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Lista de obras de Chris Mungall

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

A Census of Disease Ontologies

artículo científico publicado en 2018

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

artículo científico publicado en 2007

A Logical Model of Homology for Comparative Biology

artículo científico publicado en 2020

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

Conference paper

A Simple Standard for Sharing Ontological Mappings (SSSOM)

artículo científico publicado en 2022

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

artículo científico publicado en 2016

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

artículo científico publicado en 2013

A logical model of homology for comparative biology

artículo científico publicado en 2019

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

artículo científico publicado en 2014

A promoter-level mammalian expression atlas

artículo científico publicado en 2014

A strategy for building neuroanatomy ontologies

artículo científico

A unified anatomy ontology of the vertebrate skeletal system

artículo científico publicado en 2012

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

article

AmiGO: online access to ontology and annotation data

artículo científico publicado en 2009

An atlas of active enhancers across human cell types and tissues

artículo científico publicado en 2014

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

artículo científico publicado en 2009

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

artículo científico publicado en 2002

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

artículo científico publicado en 2017

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

artículo científico publicado en 2002

Apollo: a sequence annotation editor

artículo científico publicado en 2002

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

artículo científico publicado en 2018

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

artículo científico publicado en 2002

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

artículo científico publicado en 2017

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

artículo científico publicado en 2022

CARO – The Common Anatomy Reference Ontology

article

CLO: The cell line ontology

artículo científico publicado en 2014

Capturing phenotypes for precision medicine

artículo científico publicado en 2015

Clinical interpretation of CNVs with cross-species phenotype data

artículo científico publicado en 2014

Comparative genomics of the eukaryotes

artículo científico publicado en 2000

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

artículo científico publicado en 2015

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

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

artículo científico

Cross-product extensions of the Gene Ontology

artículo científico publicado en 2010

Dead simple OWL design patterns

artículo científico publicado en 2017

Deletions of chromosomal regulatory boundaries are associated with congenital disease

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2015

Disease insights through cross-species phenotype comparisons

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2013

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

artículo científico publicado en 2019

Emerging semantics to link phenotype and environment

artículo científico publicado en 2015

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

artículo científico publicado en 2009

Evolution of the Sequence Ontology terms and relationships

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

Extension of Roles in the ChEBI Ontology

artículo científico publicado en 2020

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

artículo científico publicado en 2018

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

artículo científico publicado en 2016

Finding our way through phenotypes

artículo científico publicado en 2015

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

artículo científico publicado en 2010

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

artículo científico

GOATOOLS: A Python library for Gene Ontology analyses

scientific article published in Scientific Reports

Gateways to the FANTOM5 promoter level mammalian expression atlas

artículo científico publicado en 2015

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

artículo científico publicado en 2012

Genome sequence of the human malaria parasite Plasmodium falciparum

artículo científico publicado en 2002

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

artículo científico publicado en 2008

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

artículo científico publicado en 2014

Hematopoietic cell types: prototype for a revised cell ontology

artículo científico publicado en 2010

Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

artículo científico publicado en 2002

High-performance web services for querying gene and variant annotation

artículo científico publicado en 2016

How many rare diseases are there?

artículo científico publicado en 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.

artículo científico

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

Improving ontologies by automatic reasoning and evaluation of logical definitions

artículo científico publicado en 2011

Integrating phenotype ontologies across multiple species

artículo científico publicado en 2010

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

JBrowse: a next-generation genome browser

artículo científico publicado en 2009

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

artículo científico publicado en 2020

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

artículo científico publicado en 2020

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

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

artículo científico publicado en 2021

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

artículo científico publicado en 2006

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

artículo científico publicado en 2009

Logical development of the cell ontology

artículo científico publicado en 2011

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

artículo científico publicado en 2018

Mapping between the OBO and OWL ontology languages

artículo científico publicado en 2011

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

artículo científico publicado en 2021

Modeling biochemical pathways in the gene ontology

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 2022

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

artículo científico publicado en 2006

Navigating the Phenotype Frontier: The Monarch Initiative

artículo científico publicado en 2016

Navigating the phenotype frontier: The Monarch Initiative

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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

OBO & OWL: Roundtrip Ontology Transformations ⬇️

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

artículo científico publicado en 2021

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

artículo científico publicado en 2010

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

artículo científico publicado en 2013

Obol: integrating language and meaning in bio-ontologies

artículo científico publicado en 2004

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

artículo científico publicado en 2012

OntoGPT

Python package for extracting structured information from text

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

artículo científico publicado en 2016

Ontologies as integrative tools for plant science

artículo científico publicado en 2012

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

artículo científico publicado en 2003

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

artículo científico publicado en 2013

Ontology engineering

artículo científico publicado en 2010

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

artículo científico publicado en 2013

Phenotype ontologies: the bridge between genomics and evolution

artículo científico

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

artículo científico publicado en 2012

Plain-language medical vocabulary for precision diagnosis.

artículo científico publicado en 2018

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

Relations in biomedical ontologies ⬇️

artículo científico publicado en 2005

Representing kidney development using the gene ontology

artículo científico publicado en 2014

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)

artículo científico publicado en 2014

String of PURLs – frugal migration and maintenance of persistent identifiers

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2014

The ARKdb: genome databases for farmed and other animals

artículo científico publicado en 2001

The Bioperl toolkit: Perl modules for the life sciences

artículo científico publicado en 2002

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

artículo científico publicado en 2016

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

artículo científico publicado en 2013

The Gene Ontology (GO) database and informatics resource

artículo científico publicado en 2004

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The Human Phenotype Ontology in 2017

artículo científico publicado en 2016

The Human Phenotype Ontology in 2021

artículo científico publicado en 2020

The Human Phenotype Ontology in 2024: phenotypes around the world

artículo científico publicado en 2023

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

The Matchmaker Exchange: a platform for rare disease gene discovery

artículo científico publicado en 2015

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

artículo científico publicado en 2020

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 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

artículo científico publicado en 2017

The National Microbiome Data Collaborative: enabling microbiome science

artículo científico publicado en 2020

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

artículo científico publicado en 2007

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

artículo científico publicado en 2020

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

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

artículo científico publicado en 2019

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

The Release 5.1 annotation of Drosophila melanogaster heterochromatin

artículo científico publicado en 2007

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

artículo científico publicado en 2005

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

artículo científico publicado en 2016

The environment ontology: contextualising biological and biomedical entities

article

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

artículo científico publicado en 2002

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 health care and life sciences community profile for dataset descriptions

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2012

Tools for exploring mouse models of human disease

artículo científico publicado en 2017

Tools for neuroanatomy and neurogenetics in Drosophila

artículo científico publicado en 2008

Toward a minimal information reporting standard about new cell types ⬇️

artículo científico publicado en 2022

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

artículo científico publicado en 2015

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

artículo científico publicado en 2020

Uberon, an integrative multi-species anatomy ontology

artículo científico publicado en 2012

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

artículo científico publicado en 2014

Unifying the Identification of Biomedical Entities with the Bioregistry ⬇️

preprint published on 10 July 2022

Unifying the identification of biomedical entities with the Bioregistry ⬇️

artículo científico publicado en 2022

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

artículo científico publicado en 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

artículo científico publicado en 2015

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?

artículo científico publicado en 2013

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

Uberon

ontología

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