Works by Balhoff, James P

Results: 41

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.

Published in:

Genetics, 2025, v. 229, n. 3, p. 1, doi. 10.1093/genetics/iyaf027

By:

Matentzoglu, Nicolas;
Bello, Susan M;
Stefancsik, Ray;
Alghamdi, Sarah M;
Anagnostopoulos, Anna V;
Balhoff, James P;
Balk, Meghan A;
Bradford, Yvonne M;
Bridges, Yasemin;
Callahan, Tiffany J;
Caufield, Harry;
Cuzick, Alayne;
Carmody, Leigh C;
Caron, Anita R;
Souza, Vinicius de;
Engel, Stacia R;
Fey, Petra;
Fisher, Malcolm;
Gehrke, Sarah;
Grove, Christian

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

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

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