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

https://doi.org/10.1101/055756
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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ZFIN , The zebrafish model organism database: Updates and new directions
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Cross‐organism analysis using InterMine
inferredcites →https://doi.org/10.1002/humu.22078openalex-snapshot
Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users
inferredcites →https://doi.org/10.1002/humu.22347openalex-snapshot
PhenoTips: Patient Phenotyping Software for Clinical and Research Use
inferredcites →https://doi.org/10.1002/humu.22857openalex-snapshot
Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery
inferredcites →https://doi.org/10.1007/978-1-4939-6427-7_4openalex-snapshot
GeneNetwork: A Toolbox for Systems Genetics
inferredcites →https://doi.org/10.1007/978-3-540-69828-9_12openalex-snapshot
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species
inferredcites →https://doi.org/10.1007/s00335-015-9582-yopenalex-snapshot
Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis
inferredcites →https://doi.org/10.1007/s00335-015-9584-9openalex-snapshot
Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data
inferredcites →https://doi.org/10.1007/s00335-015-9589-4openalex-snapshot
Mouse Genome Informatics (MGI): reflecting on 25 years
inferredcites →https://doi.org/10.1016/j.ajhg.2015.05.020openalex-snapshot
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease
inferredcites →https://doi.org/10.1016/j.ajhg.2016.07.005openalex-snapshot
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease
inferredcites →https://doi.org/10.1016/j.jbi.2010.03.002openalex-snapshot
Evolution of the Sequence Ontology terms and relationships
inferredcites →https://doi.org/10.1016/s0140-6736(14)61705-0openalex-snapshot
Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data
inferredcites →https://doi.org/10.1038/gim.2015.137openalex-snapshot
Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency
inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot
Analysis of protein-coding genetic variation in 60,706 humans
inferredcites →https://doi.org/10.1038/nbt1346openalex-snapshot
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
inferredcites →https://doi.org/10.1038/nrg2897openalex-snapshot
Phenomics: the next challenge
inferredcites →https://doi.org/10.1056/nejmsr1406261openalex-snapshot
ClinGen — The Clinical Genome Resource
inferredcites →https://doi.org/10.1073/pnas.0910200107openalex-snapshot
Systematic discovery of nonobvious human disease models through orthologous phenotypes
inferredcites →https://doi.org/10.1093/database/bar066openalex-snapshot
The mouse-human anatomy ontology mapping project
inferredcites →https://doi.org/10.1093/database/bat025openalex-snapshot
PhenoDigm: analyzing curated annotations to associate animal models with human diseases
inferredcites →https://doi.org/10.1093/database/bau075openalex-snapshot
Standardized description of scientific evidence using the Evidence Ontology (ECO)
inferredcites →https://doi.org/10.1093/database/bav005openalex-snapshot
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora
inferredcites →https://doi.org/10.1093/nar/gkt1026openalex-snapshot
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
inferredcites →https://doi.org/10.1093/nar/gkt1076openalex-snapshot
Data, information, knowledge and principle: back to metabolism in KEGG
inferredcites →https://doi.org/10.1093/nar/gkt1159openalex-snapshot
Mouse Phenome Database
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/nar/gku1179openalex-snapshot
Gene Ontology Consortium: going forward
inferredcites →https://doi.org/10.1093/nar/gku1204openalex-snapshot
The BioGRID interaction database: 2015 update
inferredcites →https://doi.org/10.1093/nar/gku1205openalex-snapshot
OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders
inferredcites →https://doi.org/10.1093/nar/gku301openalex-snapshot
InterMine: extensive web services for modern biology
inferredcites →https://doi.org/10.1093/nar/gkv1046openalex-snapshot
FlyBase: establishing a Gene Group resource for Drosophila melanogaster
inferredcites →https://doi.org/10.1093/nar/gkv1194openalex-snapshot
PANTHER version 10: expanded protein families and functions, and analysis tools
inferredcites →https://doi.org/10.1093/nar/gkv1208openalex-snapshot
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine
inferredcites →https://doi.org/10.1093/nar/gkv1217openalex-snapshot
WormBase 2016: expanding to enable helminth genomic research
inferredcites →https://doi.org/10.1093/nar/gkv1222openalex-snapshot
ClinVar: public archive of interpretations of clinically relevant variants
inferredcites →https://doi.org/10.1093/nar/gkw838openalex-snapshot
The Comparative Toxicogenomics Database: update 2017
inferredcites →https://doi.org/10.1101/048843openalex-snapshot
k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction
inferredcites →https://doi.org/10.1101/gr.160325.113openalex-snapshot
Improved exome prioritization of disease genes through cross-species phenotype comparison
