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Using ontologies to describe mouse phenotypes

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Phenotype ontologies for mouse and man: bridging the semantic gap

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Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition

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An integer programming framework for inferring disease complexes from network data

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EMMA--mouse mutant resources for the international scientific community

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A common layer of interoperability for biomedical ontologies based on OWL EL

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Gene prioritization and clustering by multi-view text mining

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Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning

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What everybody should know about the rat genome and its online resources

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Liver-innervating vagal sensory neurons are indispensable for the development of hepatic steatosis and anxiety-like behavior in diet-induced obese mice

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Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base

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The cellular microscopy phenotype ontology

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Computational approaches for predicting variant impact: An overview from resources, principles to applications

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Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge

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Improving ontologies by automatic reasoning and evaluation of logical definitions

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Improving the interoperability of biomedical ontologies with compound alignments

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HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences

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p300 and cAMP response element‐binding protein‐binding protein in skeletal muscle homeostasis, contractile function, and survival

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Searching the Mouse Genome Informatics ( MGI ) Resources for Information on Mouse Biology from Genotype to Phenotype

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Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology

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Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle

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Disease classification: from phenotypic similarity to integrative genomics and beyond

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Supervised learning is an accurate method for network-based gene classification

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Ontological discovery environment: A system for integrating gene–phenotype associations

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PhenoGO: an integrated resource for the multiscale mining of clinical and biological data

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Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics

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PhenoMiner: from text to a database of phenotypes associated with OMIM diseases

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Network topology measures for identifying disease-gene association in breast cancer

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HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology

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Integrating phenotype ontologies with PhenomeNET

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PhenoRank: reducing study bias in gene prioritization through simulation

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Text Mining in Cancer Gene and Pathway Prioritization

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Disease gene prediction for molecularly uncharacterized diseases

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Representing Phenotypes in OWL.

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Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research

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Commentary: Mouse Genetic Nomenclature: Standardization of Strain, Gene, and Protein Symbols

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MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies

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Matrix Metalloproteinase-28 Is a Key Contributor to Emphysema Pathogenesis

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Identification of Genes Important for Cutaneous Function Revealed by a Large Scale Reverse Genetic Screen in the Mouse

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RelB deficiency causes combined immunodeficiency

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PhenoMiner: quantitative phenotype curation at the rat genome database

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Transcriptome profiling in engrailed-2 mutant mice reveals common molecular pathways associated with autism spectrum disorders

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A mouse protein interactome through combined literature mining with multiple sources of interaction evidence

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Bio-Ontology and text: bridging the modeling gap

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ATOL: The Multi-species Livestock Trait Ontology

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The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database

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The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions

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Building a developmental toxicity ontology

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Functional Enrichment Analysis with Structural Variants: Pitfalls and Strategies

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Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology

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The RIKEN integrated database of mammals

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Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data

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Rummagene: massive mining of gene sets from supporting materials of biomedical research publications

Clarke, D. J. B., Marino, G. B., Deng, E. Z., Xie, Z., Evangelista, J. E., & Ma’ayan, A. (2024) · Communications Biology · doi:10.1038/s42003-024-06177-7 · Cited by 37

Laboratory Mouse Models for the Human Genome-Wide Associations

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GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

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The Rat Genome Database Curators: Who, What, Where, Why

Shimoyama, M. E., Hayman, G. T., Laulederkind, S. J. F., Nigam, R., Lowry, T. F., Petri, V., Smith, J. R., Wang, S., Munzenmaier, D. H., Dwinell, M. R., et al. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000582 · Cited by 25

Data management pipeline for plant phenotyping in a multisite project

Billiau, K., Sprenger, H., Schudoma, C., Walther, D., & Köhl, K. I. (2012) · Functional Plant Biology · doi:10.1071/fp12009 · Cited by 25

Ontology-based prediction of cancer driver genes

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Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function

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Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype

Shaw, D. R. (2009) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0107s25 · Cited by 24

Computational tools for comparative phenomics: the role and promise of ontologies

Gkoutos, G. V., Schofield, P. N., & Hoehndorf, R. (2012) · Mammalian Genome · doi:10.1007/s00335-012-9404-4 · Cited by 24

Measuring the wisdom of the crowds in network-based gene function inference

Verleyen, W., Ballouz, S., & Gillis, J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu715 · Cited by 23

Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes

Shaikh, T. H., Haldeman‐Englert, C. R., Geiger, E. A., Ponting, C. P., & Webber, C. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq527 · Cited by 24

An en masse phenotype and function prediction system for Mus musculus

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Linking MedDRA®-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors

Sarntivijai, S., Zhang, S., Jagannathan, D., Zaman, S., Burkhart, K., Omenn, G. S., He, Y. O., Athey, B. D., & Abernethy, D. R. (2016) · Drug Safety · doi:10.1007/s40264-016-0414-0 · Cited by 24

