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

View ORCID ProfileNikolas 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, David S Gregory, Andrea Nemeth, Stephanie Halford, Susan Downes, Graeme C Black, Andrew R Webster, Alison Hardcastle, Vincent Plagnol
doi: https://doi.org/10.1101/084582
Nikolas Pontikos
1UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
2UCL Genetics Institute, University College London, London WC1E 6BT, UK.
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  • ORCID record for Nikolas Pontikos
Jing Yu
3Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford, United Kingdom, OX3 9DU, UK.
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Fiona Blanco-Kelly
1UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
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Tom Vulliamy
4Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
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Tsz Lun Wong
4Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
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Cian Murphy
2UCL Genetics Institute, University College London, London WC1E 6BT, UK.
8Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK.
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Valentina Cipriani
1UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
2UCL Genetics Institute, University College London, London WC1E 6BT, UK.
9Moorfields Eye Hospital, London EC1V 2PD, UK
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Alessia Fiorentino
1UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
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Gavin Arno
1UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
9Moorfields Eye Hospital, London EC1V 2PD, UK
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Daniel Greene
6Department of Haematology, University of Cambridge, NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.
7Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK.
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Julius OB Jacobsen
12William Harvey Research Institute, Barts and The London, Queen Mary's School of Medicine and Dentistry, John Vane Building, Charterhouse Square, London, EC1M 6BQ.
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Tristan Clark
5Computer Science Department, University College London, Gower Street, London, WC1E 6BT, UK.
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David S Gregory
5Computer Science Department, University College London, Gower Street, London, WC1E 6BT, UK.
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Andrea Nemeth
3Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford, United Kingdom, OX3 9DU, UK.
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Stephanie Halford
10Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences University of Oxford, Level 6 West Wing, John Radcliffe Hospital, Oxford OX3 9DU UK.
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Susan Downes
11Oxford Eye Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
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Graeme C Black
13Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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Andrew R Webster
1UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
9Moorfields Eye Hospital, London EC1V 2PD, UK
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Alison Hardcastle
1UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
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Vincent Plagnol
2UCL Genetics Institute, University College London, London WC1E 6BT, UK.
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Abstract

Summary Phenopolis is an open-source web server which provides an intuitive interface to genetic and phenotypic databases. It integrates analysis tools which include variant filtering and gene prioritisation based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare disease.

Availability and Implementation A demo of the website is available at http://phenopolis.github.io (username: demo, password: demo123). If you wish to install a local copy, souce code and installation instruction are available at https://github.com/pontikos/phenopolis. The software is implemented using Python, MongoDB, HTML/Javascript and various bash shell scripts.

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

Footnotes

  • 14 Centre for Ophthalmology & Vision Sciences, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester Manchester, UK.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 31, 2016.
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Phenopolis: an open platform for harmonization and analysis of sequencing and phenotype data
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, David S Gregory, Andrea Nemeth, Stephanie Halford, Susan Downes, Graeme C Black, Andrew R Webster, Alison Hardcastle, Vincent Plagnol
bioRxiv 084582; doi: https://doi.org/10.1101/084582
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Phenopolis: an open platform for harmonization and analysis of sequencing and phenotype data
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, David S Gregory, Andrea Nemeth, Stephanie Halford, Susan Downes, Graeme C Black, Andrew R Webster, Alison Hardcastle, Vincent Plagnol
bioRxiv 084582; doi: https://doi.org/10.1101/084582

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