Lista de obras - James P. Balhoff - Dominio Público Uruguay

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

artículo científico publicado en 2012

A Logical Model of Homology for Comparative Biology

artículo científico publicado en 2020

A Simple Standard for Sharing Ontological Mappings (SSSOM)

artículo científico publicado en 2022

A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

scientific article

A logical model of homology for comparative biology

artículo científico publicado en 2019

A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation

artículo científico publicado en 2012

A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia

artículo científico publicado en 2013

A unified anatomy ontology of the vertebrate skeletal system

artículo científico publicado en 2012

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

artículo científico publicado en 2013

Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems

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

artículo científico publicado en 2018

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

artículo científico publicado en 2014

Application of MCAT questions as a testing tool and evaluation metric for knowledge graph–based reasoning systems

artículo científico publicado en 2021

Arachne: an OWL RL Reasoner Applied to Gene Ontology Causal Activity Models (and Beyond)

artículo científico publicado en 2018

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

artículo científico publicado en 2022

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

artículo científico publicado en 2018

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science ⬇️

artículo científico publicado en 2022

CharaParser+EQ: Performance evaluation without gold standard

article by Hong Cui et al published 2015 in Proceedings of the Association for Information Science and Technology

Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae)

artículo científico publicado en 2024

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

artículo científico publicado en 2013

Dead simple OWL design patterns

artículo científico publicado en 2017

Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

scientific article published on 13 March 2019

Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs

artículo científico publicado en 2008

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

artículo científico publicado en 2023

Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites

artículo científico publicado en 2005

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature

artículo científico publicado en 2010

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

article by Sebastian Köhler et al published 8 January 2019 in Nucleic Acids Research

Finding our way through phenotypes

artículo científico publicado en 2015

Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania)

artículo científico publicado en 2014

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

scientific article published on 01 October 2019

Highly specific and quantitative activation of STATs in 3T3-L1 adipocytes

artículo científico publicado en 1998

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

artículo científico

Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

artículo científico publicado en 2020

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

preprint published in 2023

KG-Hub—building and exchanging biological knowledge graphs

artículo científico publicado en 2023

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

artículo científico publicado en 2013

Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles

Mondo: Unifying diseases for the world, by the world

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

artículo científico publicado en 2016

Navigating the Phenotype Frontier: The Monarch Initiative

artículo científico publicado en 2016

Navigating the phenotype frontier: The Monarch Initiative

NeXML: rich, extensible, and verifiable representation of comparative data and metadata

artículo científico publicado en 2012

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

artículo científico publicado en 2021

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies

preprint published on 06 July 2022

Phenex: Ontological Annotation of Phenotypic Diversity

artículo científico publicado en 2009

Phenex: ontological annotation of phenotypic diversity

artículo científico publicado en 2010

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

artículo científico publicado en 2016

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets

artículo científico publicado en 2009

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology

scholarly article published 13 June 2018

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology

article

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

artículo científico publicado en 2013

ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources

scientific article published on 12 December 2019

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering

artículo científico publicado en 2019

ROBOT: A Tool for Automating Ontology Workflows

artículo científico publicado en 2019

Reactome and the Gene Ontology: digital convergence of data resources

artículo científico publicado en 2021

Scowl: a Scala DSL for programming with the OWL API

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

article

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The Human Phenotype Ontology in 2024: phenotypes around the world

artículo científico publicado en 2023

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

artículo científico publicado en 2020

The Monarch Initiative: Insights across species reveal human disease mechanisms

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

artículo científico publicado en 2017

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

artículo científico publicado en 2023

The Teleost Taxonomy Ontology

artículo científico publicado en 2010

The evolution of transcriptional regulation in eukaryotes

artículo científico publicado en 2003

The teleost anatomy ontology: anatomical representation for the genomics age

artículo científico publicado en 2010

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

artículo científico publicado en 2013

Time to change how we describe biodiversity

artículo científico publicado en 2011

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

artículo científico publicado en 2015

Transforming the study of organisms: Phenomic data models and knowledge bases

artículo científico publicado en 2020

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

artículo científico publicado en 2014

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

artículo científico

Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface

artículo científico publicado en 2020

rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits

scientific article published in 2023

The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms

articulo publicado en 2016

Lista de obras de James P. Balhoff

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

A Logical Model of Homology for Comparative Biology

A Simple Standard for Sharing Ontological Mappings (SSSOM)

A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

A logical model of homology for comparative biology

A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation

A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia

A unified anatomy ontology of the vertebrate skeletal system

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

Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems

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

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

Application of MCAT questions as a testing tool and evaluation metric for knowledge graph–based reasoning systems

Arachne: an OWL RL Reasoner Applied to Gene Ontology Causal Activity Models (and Beyond)

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

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

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science ⬇️

CharaParser+EQ: Performance evaluation without gold standard

Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae)

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

Dead simple OWL design patterns

Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature

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

Finding our way through phenotypes

Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania)

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Highly specific and quantitative activation of STATs in 3T3-L1 adipocytes

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

KG-Hub—building and exchanging biological knowledge graphs

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

Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles

Mondo: Unifying diseases for the world, by the world

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

Navigating the Phenotype Frontier: The Monarch Initiative

Navigating the phenotype frontier: The Monarch Initiative

NeXML: rich, extensible, and verifiable representation of comparative data and metadata

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

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies

Phenex: Ontological Annotation of Phenotypic Diversity

Phenex: ontological annotation of phenotypic diversity

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering

ROBOT: A Tool for Automating Ontology Workflows

Reactome and the Gene Ontology: digital convergence of data resources

Scowl: a Scala DSL for programming with the OWL API

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

The Gene Ontology knowledgebase in 2023

The Human Phenotype Ontology in 2024: phenotypes around the world

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

The Monarch Initiative: Insights across species reveal human disease mechanisms

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

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

The Teleost Taxonomy Ontology

The evolution of transcriptional regulation in eukaryotes

The teleost anatomy ontology: anatomical representation for the genomics age

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

Time to change how we describe biodiversity

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

Transforming the study of organisms: Phenomic data models and knowledge bases

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface

rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits

The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms