;
Lapp, Hilmar

Publication type:

Proceeding

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).

Published in:

Journal of Biomedical Semantics, 2024, v. 15, n. 1, p. 1, doi. 10.1186/s13326-024-00320-3

By:

Toro, Sabrina;
Anagnostopoulos, Anna V.;
Bello, Susan M.;
Blumberg, Kai;
Cameron, Rhiannon;
Carmody, Leigh;
Diehl, Alexander D.;
Dooley, Damion M.;
Duncan, William D.;
Fey, Petra;
Gaudet, Pascale;
Harris, Nomi L.;
Joachimiak, Marcin P.;
Kiani, Leila;
Lubiana, Tiago;
Munoz-Torres, Monica C.;
O'Neil, Shawn;
Osumi-Sutherland, David;
Puig-Barbe, Aleix;
Reese, Justin T.

Publication type:

Article

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.

Published in:

CTS: Clinical & Translational Science, 2022, v. 15, n. 8, p. 1848, doi. 10.1111/cts.13302

By:

Unni, Deepak R.;
Moxon, Sierra A. T.;
Bada, Michael;
Brush, Matthew;
Bruskiewich, Richard;
Caufield, J. Harry;
Clemons, Paul A.;
Dancik, Vlado;
Dumontier, Michel;
Fecho, Karamarie;
Glusman, Gustavo;
Hadlock, Jennifer J.;
Harris, Nomi L.;
Joshi, Arpita;
Putman, Tim;
Qin, Guangrong;
Ramsey, Stephen A.;
Shefchek, Kent A.;
Solbrig, Harold;
Soman, Karthik

Publication type:

Article

Progress toward a universal biomedical data translator.

Published in:

CTS: Clinical & Translational Science, 2022, v. 15, n. 8, p. 1838, doi. 10.1111/cts.13301

By:

Fecho, Karamarie;
Thessen, Anne E.;
Baranzini, Sergio E.;
Bizon, Chris;
Hadlock, Jennifer J.;
Huang, Sui;
Roper, Ryan T.;
Southall, Noel;
Ta, Casey;
Watkins, Paul B.;
Williams, Mark D.;
Xu, Hao;
Byrd, William;
Dančík, Vlado;
Duby, Marc P.;
Dumontier, Michel;
Glusman, Gustavo;
Harris, Nomi L.;
Hinderer, Eugene W.;
Hyde, Greg

Publication type:

Article

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Published in:

2016

By:

Harris, Nomi L.;
Cock, Peter J. A.;
Lapp, Hilmar;
Chapman, Brad;
Davey, Rob;
Fields, Christopher;
Hokamp, Karsten;
Munoz-Torres, Monica

Publication type:

Proceeding

Efficient reinterpretation of rare disease cases using Exomiser.

Published in:

NPJ Genomic Medicine, 2024, v. 9, n. 1, p. 1, doi. 10.1038/s41525-024-00456-2

By:

Vestito, Letizia;
Jacobsen, Julius O. B.;
Walker, Susan;
Cipriani, Valentina;
Harris, Nomi L.;
Haendel, Melissa A.;
Mungall, Christopher J.;
Robinson, Peter;
Smedley, Damian

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

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

Phenopacket-tools: Building and validating GA4GH Phenopackets.

Published in:

PLoS ONE, 2023, v. 18, 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

Apollo: Democratizing genome annotation.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006790

By:

Dunn, Nathan A.;
Unni, Deepak R.;
Diesh, Colin;
Munoz-Torres, Monica;
Harris, Nomi L.;
Yao, Eric;
Rasche, Helena;
Holmes, Ian H.;
Elsik, Christine G.;
Lewis, Suzanna E.

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

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06105-4

By:

Bridges, Yasemin;
Souza, Vinicius de;
Cortes, Katherina G.;
Haendel, Melissa;
Harris, Nomi L.;
Korn, Daniel R.;
Marinakis, Nikolaos M.;
Matentzoglu, Nicolas;
McLaughlin, James A.;
Mungall, Christopher J.;
Odell, Aaron;
Osumi-Sutherland, David;
Robinson, Peter N.;
Smedley, Damian;
Jacobsen, Julius O. B.

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

Association of post-COVID phenotypic manifestations with new-onset psychiatric disease.

Published in:

Translational Psychiatry, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41398-024-02967-z

By:

Coleman, Ben;
Casiraghi, Elena;
Callahan, Tiffany J.;
Blau, Hannah;
Chan, Lauren E.;
Laraway, Bryan;
Clark, Kevin B.;
Re'em, Yochai;
Gersing, Ken R.;
Wilkins, Kenneth J.;
Harris, Nomi L.;
Valentini, Giorgio;
Haendel, Melissa A.;
Reese, Justin T.;
Robinson, Peter N.

Publication type:

Article

The GA4GH Phenopacket schema defines a computable representation of clinical data.

Published in:

2022

By:

Jacobsen, Julius O. B.;
Baudis, Michael;
Baynam, Gareth S.;
Beckmann, Jacques S.;
Beltran, Sergi;
Buske, Orion J.;
Callahan, Tiffany J.;
Chute, Christopher G.;
Courtot, Mélanie;
Danis, Daniel;
Elemento, Olivier;
Essenwanger, Andrea;
Freimuth, Robert R.;
Gargano, Michael A.;
Groza, Tudor;
Hamosh, Ada;
Harris, Nomi L.;
Kaliyaperumal, Rajaram;
Lloyd, Kevin C. Kent;
Khalifa, Aly

Publication type:

Letter

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Published in:

Nature Biotechnology, 2018, v. 36, n. 7, p. 566, doi. 10.1038/nbt.4163

By:

Arkin, Adam P;
Cottingham, Robert W;
Henry, Christopher S;
Harris, Nomi L;
Stevens, Rick L;
Maslov, Sergei;
Dehal, Paramvir;
Ware, Doreen;
Perez, Fernando;
Canon, Shane;
Sneddon, Michael W;
Henderson, Matthew L;
Riehl, William J;
Murphy-Olson, Dan;
Chan, Stephen Y;
Kamimura, Roy T;
Kumari, Sunita;
Drake, Meghan M;
Brettin, Thomas S;
Glass, Elizabeth M

Publication type:

Article