List of works by Christopher J. Mungall

"Opposite-of"-information improves similarity calculations in phenotype ontologies

A Census of Disease Ontologies

scientific article published on 09 May 2018

A Chado case study: an ontology-based modular schema for representing genome-associated biological information

scientific article (publication date: July 2007)

A Logical Model of Homology for Comparative Biology

scientific article published on 01 March 2020

A Simple Standard for Ontological Mappings 2022: Updates of data model and outlook ⬇️

Conference paper

A Simple Standard for Sharing Ontological Mappings (SSSOM)

preprint published on 15 December 2021

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

scientific article published on 25 August 2016

A knowledge based approach to matching human neurodegenerative disease and animal models

scientific article published on 14 May 2013

A logical model of homology for comparative biology

scientific article published on 26 March 2019

A method for increasing expressivity of Gene Ontology annotations using a compositional approach

scientific article

A promoter-level mammalian expression atlas

scientific article

A strategy for building neuroanatomy ontologies

scientific article published on 07 March 2012

A unified anatomy ontology of the vertebrate skeletal system

scientific article (publication date: 2012)

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

article

AmiGO: online access to ontology and annotation data

scientific article (publication date: 15 January 2009)

An atlas of active enhancers across human cell types and tissues

scientific article

An improved ontological representation of dendritic cells as a paradigm for all cell types

scientific article

An integrated computational pipeline and database to support whole-genome sequence annotation

scientific article

An integrated expression atlas of miRNAs and their promoters in human and mouse.

scientific article

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

scientific article

Apollo: a sequence annotation editor

scientific article

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 the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

scientific article

BioMake: a GNU make-compatible utility for declarative workflow management.

scientific article published on 9 May 2017

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

scientific article

CARO – The Common Anatomy Reference Ontology

article

CLO: The cell line ontology

scientific article

Capturing phenotypes for precision medicine

scientific article

Clinical interpretation of CNVs with cross-species phenotype data

scientific article

Comparative genomics of the eukaryotes

scientific article (publication date: 24 March 2000)

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.

scientific article

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

scientific article published on February 2013

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

article

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

scientific article published on 09 May 2013

Cross-product extensions of the Gene Ontology

scientific article

Dead simple OWL design patterns

scientific article

Deletions of chromosomal regulatory boundaries are associated with congenital disease

scientific article

Design and implementation of a CORBA-based genome mapping system prototype

scientific article published on January 1998

Development of an Ontology of Microbial Phenotypes (OMP)

article

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

scientific article

Disease insights through cross-species phenotype comparisons

scientific article

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

scientific article published on 26 June 2017

Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience

scientific article published on 12 October 2016

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

scientific article

ECO, the Evidence & Conclusion Ontology: community standard for evidence information

scholarly article

Emerging semantics to link phenotype and environment

scientific article

Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics

scientific article published on 01 September 2019

Entity/quality-based logical definitions for the human skeletal phenome using PATO

scientific article

Evolution of the Sequence Ontology terms and relationships

scientific article

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

Extension of Roles in the ChEBI Ontology

scholarly article

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

scientific article published on 19 February 2018

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

scientific article published on 13 June 2016

Finding our way through phenotypes

scientific article

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

scientific article

From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies

scientific article published on 19 May 2017

GOATOOLS: A Python library for Gene Ontology analyses

scientific article published in Scientific Reports

Gateways to the FANTOM5 promoter level mammalian expression atlas

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

Gene Ontology annotations and resources

scientific article

Genome sequence of the human malaria parasite Plasmodium falciparum

scientific article

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins

scientific article

Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets ⬇️

scientific article published November 2014

Hematopoietic cell types: prototype for a revised cell ontology

scientific article

Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

scientific article

High-performance web services for querying gene and variant annotation

scientific article (publication date: 6 May 2016)

How many rare diseases are there?

scientific article published on 01 February 2020

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

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Improved exome prioritization of disease genes through cross-species phenotype comparison

scientific article

Improving ontologies by automatic reasoning and evaluation of logical definitions

scientific article

Integrating phenotype ontologies across multiple species

scientific article

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

JBrowse: a next-generation genome browser

scientific article

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response

scientific article published on 01 October 2020

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

scientific article published on 18 August 2020

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

Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge

scientific article published on 23 March 2021

Large-scale trends in the evolution of gene structures within 11 animal genomes

scientific article

LinkML

A flexible modeling framework that allow for working with semantic web standards alongside a modern data stack

Linking human diseases to animal models using ontology-based phenotype annotation

scientific article

Logical development of the cell ontology

scientific article

MIRO: guidelines for minimum information for the reporting of an ontology

scientific article published on 18 January 2018

Mapping between the OBO and OWL ontology languages

scientific article

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

scientific article published on 22 February 2021

Modeling biochemical pathways in the gene ontology

scientific article published on September 2016

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

scientific article published on 16 September 2020

Modularization for the Cell Ontology

Modularization for the Cell Ontology

scientific article published on 12 December 2011

Mondo: Unifying diseases for the world, by the world

Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease

scientific article published on 02 August 2009

MouseFinder: Candidate disease genes from mouse phenotype data

scientific article

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

scientific article

MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services

article

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

scientific article published on 15 May 2022

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge

scientific article

Navigating the Phenotype Frontier: The Monarch Initiative

scientific article

Navigating the phenotype frontier: The Monarch Initiative

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

scientific article

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis

scientific article

OBO & OWL: Roundtrip Ontology Transformations ⬇️

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

scientific article published on 13 October 2021

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

scientific article

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

scientific article published on 4 January 2013

Obol: integrating language and meaning in bio-ontologies

scientific article (publication date: 2004)

