Appendix 81. From OPENFLU to OPENFMD. Open Session of the EuFMD: 2012, Jerez de la Frontera, Spain 1. Conclusions and recommendations
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1 From OPENFLU to OPENFMD a resource for automatic and curated nomenclature and tools for the FMD community Filip Claes, Philippe Le Mercier, Dmitry Kuznetsov, Robin Liechti, Anne Gleizes, Ioannis Xenarios, Gwenaelle Dauphin Conclusions and recommendations Complete collection of FMDV (genetic) data is necessary for: - Surveillance of disease evolutionary trends - Scientific analysis - Infer gaps in epidemiological data OPENFLU-EMPRESi experience may be useful for FMDV community OPENFMD might become a central portal for the community to store and share FMDV data - and move towards harmonized nomenclature OpenFLU - an open database of influenza data Contains only public data All data are accessible for browsing All users are welcome - standard free web registration is needed to upload and manage own or laboratory data OpenFLU: an adequate data model for Influenza virus Sequences grouped per isolates Isolates accompanied by a comprehensive record of data for epidemiology: - Minimal data required: year, host species, country - Support for much more data: vaccination, patient status, resistance to antibiotics, animal domestication status, etc Influenza-specific genetic knowledge and algorithms - Translation to viral proteins - Key mutations OpenFLU: data import/export OpenFLU: easy to find your isolate Import: - GENBANK - USER SUBMISSIONS daily CURATION! GenBank OpenFlu Export: GenBank, data as a structured comment Dynamic fields showing an estimation 1
2 OpenFLU: more search criteria OpenFlu: analysis of the data found Multiple sequence alignment, BLAST, phylogenetic tree, SSM OpenFLU example: SSM for H7N3 OpenFLU example: SSM for H7N3 South American Eurasian A/Mexico/InDRE7218/ North American 2012 A/chicken/Jalisco/CPA1/ Each sequence is a point on the map Similar sequences are close to each other Zoom into a geo region also selects and highlights corresponding sequences on SSM Epidemiological information EMPRES-i Genetic Module Linking epi and genetics On outbreaks: date, location, species, On surveillance Generated by field teams the day of the event, compiled and reported by vet services (epi unit) within a short time Stored in databases: local, national, regional, global 2
3 Virus information How does it work Generated by labs: - Detection of influenza virus, subtyping, RNA sequencing - Can take a few days (more) Sequence information deposited in a database - Genbank: universal repository - Other genetic databases, eg influenza specialized 3
4 OpenFMD: the project A public database that will - Store FMDV sequences and epidemiological data from various sources Import from public repositories (like GenBank) Direct user submission - Verify data consistency (e.g. control of user-submitted serotype by sequence similarity vs. collections of reference strain sequences - Eventually manually curate records - Analyse data using tools like phylo-trees or SSM - Serve all the curated and organized data together with analysis results back to the FMDV community - Towards a harmonized nomenclature (with parallel current names) OpenFMD: a live DB OpenFMD: a sandbox trial To be daily synchronized with all data sources GenBank (EFetch) allows data export in computer-friendly form (XML) suitable for daily incremental updates Precision of epidemiological data varies, but GenBank team collects and merges author s updates Authors might also correct/update data directly Already >4000 (full and partial) sequences available in GenBank FMDV specific data model Simplified partial GenBank import 257 full genome sequences All 7 serotypes 2 un-typed sequences - one is HKN/2002 SEROTYPE SEROSUBTYPE CNT A 72 Asia 1 41 C 1,3,4,5 17 O 113 SAT 1 10 SAT 2 5 SAT 3 5 -N/A- 2 OpenFMD: SSM try-out Color-coded by the available from GenBank serotype data N/A A Asia 1 C 1,3,4,5 O SAT 1,2,3 Serotype SAT 1,2,3 Serotypes A and C HKN/200 2 Serotype Asia 1 OpenFMD: a closer look on the map for the type O Clusters (topotypes) No more precise annotation in the GenBank records No serotype for HKN/2002 (pink) The serotype can be inferred from its neighbors, i.e. O Serotype O The phylogenetic tree from Samuel and Knowles, J Gen Virol 2001, vol. 82 no. 3 ( ) 4
5 How can it work? DBASE A DBASE (P)B DBASE C Genetic info Genetic info Genetic info OpenFMD: HNK/2002 serotype? Indeed, no serotype info in the GenBank record Transfer public data Expert inputs OPENFMD Interface - Bioinformatic tools - Curation Science Comm. Transfer public data EMPRES-i Epi info OpenFMD: HNK/2002 serotype? Conclusions and recommendations Complete collection of FMDV (genetic) data is necessary for: - Surveillance of disease evolutionary trends - Scientific analysis - Infer gaps in epidemiological data OPENFLU-EMPRESi experience may be useful for FMDV community OPENFMD might become a central portal for the community to store and share FMDV data Screenshots from Biochem Biophys Res Commun Oct 8;323(1):
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