Nikolas Pontikos1,2,3, Jing Yu4, Ismail Moghul5, Lucy Withington6, Fiona Blanco-Kelly2,3, Tom Vulliamy7, Tsz Lun Ernest Wong7, Cian Murphy1,8, Valentina Cipriani1,2,3, Alessia Fiorentino2, Gavin Arno2,3, Daniel Greene9,10, Julius O B Jacobsen11, Tristan Clark12, David S Gregory12, Andrea M Nemeth4, Stephanie Halford13, Chris F Inglehearn14, Susan Downes15, Graeme C Black16, Andrew R Webster2,3, Alison J Hardcastle2, Vincent Plagnol1. 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.
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.
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.
Authors: Vanita Berry; Alexander C W Ionides; Nikolas Pontikos; Ismail Moghul; Anthony T Moore; Michael E Cheetham; Michel Michaelides Journal: Eye (Lond) Date: 2018-05-01 Impact factor: 3.775
Authors: Petra Liskova; Lubica Dudakova; Cerys J Evans; Karla E Rojas Lopez; Nikolas Pontikos; Dimitra Athanasiou; Hodan Jama; Josef Sach; Pavlina Skalicka; Viktor Stranecky; Stanislav Kmoch; Caroline Thaung; Martin Filipec; Michael E Cheetham; Alice E Davidson; Stephen J Tuft; Alison J Hardcastle Journal: Am J Hum Genet Date: 2018-03-01 Impact factor: 11.025
Authors: Valentina Cipriani; Nikolas Pontikos; Gavin Arno; Panagiotis I Sergouniotis; Eva Lenassi; Penpitcha Thawong; Daniel Danis; Michel Michaelides; Andrew R Webster; Anthony T Moore; Peter N Robinson; Julius O B Jacobsen; Damian Smedley Journal: Genes (Basel) Date: 2020-04-23 Impact factor: 4.096
Authors: Alessia Fiorentino; Jing Yu; Gavin Arno; Nikolas Pontikos; Stephanie Halford; Suzanne Broadgate; Michel Michaelides; Keren J Carss; F Lucy Raymond; Michael E Cheetham; Andrew R Webster; Susan M Downes; Alison J Hardcastle Journal: Mol Vis Date: 2018-08-31 Impact factor: 2.367
Authors: E R Schiff; M Frampton; N Ben-Yosef; B E Avila; F Semplici; N Pontikos; S L Bloom; S A McCartney; R Vega; L B Lovat; E Wood; A Hart; E Israeli; D Crespi; M A Furman; S Mann; C D Murray; A W Segal; A P Levine Journal: Hum Genet Date: 2018-08-22 Impact factor: 4.132
Authors: Mathena Vinayaga-Pavan; Matthew Frampton; Nikolas Pontikos; Adam P Levine; Phillip J Smith; Jon G Jonasson; Einar S Björnsson; Anthony W Segal; Andrew M Smith Journal: Inflamm Bowel Dis Date: 2019-01-10 Impact factor: 5.325
Authors: Ana Rio-Machin; Tom Vulliamy; Nele Hug; Amanda Walne; Kiran Tawana; Shirleny Cardoso; Alicia Ellison; Nikolas Pontikos; Jun Wang; Hemanth Tummala; Ahad Fahad H Al Seraihi; Jenna Alnajar; Findlay Bewicke-Copley; Hannah Armes; Michael Barnett; Adrian Bloor; Csaba Bödör; David Bowen; Pierre Fenaux; Andrew Green; Andrew Hallahan; Henrik Hjorth-Hansen; Upal Hossain; Sally Killick; Sarah Lawson; Mark Layton; Alison M Male; Judith Marsh; Priyanka Mehta; Rogier Mous; Josep F Nomdedéu; Carolyn Owen; Jiri Pavlu; Elspeth M Payne; Rachel E Protheroe; Claude Preudhomme; Nuria Pujol-Moix; Aline Renneville; Nigel Russell; Anand Saggar; Gabriela Sciuccati; David Taussig; Cynthia L Toze; Anne Uyttebroeck; Peter Vandenberghe; Brigitte Schlegelberger; Tim Ripperger; Doris Steinemann; John Wu; Joanne Mason; Paula Page; Susanna Akiki; Kim Reay; Jamie D Cavenagh; Vincent Plagnol; Javier F Caceres; Jude Fitzgibbon; Inderjeet Dokal Journal: Nat Commun Date: 2020-02-25 Impact factor: 14.919