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

2019 Nucleic Acids Research  
The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search.  ...  Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.  ...  ACKNOWLEDGEMENTS We would like to thank the many people who have contributed to the improvements and updates we have reported here, including (but not limited to) Donna Maglott, Anne Pariser and Janine  ... 
doi:10.1093/nar/gkz997 pmid:31701156 pmcid:PMC7056945 fatcat:tramusfgz5eufn2aguuzzasafi

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

Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J.P. Gourdine (+14 others)
2016 Nucleic Acids Research  
The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to se-mantically integrate genotype-phenotype data from many species and sources in order to support precision  ...  Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.  ...  ACKNOWLEDGEMENTS We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1093/nar/gkw1128 pmid:27899636 pmcid:PMC5210586 fatcat:tbsgmbgu4vfmpiwwsenemxj2cm

The Monarch Initiative: Insights across species reveal human disease mechanisms [article]

Christopher Mungall, Julie McMurry, Sebastian Koehler, James Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, TOM CONLIN, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine (+14 others)
2016 bioRxiv   pre-print
The Monarch Initiative (https://monarchinitiative.org) is an international consortium dedicated to providing computational tools that leverage a computational representation of phenotypic data for genotype-phenotype  ...  analysis, genomic diagnostics, and precision medicine on the basis of a large-scale platform of multimodal data that is deeply integrated across species and covering broad areas of disease.  ...  Acknowledgments We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1101/055756 fatcat:26ov5gydkvgmxekc5z7yvcqzly

Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues

Sabina Gainotti, Deborah Mascalzoni, Virginie Bros-Facer, Carlo Petrini, Giovanna Floridia, Marco Roos, Marco Salvatore, Domenica Taruscio
2018 International Journal of Environmental Research and Public Health  
The contribution of patients to collecting and coding data comprehensively is critical for efficient use of data downstream of data collection.  ...  In-depth analysis of the genotype through next generation sequencing, together with a standardized in-depth phenotype description and sophisticated high-throughput approaches, have been applied as diagnostic  ...  We thank the RD-Connect  ... 
doi:10.3390/ijerph15102072 pmid:30248891 pmcid:PMC6210164 fatcat:uhjpb4pm25h4hbrtsto6o3lvdu

A Baseline Measurement for Endpoint Consistency Across Zebrafish Laboratories

Anne E Thessen, Melissa A Haendel, Lisa Truong, David Reif, Kristen Ryan, Jon Hamm, Stefan Scholz, Nils Klüver
2020 Zenodo  
This poses a problem for integrating and comparing data across labs, which could support more robust corroboration in the confidence of results from toxicological assessments.  ...  The free text results included 1748 terms which were mapped to 48 traits from the Zebrafish Phenotype Ontology (ZP) for comparison.  ...  The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nuc Acids Res, https://doi.org/10.1093/nar/gkz997 • Tice et al 2013.  ... 
doi:10.5281/zenodo.3713388 fatcat:hkshdnschbetray3cmcxv5dpte

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

Keywan Hassani-Pak, Christopher Rawlings
2017 Journal of Integrative Bioinformatics  
AbstractGenetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden.  ...  Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological  ...  The Monarch Initiative [67] is an outstanding example of how RDF and semantic web technolgies can be harnessed to build analytical tools that connect genotype to phenotype across species.  ... 
doi:10.1515/jib-2016-0002 pmid:28609292 pmcid:PMC6042805 fatcat:5n6hsndt5fecpkolgctalg4oca

Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice

Molly A Bogue, Stephen C Grubb, David O Walton, Vivek M Philip, Georgi Kolishovski, Tim Stearns, Matthew H Dunn, Daniel A Skelly, Beena Kadakkuzha, Gregg TeHennepe, Govindarajan Kunde-Ramamoorthy, Elissa J Chesler
2017 Nucleic Acids Research  
The resource has been expanded to include the QTL Archive and other primary phenotype data from mapping crosses as well as advanced high-diversity mouse populations including the Collaborative Cross and  ...  Most data in MPD are from inbreds and other reproducible strains such that the data are cumulative over time and across laboratories.  ...  Further, phenotypic abnormalities have been accessed and integrated into analyses by the Monarch Initiative which aims to integrate, align, and re-distribute cross-species phenotype data (7) .  ... 
doi:10.1093/nar/gkx1082 pmid:29136208 pmcid:PMC5753241 fatcat:kzcgzwce7bdxhbyxwwdyiq5wpe

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery

2019 Database: The Journal of Biological Databases and Curation  
Ontology (HPO), and model organism ontologies such as Mammalian Phenotype Ontology (MP) in the context of the Monarch Initiative.  ...  Diagnosis of rare diseases by computational cross-species comparison of genotype-phenotype data has been facilitated by leveraging ontological representations of clinical phenotypes, using Human Phenotype  ...  Acknowledgement We would like to thank our colleagues from the Monarch Initiative for comments and suggestions, KidsFirst (U2CHL138346) and Undiagnosed Disease Networks Metabolomics (U01-TR001395-02) for  ... 
doi:10.1093/database/baz114 pmid:31735951 pmcid:PMC6859258 fatcat:tg4c755iuzb35ct5be42k3xnp4

Knowledge Representation and Management: Interest in New Solutions for Ontology Curation

