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Authors whose works are in public domain in at least one jurisdiction

List of works by James P. Balhoff

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

scientific article (publication date: June 2012)

A Logical Model of Homology for Comparative Biology

scientific article published on 01 March 2020

A Simple Standard for Sharing Ontological Mappings (SSSOM)

preprint published on 15 December 2021

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

scientific article

A logical model of homology for comparative biology

scientific article published on 26 March 2019

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

scientific article

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

scientific article (publication date: September 2013)

A unified anatomy ontology of the vertebrate skeletal system

scientific article (publication date: 2012)

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

scientific article published on 17 January 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

scientific article published on 01 January 2018

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

scientific article

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

scientific article published on 20 March 2021

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

scientific article published in proceedings of the iswc 2018 posters & demonstrations, industry and blue sky ideas tracks

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

scientific article published on 10 March 2022

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

scientific article published on 9 January 2018

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

scientific article

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)

scientific article published on 13 June 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

scientific article

Dead simple OWL design patterns

scientific article

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

scientific article

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

scientific article published on 04 August 2023

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

scientific article

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

scientific article (publication date: 20 May 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

scientific article

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

scientific article

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

scientific article published on June 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.

scientific article published on January 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

scientific article published on 9 November 2020

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

preprint published in 2023

KG-Hub—building and exchanging biological knowledge graphs

scientific article published in 2023

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

scientific article published on 9 January 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

scientific article

Navigating the Phenotype Frontier: The Monarch Initiative

scientific article

Navigating the phenotype frontier: The Monarch Initiative

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

scientific article (publication date: July 2012)

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

scientific article published on 13 October 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

scientific article published in 2009

Phenex: ontological annotation of phenotypic diversity

scientific article (publication date: 5 May 2010)

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

scientific article

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets

scientific article published on 14 August 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

scientific article (publication date: 13 May 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

scientific article published on 01 December 2019

ROBOT: A Tool for Automating Ontology Workflows

scientific article published on 29 July 2019

Reactome and the Gene Ontology: digital convergence of data resources

scientific article

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

scientific article published in 2023

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

scientific article published on 01 January 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

scientific article

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

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

scientific article published in 2023

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

The Teleost Taxonomy Ontology

scientific article published on 6 July 2010

The evolution of transcriptional regulation in eukaryotes

scientific article (publication date: September 2003)

The teleost anatomy ontology: anatomical representation for the genomics age

scientific article

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

scientific article

Time to change how we describe biodiversity

scientific article

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

scientific article

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

scientific article published on 24 November 2020

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

scientific article

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

scientific article published on 28 July 2015

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

scientific article published on 23 November 2020

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

scientific article published in 2023

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