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

scientific article

OntoGPT

Python package for extracting structured information from text

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

scientific article (publication date: 12 October 2016)

Ontologies as integrative tools for plant science

scientific article

Ontologies for biologists: a community model for the annotation of genomic data

scientific article

Ontology Development Kit

The Ontology Development Kit is a toolbox of various ontology related tools such as ROBOT and dosdp-tools, bundled as a docker image. It provides executable workflows for managing ontologies continuous integration, releases and dynamic imports.

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

preprint published on 06 July 2022

Ontology based molecular signatures for immune cell types via gene expression analysis

scientific article

Ontology engineering

scientific article

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

scientific article published on 9 May 2013

Phenotype ontologies: the bridge between genomics and evolution

scientific article published on 09 April 2007

Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish

scientific article published on 25 October 2012

Plain-language medical vocabulary for precision diagnosis.

scientific article published in April 2018

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

Relations in biomedical ontologies ⬇️

scientific article published on 28 April 2005

Representing kidney development using the gene ontology

scientific article

SSSOM-py

Python package

Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery: Supplementary materials

article

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

article

Simple Standard for Sharing Ontology Mappings

Metadata standard

Standardized description of scientific evidence using the Evidence Ontology (ECO)

scientific article

String of PURLs – frugal migration and maintenance of persistent identifiers

scientific article published on 12 June 2020

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

scientific article published on 21 February 2024

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

scientific article published on 08 December 2021

Survey-based naming conventions for use in OBO Foundry ontology development

scientific article (publication date: 27 April 2009)

SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

scientific article published on 28 April 2022

Taking shortcuts with OWL using safe macros

Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

scientific article published on 02 September 2020

TermGenie - a web-application for pattern-based ontology class generation

scientific article published on 11 December 2014

The ARKdb: genome databases for farmed and other animals

scientific article

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

scientific article

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

scientific article (publication date: 7 October 2013)

The Gene Ontology (GO) database and informatics resource

scientific article (publication date: 2004)

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The Human Phenotype Ontology in 2017

scientific article (publication date: 28 November 2016)

The Human Phenotype Ontology in 2021

scientific article published on 02 December 2020

The Human Phenotype Ontology in 2024: phenotypes around the world

scientific article published in 2023

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

scientific article (publication date: 2014)

The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles

scientific article

The Matchmaker Exchange: a platform for rare disease gene discovery

scientific article

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

scientific article published on 30 June 2020

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 in 2024: an analytic platform integrating phenotypes, genes and diseases 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

scientific article

The National Microbiome Data Collaborative: enabling microbiome science

scientific article published on 29 April 2020

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

scientific article published in November 2007

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

scientific article published on 25 September 2020

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

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

scientific article published on 04 June 2019

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

scientific article

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

scientific article

The Release 5.1 annotation of Drosophila melanogaster heterochromatin

scientific article

The Sequence Ontology: a tool for the unification of genome annotations

scientific article published in 2005

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

scientific article

The environment ontology: contextualising biological and biomedical entities

article

The generic genome browser: a building block for a model organism system database

scientific article

The health care and life sciences community profile for dataset descriptions

scientific article (publication date: 2016)

The health care and life sciences community profile for dataset descriptions

The health care and life sciences community profile for dataset descriptions

The health care and life sciences community profile for dataset descriptions

article published in 2016

The influence of disease categories on gene candidate predictions from model organism phenotypes

scientific article

The plant ontology as a tool for comparative plant anatomy and genomic analyses

scientific article published on 5 December 2012

Tools for exploring mouse models of human disease

scientific article published on 30 August 2017

Tools for neuroanatomy and neurogenetics in Drosophila

scholarly article

Toward a minimal information reporting standard about new cell types ⬇️

preprint

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

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

scientific article published on 24 November 2020

Uberon

ontology

Uberon, an integrative multi-species anatomy ontology

scientific article

Uberon: towards a comprehensive multi-species anatomy ontology

Uberon: towards a comprehensive multi-species anatomy ontology

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

scientific article

Unifying the Identification of Biomedical Entities with the Bioregistry ⬇️

preprint published on 10 July 2022

Unifying the identification of biomedical entities with the Bioregistry ⬇️

scientific article published on 19 November 2022

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

scientific article published on 27 October 2016

Use of animal models for exome prioritization of rare disease genes

article

Use of model organism and disease databases to support matchmaking for human disease gene discovery

scientific article

Using ontologies to define the relation between neurodegenerative disease and associated animal model phenotypes

VO: Vaccine Ontology

VO: Vaccine Ontology

VO: Vaccine Ontology

VO: Vaccine Ontology

WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis

article

What is an anatomy ontology?

scientific article

k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction

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