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Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data

Nikolas Pontikos, Jing Yu, Ismail Moghul, Lucy Withington, Fiona Blanco-Kelly, Tom Vulliamy, Tsz Lun Ernest Wong, Cian Murphy, Valentina Cipriani, Alessia Fiorentino, Gavin Arno, Daniel Greene (+12 others)
2017 Bioinformatics  
We also acknowledge the Computer Science High Performance Cluster for providing us with the computing platform on which to analyse our data and host our webserver.  ...  DG carried out the SimReg analysis. JJ and VC helped with the Exomiser analysis. FBK, TV, VC, JY and GA provided the clinical patient data in HPO format.  ...  The molecular diagnosis of rare genetic diseases requires detailed clinical phenotypes and processing of large amounts of genetic data.  ... 
doi:10.1093/bioinformatics/btx147 pmid:28334266 fatcat:27kybrmkhfdijdua73n5ekek6a

Phenopolis: an open platform for harmonization and analysis of sequencing and phenotype data [article]

Nikolas Pontikos, Jing Yu, Fiona Blanco-Kelly, Tom Vulliamy, Tsz Lun Wong, Cian Murphy, Valentina Cipriani, Alessia Fiorentino, Gavin Arno, Daniel Greene, Julius OB Jacobsen, Tristan Clark (+8 others)
2016 bioRxiv   pre-print
Summary:Phenopolis is an open-source web server which provides an intuitive interface to genetic and phenotypic databases.  ...  The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare disease.  ...  We have integrated these approaches into Phenopolis, an interactive website built on genetic and phenotypic databases.  ... 
doi:10.1101/084582 fatcat:7scmbnlcmngb3k7jyl2g56e44q

The Human Phenotype Ontology in 2017

Sebastian Köhler, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske (+47 others)
2016 Nucleic Acids Research  
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described.  ...  algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition  ...  ACKNOWLEDGEMENTS The authors are grateful for the work of Miranda Jarnot and Tammy Powell at the National Library of Medicine for leading the work to import the HPO into the UMLS.  ... 
doi:10.1093/nar/gkw1039 pmid:27899602 pmcid:PMC5210535 fatcat:55iggw3tzvei7ispy3gu6rwqum

The Human Phenotype Ontology

PN Robinson, S Mundlos
2010 Clinical Genetics  
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described.  ...  algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition  ...  ACKNOWLEDGEMENTS The authors are grateful for the work of Miranda Jarnot and Tammy Powell at the National Library of Medicine for leading the work to import the HPO into the UMLS.  ... 
doi:10.1111/j.1399-0004.2010.01436.x pmid:20412080 fatcat:ltjtumlbpnfqdkp6vjahbzu35u

An overview of graph databases and their applications in the biomedical domain

Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás
2021 Database: The Journal of Biological Databases and Curation  
, exploration and analysis facilities.  ...  Because of the interconnected nature of its data, the biomedical domain has been one of the early adopters of graph databases, enabling more natural representation models and better data integration workflows  ...  models to graphs Pheno4J (75) https://github.com/phenopolis/pheno4j Java library to load patient genetic variants and phenotype data into Neo4j Recon2Neo4j (76) https://github.com/ibalaur/Recon2Neo4j  ... 
doi:10.1093/database/baab026 pmid:34003247 pmcid:PMC8130509 fatcat:xku5npedwzgs3ayzsuvz6iattq

PhenPath: a tool for characterizing biological functions underlying different phenotypes

Giulia Babbi, Pier Luigi Martelli, Rita Casadio
2019 BMC Genomics  
Furthermore, 58.8 and 77.8% of HPO phenotypes are also enriched for KEGG and Reactome pathways, respectively.  ...  Phenotypes are then associated with biological functions and pathways by means of NET-GE, a network-based method for functional enrichment of sets of genes.  ...  About this supplement This article has been published as part of BMC Genomics Volume 20 Supplement 8, 2019: Proceedings of VarI-COSI 2018: identification and annotation of genetic variants in the context  ... 
doi:10.1186/s12864-019-5868-x pmid:31307376 pmcid:PMC6631446 fatcat:tn7yypcvfzbmdfwfeibttwznxq

Methods for Determining the Genetic Causes of Rare Diseases

Daniel Greene, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Ernest Turro, Sylvia Richardson, Willem Ouwehand
2018
This thesis presents research into statistical and computational methods for determining the genetic causes of rare diseases.  ...  I developed a suite of software packages dubbed 'ontologyX' in order to simplify analysis and visualisation of such ontologically encoded data, and enable them to be incorporated into complex analysis  ...  "Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data". Bioinformatics.  ... 
doi:10.17863/cam.17443 fatcat:edfiw335lrecxefa3inveewosq