inferredcites →https://doi.org/10.1109/tvcg.2011.185openalex-snapshot
D³ Data-Driven Documents
inferredcites →https://doi.org/10.1126/science.1070534openalex-snapshot
Maneuvering in the Complex Path from Genotype to Phenotype
inferredcites →https://doi.org/10.1126/scitranslmed.3009262openalex-snapshot
Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome
inferredcites →https://doi.org/10.1186/1471-2105-14-203openalex-snapshot
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs
inferredcites →https://doi.org/10.1186/2041-1480-5-21openalex-snapshot
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
inferredcites →https://doi.org/10.1186/gb-2005-6-5-r46openalex-snapshot
Relations in biomedical ontologies
inferredcites →https://doi.org/10.1186/gb-2010-11-1-r2openalex-snapshot
Integrating phenotype ontologies across multiple species
inferredcites →https://doi.org/10.1186/s12859-015-0559-3openalex-snapshot
KaBOB: ontology-based semantic integration of biomedical databases
inferredcites →https://doi.org/10.1186/s13059-016-0953-9openalex-snapshot
High-performance web services for querying gene and variant annotation
inferredcites →https://doi.org/10.1186/s13326-015-0009-1openalex-snapshot
Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens
inferredcites →https://doi.org/10.1186/s13326-016-0067-zopenalex-snapshot
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
inferredcites →https://doi.org/10.1186/s13326-016-0088-7openalex-snapshot
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
inferredcites →https://doi.org/10.12688/f1000research.2-30.v1openalex-snapshot
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research
inferredcites →https://doi.org/10.12688/f1000research.2-30.v2openalex-snapshot
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research
inferredcites →https://doi.org/10.1371/journal.pbio.1000247openalex-snapshot
Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation
inferredcites →https://doi.org/10.1371/journal.pone.0154556openalex-snapshot
The Ontology for Biomedical Investigations
inferredcites →https://doi.org/10.1534/genetics.116.188870openalex-snapshot
Navigating the Phenotype Frontier: The Monarch Initiative
inferredcites →https://doi.org/10.5281/zenodo.610288openalex-snapshot
10 Simple Rules For Design, Provision, And Reuse Of Identifiers For Web-Based Life Science Data
inferredcites →https://doi.org/10.6083/m4z60n1wopenalex-snapshot
Comparative analysis of semantic similarity and gene orthology tools for identification of gene candidates for human diseases

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.ajhg.2017.04.010openalex-snapshot
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome
inferred← citeshttps://doi.org/10.1038/s41559-020-1167-9openalex-snapshot
Publisher Correction: Open Science principles for accelerating trait-based science across the Tree of Life
inferred← citeshttps://doi.org/10.20868/upm.thesis.71764openalex-snapshot
Creation of Networks for the Analysis of Disease Similarities
inferred← citeshttps://doi.org/10.3389/fpubh.2022.902123openalex-snapshot
SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19
inferred← citeshttps://doi.org/10.3410/f.734199035.793552161openalex-snapshot
Faculty Opinions recommendation of Classification, ontology, and precision medicine.
inferred← citeshttps://doi.org/10.3410/f.734944792.793567131openalex-snapshot
Faculty Opinions recommendation of Data lakes, clouds, and commons: A review of platforms for analyzing and sharing genomic data.
inferred← citeshttps://doi.org/10.3410/f.736064114.793562214openalex-snapshot
Faculty Opinions recommendation of A genetics-led approach defines the drug target landscape of 30 immune-related traits.
inferred← citeshttps://doi.org/10.3410/f.736064114.793562879openalex-snapshot
Faculty Opinions recommendation of A genetics-led approach defines the drug target landscape of 30 immune-related traits.
inferred← citeshttps://doi.org/10.3410/f.736064114.793565046openalex-snapshot
Faculty Opinions recommendation of A genetics-led approach defines the drug target landscape of 30 immune-related traits.
inferred← citeshttps://doi.org/10.5121/csit.2022.1209openalex-snapshot
Artificial Intelligence and Applications
inferred← citeshttps://doi.org/10.5121/csit.2022.120912openalex-snapshot
Automatized Bioinformatics Data Integration in a Hadoop-based Data Lake
inferred← citeshttps://doi.org/10.5121/ijdkp.2022.122openalex-snapshot
inferred← citeshttps://doi.org/10.5121/ijdkp.2022.123openalex-snapshot
inferred← citeshttps://doi.org/10.5121/ijdkp.2022.12401openalex-snapshot
Data integration in a Hadoop-based data lake: A bioinformatics case
inferred← citeshttps://doi.org/10.7554/elife.88229.1.sa0openalex-snapshot
Reviewer #3 (Public Review): Broad functional profiling of fission yeast proteins using phenomics and machine learning
inferred← citeshttps://doi.org/10.7554/elife.88229.1.sa3openalex-snapshot
eLife Assessment: Broad functional profiling of fission yeast proteins using phenomics and machine learning
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.