ResistVir-Db

The database ofResistVir European Project

Co-ordination of Research on Genetic Resistance to Plant Pathogenic

Viruses, and their Vectors, in European Crops

Work Package no 2Survey and database of European resources and centres of activity

Organization

Scientists andother 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 systemhttp://www.postgresql.org

• eZ publishopen source content management system and development frameworkhttp://ez.no

• Apacheopen source web serverhttp://www.apache.org

• Linux

An Object-Relational Database• User’s view :

– Tablesrows = instances of objects of the same typecolumns = fields for this type of datarows can be ordered by fields valuescolumns can be chosen and ordered

– Forms (pages)one instance per pageall available fields

– Linksa table row -> an instance forman instance form field -> another instance forman 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 languagesAcceptance criteria for another language :– Provide reference data and all interface terms– Second set of questionnaires

• Technical choices :– ISO 639 2-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, email, 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– http://www.resistvir-db.org/query?

id=rstvr:0000123&lang=ES

• Specific Identifier– Identify both data type and instance

– http://www.resistvir-db.org/query? id=GR0000067&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 DiagramObject current and new versions

Current andprivate new

versions

Dismissed

Consortiumsubmitted

Public submitted

Public validated

Consortium validated

Privatecurrentversion

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