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; Julius O B Jacobsen; Tristan Clark; David S Gregory; Andrea M Nemeth; Stephanie Halford; Chris F Inglehearn; Susan Downes; Graeme C Black; Andrew R Webster; Alison J Hardcastle; UKIRDC; Vincent Plagnol

doi:10.1093/bioinformatics/btx147

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

Bioinformatics. 2017 Aug 1;33(15):2421-2423. doi: 10.1093/bioinformatics/btx147.

Authors

Nikolas Pontikos^{1

2

3}, Jing Yu⁴, Ismail Moghul⁵, Lucy Withington⁶, Fiona Blanco-Kelly^{2

3}, Tom Vulliamy⁷, Tsz Lun Ernest Wong⁷, Cian Murphy^{1

8}, Valentina Cipriani^{1

2

3}, Alessia Fiorentino², Gavin Arno^{2

3}, Daniel Greene^{9

10}, Julius O B Jacobsen¹¹, Tristan Clark¹², David S Gregory¹², Andrea M Nemeth⁴, Stephanie Halford¹³, Chris F Inglehearn¹⁴, Susan Downes¹⁵, Graeme C Black¹⁶, Andrew R Webster^{2

3}, Alison J Hardcastle²; UKIRDC; Vincent Plagnol¹

Affiliations

¹ UCL Genetics Institute, University College London, London WC1E 6BT, UK.
² Institute of Ophthalmology, University College London, London EC1V 9EL, UK.
³ Moorfields Eye Hospital, London EC1V 2PD, UK.
⁴ Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
⁵ UCL Cancer Institute, University College London, London WC1E 6DD, UK.
⁶ RP Fighting Blindness, PO Box 350, Buckingham, MK18 1GZ, UK.
⁷ Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London E1 2AT, UK.
⁸ Warwick Medical School, The University of Warwick, Coventry CV4 7AL, UK.
⁹ Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.
¹⁰ Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK.
¹¹ Barts and The London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, John Vane Building, Charterhouse Square, London EC1M 6BQ, UK.
¹² Computer Science Department, University College London, London WC1E 6BT, UK.
¹³ Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
¹⁴ Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St James's University Hospital, Leeds LS9 7TF, UK.
¹⁵ Oxford Eye Hospital, John Radcliffe Hospital, Oxford OX3 9DU, UK.
¹⁶ Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK.

PMID: 28334266
DOI: 10.1093/bioinformatics/btx147

Abstract

Summary: Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritization 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 genetic diseases.

Availability and implementation: A demo of the website is available at https://phenopolis.github.io . If you wish to install a local copy, source code and installation instruction are available at https://github.com/phenopolis . The software is implemented using Python, MongoDB, HTML/Javascript and various bash shell scripts.

Contact: n.pontikos@ucl.ac.uk.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Computational Biology / methods*
Databases, Factual
Genetic Diseases, Inborn / diagnosis
Genetic Diseases, Inborn / genetics*
Genetic Diseases, Inborn / pathology
Humans
Phenotype*
Rare Diseases / diagnosis
Rare Diseases / genetics
Rare Diseases / pathology
Software*