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Authors: James P. Balhoff
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Journal Article

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

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Nicolas Matentzoglu and others
Genetics, Volume 229, Issue 3, March 2025, iyaf027, https://doi.org/10.1093/genetics/iyaf027
Published: 06 March 2025
Journal Article

The Human Phenotype Ontology in 2024: phenotypes around the world Open Access

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Michael A Gargano and others
Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D1333–D1346, https://doi.org/10.1093/nar/gkad1005
Published: 11 November 2023
Journal Article

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies Open Access

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Nicolas Matentzoglu and others
Database, Volume 2022, 2022, baac087, https://doi.org/10.1093/database/baac087
Published: 08 October 2022
Journal Article

A Simple Standard for Sharing Ontological Mappings (SSSOM) Open Access

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Nicolas Matentzoglu and others
Database, Volume 2022, 2022, baac035, https://doi.org/10.1093/database/baac035
Published: 25 May 2022
Journal Article

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies Open Access

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Diego S Porto and others
Systematic Biology, Volume 71, Issue 6, November 2022, Pages 1290–1306, https://doi.org/10.1093/sysbio/syac022
Published: 14 March 2022
Journal Article

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies Open Access

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Rebecca Jackson and others
Database, Volume 2021, 2021, baab069, https://doi.org/10.1093/database/baab069
Published: 26 October 2021
Journal Article

Reactome and the Gene Ontology: digital convergence of data resources Open Access

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Benjamin M Good and others
Bioinformatics, Volume 37, Issue 19, October 2021, Pages 3343–3348, https://doi.org/10.1093/bioinformatics/btab325
Published: 08 May 2021
Journal Article

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species Open Access

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Kent A Shefchek and others
Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D704–D715, https://doi.org/10.1093/nar/gkz997
Published: 08 November 2019
Journal Article

A Logical Model of Homology for Comparative Biology Open Access

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Paula M Mabee and others
Systematic Biology, Volume 69, Issue 2, March 2020, Pages 345–362, https://doi.org/10.1093/sysbio/syz067
Published: 09 October 2019
Journal Article

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems Open Access

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Wasila Dahdul and others
Database, Volume 2018, 2018, bay110, https://doi.org/10.1093/database/bay110
Published: 14 December 2018
Journal Article

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources Open Access

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Sebastian Köhler and others
Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1018–D1027, https://doi.org/10.1093/nar/gky1105
Published: 22 November 2018
Journal Article

Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes Open Access

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Laura M Jackson and others
Systematic Biology, Volume 67, Issue 4, July 2018, Pages 559–575, https://doi.org/10.1093/sysbio/syx098
Published: 09 January 2018
Journal Article

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species Open Access

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Christopher J. Mungall and others
Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D712–D722, https://doi.org/10.1093/nar/gkw1128
Published: 29 November 2016
Journal Article

Navigating the Phenotype Frontier: The Monarch Initiative Free

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Julie A McMurry and others
Genetics, Volume 203, Issue 4, 1 August 2016, Pages 1491–1495, https://doi.org/10.1534/genetics.116.188870
Published: 01 August 2016
Journal Article

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes Open Access

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Richard C. Edmunds and others
Molecular Biology and Evolution, Volume 33, Issue 1, January 2016, Pages 13–24, https://doi.org/10.1093/molbev/msv223
Published: 24 October 2015
Journal Article

Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies Open Access

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T. Alexander Dececchi and others
Systematic Biology, Volume 64, Issue 6, November 2015, Pages 936–952, https://doi.org/10.1093/sysbio/syv031
Published: 26 May 2015
Journal Article

A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia Open Access

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James P. Balhoff and others
Systematic Biology, Volume 62, Issue 5, September 2013, Pages 639–659, https://doi.org/10.1093/sysbio/syt028
Published: 31 May 2013
Journal Article

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task Open Access

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Cecilia N. Arighi and others
Database, Volume 2013, 2013, bas056, https://doi.org/10.1093/database/bas056
Published: 16 January 2013
Journal Article

Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment Open Access

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Matthew A. Bertone and others
Database, Volume 2013, 2013, bas057, https://doi.org/10.1093/database/bas057
Published: 09 January 2013
Journal Article

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata Open Access

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Rutger A. Vos and others
Systematic Biology, Volume 61, Issue 4, July 2012, Pages 675–689, https://doi.org/10.1093/sysbio/sys025
Published: 22 February 2012