Download ppt - ResistVir

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
Computer staff
• Steering committee
• DB development team
• WP2 participants
• Quadrate DM support
• Consortium members
• Consortium members
• Professional users
• Others
• Public users
Technical choices
• PostgreSQL
open source object-relational database
management system
http://www.postgresql.org
• eZ publish
open source content management system and
development framework
http://ez.no
• Apache
open source web server
http://www.apache.org
• 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 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 of Activity
Centres (1)
– 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 ?
•
•
•
•
•
Plant resources
Diagnosis services
Biotechnological resources
Agrochemical resources
Agricultural resources
Tools
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 Diagram
Object current and new versions
Consortium
submitted
Private
current
version
Current and
private new
versions
Consortium validated
Dismissed
Public submitted
Public validated
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