ResistVir-Db The database of ResistVir European Project Co-ordination of Research on Genetic Resistance to Plant Pathogenic Viruses, and their Vectors, in European Crops Work Package no 2 Survey and database of European resources and centres of activity

Organization Scientists and other DB users Steering committee WP2 participants Consortium members Professional users Public users Computer staff DB development team Quadrate DM support Consortium members Others

Technical choices PostgreSQL open source object-relational database management system eZ publish open source content management system and development framework Apache open source web server Linux

An Object-Relational Database User’s view : –Tables rows = instances of objects of the same type columns = fields for this type of data rows can be ordered by fields values columns can be chosen and ordered –Forms (pages) one instance per page all available fields –Links a table row -> an instance form an instance form field -> another instance form an instance form URL field -> a Web page

Database Web Query Interface (1) Open a session –As anonymous –As Consortium member Create a set of requests –Single criterion request Choose type of data Choose criterion Define operator and values –Combination of 2 requests Choose 2 requests (same type of data) Choose operators –Query execution -> count of instances

Database Web Query Interface (2) Display the set of instances corresponding to a request –Choose columns (or default columns) –Choose instances order –Jump scrolling Export data (.csv) Display specific instance form Display links …

A Multilingual Database Default language : English –All reference data and interface terms in English –All questionnaires in English Other languages Acceptance criteria for another language : –Provide reference data and all interface terms –Second set of questionnaires Technical choices : –ISO letters language code –Encoding system : UTF-8

Which data ?References Main Reference Entities –Disease –Virus –Vector –Plant : species, populations, lines, … –Genetic resistance –Locus –QTL –Gene Some are also research topics

Which data ?Centres (1) Centres of Activity –Organization, Research Unit, …, Team –Dependency links –Description : acronym, full name, type of centre, address, postal code, city, country, phone, fax, , url –Staff (whole centre) : total, permanent, total scientists, total permanent scientists, PhD students –Staff (ResistVir fields) : total, permanent, total scientists, total permanent scientists, PhD students

Which data ?Centres (2) Centres of Activity –Persons –Studied viruses –Studied plants –Studied vectors –Studied diseases –Studied genetic resistances –Studied genes –Research topics –Know-how and technologies

Which data ?Research results Main research results Main published bibliographic references Thesis Other documents Patents

Which data ?Tools Plant resources Diagnosis services Biotechnological resources Agrochemical resources Agricultural resources

Links with ontologies ISO Codes (countries, languages, …) Structured controlled vocabularies –Our own data … –… linked whenever possible with existing ontologies databases (GO, TO, PO, taxon, …) When ontologies databases don’t exist today : –Simple reference tables –Creation of new ontologies ?

Identifiers General Identifier –Identify one instance whatever its type – id=rstvr: &lang=ES Specific Identifier –Identify both data type and instance – id=GR &lang=CA

Data Access Policy Public –Some instances will be hidden –Some fields will be hidden Consortium –Personal accounts with password (and term ?) –All (validated ?) instances –All fields Private Project –Consortium view + specific data DBA

Origin of Data Initial loading period –Questionnaires (spreadsheet.sxc,.xls,.csv) –Specific files from existing databases –Batch loading Then –Questionnaires with batch loading –Web Update Interface (?) only by authorized for update accounts only for data of each one’s organization

Data Validation Policy Restrictive policy –No data published without Committee agreement –An a priori control –Least update requires new validation Laxist policy –Data published under provider responsibility –An a fortiori control –Updated instances remain validated –Good practice agreement

State Transition Diagram Object current and new versions Current and private new versions Dismissed Consortium submitted Public submitted Public validated Consortium validated Private current version

Data Traceability Minimal level –Person and organization responsible for each instance –Creation and last update dates Increased traceability –Description of all state change events Maximal traceability –Record all consecutive versions of each instance