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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 ( integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search.  ...  Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies  ...  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


C. Titus Brown, Amanda Charbonneau, Owen White
2019 Figshare  
July 2019 Assessment Report for the Common Fund Data Ecosystem.  ...  Many members of the CFDE tech team participated in data gathering; in particular we would like to cite Lee Liming for his review of the report and assistance with data collection, as well as Theresa Hodges  ...  Acknowledgements We are grateful to Brian Osbourne and Brian O'Connor for their assistance in preparation of this document.  ... 
doi:10.6084/m9.figshare.9588374 fatcat:o6kr3ku2eff2tlnv6uep7eotbm

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

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.  ...  Toxicology as a discipline is moving toward increased standardization of methods for testing and reporting end points in model organisms for improved, cross-laboratory data integration.  ...  The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nuc Acids Res, • Tice et al 2013.  ... 
doi:10.5281/zenodo.3713388 fatcat:hkshdnschbetray3cmcxv5dpte

A Common Dialect for Infrastructure and Services in Translator

Melissa Haendel, Julie McMurry, Anne Thessen, Chris Bizon, Nomi Harris, Chris Mungall
2019 Zenodo  
be developed with community buy-in to ensure an effective collaborative environment, and drive consortium-wide consensus on the other components.  ...  Next-generation Shared Translator Services will integrate features of ROBOKOP [3], Monarch [4], BioLink [5], and the reasoner APIs to remove integration barriers.  ...  Mungall), a cross-species genotype-to-phenotype discovery consortium, and was also a multi-PI for the Orange team in the first phase of the NCATS Translator project (with Dr. Mungall).  ... 
doi:10.5281/zenodo.3546914 fatcat:uzgj6bckgbdyxb43a4yneu3kcm

Abstracts from the 2019 OAS Annual Meeting

The Ohio Academy of Science
2019 The Ohio journal of science  
Abstracts from the 2019 Ohio Academy of Science Annual Meeting  ...  Data were collected using the iNaturalist platform within the state from 2012 to 2018.  ...  This study will assess the effect of road salt on freshwater streams during the winter of 2018-2019 using similar sites and methodology as the initial study.  ... 
doi:10.18061/ojs.v119i1.6832 fatcat:orhiawvtpbdzrahia4zpftme6q

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

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 (, 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 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

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 (, 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. is focused on the integration of genotypic and phenotypic data across  ... 
doi:10.1093/bioinformatics/btaa961 pmid:33165574 pmcid:PMC8189674 fatcat:vyx3sxz635d6vjwc43y34murv4

Integration of Evidence across Human and Model Organism Studies: A Meeting Report

Rohan H C Palmer, Emma C Johnson, Hyejung Won, Renato Polimanti, Manav Kapoor, Apurva Chitre, Molly A Bogue, Chelsie E Benca-Bachman, Clarissa C Parker, Oana Ursu, Anurag Verma, Timothy Reynolds (+39 others)
2021 Genes, Brain and Behavior  
species and data types, (c) identify current tools and resources for integration of genetic, epigenetic, and phenotypic data, (d) discuss steps and impediment related to data integration, and (e) outline  ...  The meeting's objective was to discuss and evaluate better strategies to integrate genetic, epigenetic, and 'omics data across human and model organisms to achieve deeper mechanistic insight into SUDs.  ...  Continued research in integrative platforms will allow the examination of various use cases that will help develop an understanding of the difficulties and opportunities in data integration.  ... 
doi:10.1111/gbb.12738 pmid:33893716 fatcat:h2ozonod25ax5ksurweizt3d5y

The Global Museum: natural history collections and the future of evolutionary science and public education

Freek T. Bakker, Alexandre Antonelli, Julia A. Clarke, Joseph A. Cook, Scott V. Edwards, Per G.P. Ericson, Søren Faurby, Nuno Ferrand, Magnus Gelang, Rosemary G. Gillespie, Martin Irestedt, Kennet Lundin (+9 others)
2020 PeerJ  
We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth.  ...  insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life.  ...  We are very thankful to Karin Hårding, Gunnar Nyman, and Mattias Marklund for their continuous support and assistance in the program as GoCAS organizers.  ... 
doi:10.7717/peerj.8225 pmid:32025365 pmcid:PMC6993751 fatcat:aib5i2ihareuve46a46f2kpaiq

Report on 4 INFRAFRONTIER Annual Conferences

Asrar Ali Khan
2022 Zenodo  
Melissa Haendel, introduced the Monarch Initiative -a large-scale bioinformatics resource connecting genotypes and phenotypes from many species with the goal to aid genetic disease research and presented  ...  This conference boosted the sustainability of INFRAFRONTIER by providing an excellent opportunity to better align INFRAFRONTIER / IMPC platforms with current ageing and big data initiatives.  ... 
doi:10.5281/zenodo.6504913 fatcat:emxdpj6crjamvc6qhy4nrv5tn4

Bringing Big Data to Bear in Environmental Public Health: Challenges and Recommendations

Saskia Comess, Alexia Akbay, Melpomene Vasiliou, Ronald N. Hines, Lucas Joppa, Vasilis Vasiliou, Nicole Kleinstreuer
2020 Frontiers in Artificial Intelligence  
Leaders in the field were asked to prioritize challenges in incorporating big data in environmental public health research: inconsistent implementation of FAIR principles in data collection and sharing  ...  Understanding the role that the environment plays in influencing public health often involves collecting and studying large, complex data sets.  ...  The Monarch Initiative ( is one such collaboration to apply ontologies, or semantic descriptions, to disease phenotypes and enable intra-and inter-species comparisons and  ... 
doi:10.3389/frai.2020.00031 pmid:33184612 pmcid:PMC7654840 fatcat:xg3ev4uohfgmvf2vc4ejngmwh4

DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier

Maxat Kulmanov, Robert Hoehndorf, Casey S. Greene
2020 PLoS Computational Biology  
Both forward and reverse genetic screen are employed to identify the molecular mechanisms underlying phenotypes and disease, and these resulted in a large number of genotypephenotype association being  ...  Predicting the phenotypes resulting from molecular perturbations is one of the key challenges in genetics.  ...  Acknowledgments We acknowledge the use of computational resources from the KAUST Supercomputing Core Laboratory.  ... 
doi:10.1371/journal.pcbi.1008453 pmid:33206638 fatcat:c43pskgozvae5iflwqukglgcoe
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