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Pheno4J: a gene to phenotype graph database

Sajid Mughal, View ORCID ProfileIsmail Moghul, View ORCID ProfileJing Yu, Tristan Clark, David S Gregory, View ORCID ProfileNikolas Pontikos
doi: https://doi.org/10.1101/142257
Sajid Mughal
1Globe View 10 High Timber Street London, EC4V 3PP, UK
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Ismail Moghul
2UCL Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
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Jing Yu
3Level 6, West Wing, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
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Tristan Clark
4Computer Science Department, University College London, Gower Street, London, WC1E 6BT, UK
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David S Gregory
4Computer Science Department, University College London, Gower Street, London, WC1E 6BT, UK
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Nikolas Pontikos
5UCL Genetics Institute, University College London, London WC1E 6BT, UK
6Institute of Ophthalmology, University College London, London EC1V 9EL, UK
7Moorfields Eye Hospital, London EC1V 2PD, UK
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Abstract

Summary Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation. We have also developed an accompanying webserver with end-points to facilitate querying of the database.

Availability and Implementation The Java code and python code is available at https://github.com/phenopolis/pheno4i

Contact n.pontikos{at}ucl.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 25, 2017.
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Pheno4J: a gene to phenotype graph database
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
bioRxiv 142257; doi: https://doi.org/10.1101/142257
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Pheno4J: a gene to phenotype graph database
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
bioRxiv 142257; doi: https://doi.org/10.1101/142257

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