Ferdinand Dhombres, Jean Charlet, Section Editors for the IMIA Yearbook Section on Knowledge Representation and Management
2021 IMIA Yearbook of Medical Informatics  
As in 2019, representations serve a great variety of applications across many medical domains, with actionable results and now with growing adhesion to the open science initiative.  ...  Objective: To select, present and summarize some of the best papers in the field of Knowledge Representation and Management (KRM) published in 2020.  ...  Acknowledgements We would like to acknowledge the support of Lina Soualmia, Fleur Mougin, Adrien Ugon, Martina Hutter, and the whole IMIA Yearbook Editorial Committee as well as the numerous reviewers  ... 
doi:10.1055/s-0041-1726508 pmid:34479390 fatcat:qkgdqbj4irhcrihnhms362igkm

A Common Dialect for Infrastructure and Services in Translator

Melissa Haendel, Julie McMurry, Anne Thessen, Chris Bizon, Nomi Harris, Chris Mungall
2019 Zenodo  
Next-generation Shared Translator Services will integrate features of ROBOKOP [3], Monarch [4], BioLink [5], and the reasoner APIs to remove integration barriers.  ...  be developed with community buy-in to ensure an effective collaborative environment, and drive consortium-wide consensus on the other components.  ...  and human genotype-phenotype data using semantic technologies.  ... 
doi:10.5281/zenodo.3546914 fatcat:uzgj6bckgbdyxb43a4yneu3kcm

International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases

Kym M. Boycott, Ana Rath, Jessica X. Chong, Taila Hartley, Fowzan S. Alkuraya, Gareth Baynam, Anthony J. Brookes, Michael Brudno, Angel Carracedo, Johan T. den Dunnen, Stephanie O.M. Dyke, Xavier Estivill (+28 others)
2017 American Journal of Human Genetics  
Acknowledgments We thank the present and former staff of the IRDiRC Scientific Secretariat, Ségolène Aymé, Lilian Lau, Anneliene Jonker, Antonia Mills, Barbara Cagniard, and members of the scientific committees  ...  We also thank the former chairs of the IRDiRC Therapies Scientific Committee (Yann Le Cam and Josep Torrent i Farnell) for helpful discussions. We thank Rachel Thompson  ...  The Monarch Initiative has been working in this realm since 2009 and acts as an integrative data and analytic platform that connects phenotypes and genotypes across species.  ... 
doi:10.1016/j.ajhg.2017.04.003 pmid:28475856 pmcid:PMC5420351 fatcat:q4rcjzhz6ff4hmbc66u4u62s3y

EpiGraphDB: a database and data mining platform for health data science

Yi Liu, Benjamin Elsworth, Pau Erola, Valeriia Haberland, Gibran Hemani, Matt Lyon, Jie Zheng, Oliver Lloyd, Marina Vabistsevits, Tom R Gaunt
2020 Bioinformatics  
Results We developed EpiGraphDB (https://epigraphdb.org/), a graph database containing an array of different biomedical and epidemiological relationships and an analytical platform to support their use  ...  These opportunities are paralleled by a growing need for data integration, curation and mining to increase research efficiency, reduce mis-inference and ensure reproducible research.  ...  open nature of the platform enables users to easily work with Hetionet in parallel with EpiGraphDB. https://monarchinitiative.org/) is focused on the integration of genotypic and phenotypic data across  ... 
doi:10.1093/bioinformatics/btaa961 pmid:33165574 pmcid:PMC8189674 fatcat:vyx3sxz635d6vjwc43y34murv4

Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions

Shadia Zaman, Sirarat Sarntivijai, Darrell R Abernethy
2017 Gene Regulation and Systems Biology  
This program involves integrating data acquired during preclinical studies and clinical trials within pharmaceutical company development programs that they have agreed to put in the public domain and in  ...  The PredicTox effort is leveraging the experience gathered from these early initiatives to develop an infrastructure that allows evaluation of the hypothesis that having a mechanistic understanding underlying  ...  The Monarch Initiative The Monarch Initiative (https://monarchinitiative.org/) was developed to integrate data acquired from different species to discover new genotype-phenotype relationships for both  ... 
doi:10.1177/1177625017696075 pmid:28469412 pmcid:PMC5398297 fatcat:tioq5cn4rjaxzm22nf5s3246om

Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes

Eleanor G. Seaby, Heidi L. Rehm, Anne O'Donnell-Luria
2021 Frontiers in Genetics  
data, and gene-to-patient methods.  ...  We discuss the importance of data sharing, phenotype-driven approaches, patient-led approaches, utilization of large-scale genomic sequencing projects, constraint-based methods, integration of multi-omics  ...  ACKNOWLEDGMENTS The authors would like to thank the members of the Centers for Mendelian Genomics and the Genome Aggregation Database teams for helpful discussions in the development of approaches to novel  ... 
doi:10.3389/fgene.2021.674295 fatcat:4dwwb6iswvgqpczeiijopg7qm4

EpiGraphDB: a database and data mining platform for health data science [article]

Yi Liu, Benjamin L Elsworth, Pau Erola, Valeriia Haberland, Gibran Hemani, Matthew S Lyon, Jie Zheng, Tom R Gaunt
2020 biorxiv/medrxiv   pre-print
Results: We developed EpiGraphDB (https://epigraphdb.org/), a graph database containing an array of different biomedical and epidemiological relationships and an analytical platform to sup-port their use  ...  These opportunities are paralleled by a growing need for data integration, curation and mining to increase research efficiency, reduce mis-inference and ensure reproducible research.  ...  The Monarch Initiative (Mungall et al., 2017) (https://monarchi nitiative.org/) is focussed on the integration of genotypic and phenotypic data across species with the aim of identifying related phenotypes  ... 
doi:10.1101/2020.08.01.230193 fatcat:bcnkxoa2njdz3ckmbquwxz7cxe
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