The development of hepatic steatosis depends on the presence of liver-innervating parasympathetic cholinergic neurons in mice fed a high-fat diet

Hwang, J., Okada, J., Li, L., Pessin, J. E., Schwartz, G. J., & Jo, Y. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002865 · Cited by 23

Improving Disease Gene Prioritization by Comparing the Semantic Similarity of Phenotypes in Mice with Those of Human Diseases

Oellrich, A., Hoehndorf, R., Gkoutos, G. V., & Rebholz‐Schuhmann, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038937 · Cited by 24

Comparative Genomics for Detecting Human Disease Genes

Moreno, C., Lazar, J., Jacob, H. J., & Kwitek, A. E. (2008) · Advances in genetics · doi:10.1016/s0065-2660(07)00423-3 · Cited by 23

MouseBook: an integrated portal of mouse resources

Blake, A., Pickford, K., Greenaway, S., Thomas, S. W., Pickard, A. R., Williamson, C. M., Adams, N. C., Walling, A., Beck, T., Fray, M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp867 · Cited by 22

OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem

McLaughlin, J. A., Lagrimas, J., Iqbal, H., Parkinson, H., & Harmse, H. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf279 · Cited by 22

Phenoclustering: online mining of cross-species phenotypes

Groth, P., Kalev, I., Kirov, I., Traikov, B., Leser, U., & Weiss, B. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq311 · Cited by 22

Computational Methods for Prediction of Human Protein-Phenotype Associations: A Review

Liu, L., & Zhu, S. (2021) · Phenomics · doi:10.1007/s43657-021-00019-w · Cited by 22

POSTRE: a tool to predict the pathological effects of human structural variants

Sánchez-Gaya, V., & Rada-Iglesias, Á. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad225 · Cited by 22

Analyzing gene expression data in mice with the Neuro Behavior Ontology

Hoehndorf, R., Hancock, J. M., Hardy, N. W., Mallon, A., Schofield, P. N., & Gkoutos, G. V. (2013) · Mammalian Genome · doi:10.1007/s00335-013-9481-z · Cited by 22

LINKING PHARMGKB TO PHENOTYPE STUDIES AND ANIMAL MODELS OF DISEASE FOR DRUG REPURPOSING

Hoehndorf, R., Oellrich, A., Rebholz‐Schuhmann, D., Schofield, P. N., & Gkoutos, G. V. (2011) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789814366496_0038 · Cited by 22

Accelerated Discovery of Novel Protein Function in Cultured Human Cells

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Ontology searching and browsing at the Rat Genome Database

Laulederkind, S. J. F., Tutaj, M., Shimoyama, M. E., Hayman, G. T., Lowry, T. F., Nigam, R., Petri, V., Smith, J. R., Wang, S.-J., Pons, J. D., et al. (2012) · Database · doi:10.1093/database/bas016 · Cited by 21

Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information

Adamusiak, T., Parkinson, H., Muilu, J., Roos, E. T., van der Velde, K. J., Þórisson, G. Á., Byrne, M., Pang, C., Gollapudi, S., Ferretti, V., et al. (2012) · Human Mutation · doi:10.1002/humu.22070 · Cited by 21

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

Hancock, J. M., Mallon, A., Beck, T., Gkoutos, G. V., Mungall, C., & Schofield, P. N. (2009) · Mammalian Genome · doi:10.1007/s00335-009-9208-3 · Cited by 21

GEN3VA: aggregation and analysis of gene expression signatures from related studies

Gundersen, G. W., Jagodnik, K. M., Woodland, H., Fernandez, N. F., Sani, K., Dohlman, A. B., Ung, P. M. U., Monteiro, C. D., Schlessinger, A., & Ma’ayan, A. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1321-1 · Cited by 21

PhenoHM: human–mouse comparative phenome–genome server

Sardana, D., Vasa, S., Vepachedu, N., Chen, J., Gudivada, R. C., Aronow, B. J., & Jegga, A. G. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq472 · Cited by 20

New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models

Schofield, P. N., Sundberg, J. P., Hoehndorf, R., & Gkoutos, G. V. (2011) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr031 · Cited by 21

Annotating the human genome with Disease

Osborne, J. D., Flatow, J. M., & Holko, M. (2009) · Cited by 20

Disease Gene Prioritization

Roberto, C., Yeh, H., & Soo, V. (2011) · InTech eBooks · doi:10.5772/20049 · Cited by 22

Identification of SRC as a Potent Drug Target for Asthma, Using an Integrative Approach of Protein Interactome Analysis and In Silico Drug Discovery

Randhawa, V., & Bagler, G. (2012) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2011.0160 · Cited by 20

A method exploiting syntactic patterns and the UMLS semantics for aligning biomedical ontologies: The case of OBO disease ontologies

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An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes

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