Transcript Training Workshop on Advanced Diagnosis and Surveillance

Options for Local Databases
Dr Ian Naumann,
Office of the Chief Plant Protection Officer
Pest Lists Workshop: Kuala Lumpur, Malaysia
August 2005
D E PA R T M E N T O F A G R I C U LT U R E , F I S H E R I E S A N D F O R E S T R Y
Overview
• Major development issues
• Pacific Islands Pest List Database
• Three Australian Databases:
– West Australian Department of Agriculture Insect
Collection Database
– Biolink
– KE Emu
• National Phytosanitary Database
– Cambodia, Lao PDR, Myanmar, Vietnam
Development issues - local databases
Data standards
– Collection data
– Scientific names
– Validation of identifications
– Data entry protocols
Software
– Which database package?
– Other functions, e.g. collection management,
issue of phytosanitary certificates
– Import and export of data
– Institutional / national/ regional choices
– Changes over time
– Access, security & intellectual property
Validation of pest records
•Huge task: many thousands of records
•Requires expert skills – entomology, plant pathology,
nematology, virology, weed science
•Possible if voucher specimen available, may be impossible if
no vouchers available for re-examination or re-testing
•Standard may vary depending on who has access to the
records
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Data entry and access protocols
To provide safeguards to the integrity of the system, above
and beyond those measures provided by the design of the
system.
•Training for staff who will have access to the system.
•Comprehensive user manual.
•Specify standards, especially where these are not
incorporated into the system, e.g. as pick lists.
•One person enters data; another person checks that data has
been correctly entered.
•Record the location of specimens and other material referred
to in the system, e.g. storage cabinet number.
•Record details if specimens loaned to other institution.
•Adequate curation of specimens and other material to ensure
remains in usable condition.
•Update data as required, e.g. as names change.
•Back up – preferably daily.
•Rules for deciding who has access to data and what may be
done with the data – may prefer several levels of
access.
•Update passwords regularly.
Overview
• Major development issues
• Pacific Pest List Database
• Three Australian Databases:
– West Australian Department of Agriculture Insect
Collection Database
– Biolink
– Ke Emu
• National Phytosanitary Database
– Cambodia, Lao PDR, Myanmar, Vietnam
Information system that:
• Records pest occurrences within a country
– Specimen-based
– Literature-based
• Records quarantine interceptions
• Provides pest lists for research and trade facilitation
• Is available to research staff, plant protection and
quarantine officers, senior managers
• Based on globally supported, inexpensive database
engine
Contact
South Pacific Commission, Fiji
[email protected]
Availability and cost
Freely available from SPS
Computing platform
Microsoft Windows/Windows 98/ NT/ 2000/XP
Database
Limitations
MS Access
2GB
140 000 records
Maximum users 255
Reports
By locality, host, pest or disease
Data import and export
capabilities
MS Access import/export capabilities
Users
16 Pacific Island countries
User manual
Yes
http://www.spc.int/pps/PLD_Workshop_Materials/P
LD_User_Manual.doc
Database model documentation
Yes
The PLD has three core tables:
1. Pests – a reference set of about 6000 common pests (or
diseases) of the Pacific region
2. Hosts – about 1000 of the main crops of the Pacific region
3. Occurrences – details of each time a pest is found.
Data Entry Screen for Pest Status Records
Pest Status Records – Pest Information Screen
http://www.spc.int/pps/the_plant_protection_service.htm
Overview
• Major development issues
• Pacific Pest List Database
• Three Australian Databases:
– West Australian Department of Agriculture Insect
Collection Database
– Biolink
– Ke Emu
• National Phytosanitary Database
– Cambodia, Lao PDR, Myanmar, Vietnam
Western Australian Department of Agriculture
Insect Collection Database
Contact
Mr Robert Emery, Department of Agriculture, Perth,
Australia
[email protected]
Availability and cost
Free
Database engine
Limitations
MS Access
2GB
140 000 records
Maximum users 255
Data import and export
capabilities
MS Access capabilities
Users
WA Agriculture
User manual
Yes
http://agspsrv34.agric.wa.gov.au/ento/icdb/icdb1.i
dc
Database model documentation
Yes
Data entry
Data entry
Data entry
Data entry
Searching
Search
results
Contact
Dr Steve Shattuck, CSIRO Entomology, Canberra,
Australia [email protected]
http://www.ento.csiro.au/biolink/software.html
Availability and cost
Free
Computing platform
Microsoft Windows and Apple Macintosh
Database Engine
Limitations
Microsoft SQL Server database management system
No
Data import and export
capabilities
Wizard
From tab-delimited files, Excel spreadsheets, Access.
Export to delimited text, XML, Excel, Word, Access,
RTF
Users
About 250 users in 65 countries
User manual
Yes
http://www.ento.csiro.au/biolink/software.html
Database model documentation
Yes
Contact
KE Software, Melbourne, Australia
http://www.kesoftware.com/emu/
Availability and cost
Initial cost and annual licence fee
Computing platform
MS Windows NT/2000/XP or Macintosh
Database Engine
Limitations
KE Texpress
None
Data import and export
capabilities
Import from most formats
Users
Hundreds of museums, herbaria and art galleries
globally
User manual
Provided during training by KE software
Database model documentation
No
KE EMu Modules
Catalogue
Parties
Loans
Multimedia
KE EMu Modules
Catalogue
Parties
Pathogen and host.
Collection details.
Specimen information.
Personal details.
Address and biography.
Roles and associations.
Loans
Multimedia
Loan number.
Type and purpose.
Due date.
Images and documents.
Sounds and movies.
Executable files.
KE EMu Catalogue Module
KE EMu Multimedia Module
Image formats - jpg, gif, bmp, tiff, etc
KE EMu Multimedia Module
Molecular information - DNA sequences, chromatograms, etc
Query Form
Search Results
Mapping Module
Overview
• Major development issues
• Pacific Pest List Database
• Three Australian Databases:
– West Australian Department of Agriculture Insect
Collection Database
– Biolink
– Ke Emu
• National Phytosanitary Database
– Cambodia, Lao PDR, Myanmar, Vietnam
National Phytosanitary
Database
Contact
GBS & Associates, Palmerston North, New Zealand
[email protected]
Availability and cost
Under license from GBS & Associates
Initial cost and cost to modify/ upgrade
Database Engine
Limitations
SQL Server database system
None
Data import and export
capabilities
Import from Excel spreadsheet
Users
Cambodia, Lao PDR, Myanmar, Vietnam, Bhutan, UAE
User manual
Yes
Database model documentation
No
National Phytosanitary
Database
National Phytosanitary
Database
Concept Diagram - National Phytosanitary Database
Copyright © GBS & Associates 2002
Intranet - access within the NPPO
Extranet (user authenticated access only)
Export Certification and
Country-Commodity
Specific Specifications
Import Certification and
Country-Commodity
Specific Import
Specifications
Internet – open access
Pest Risk Analysis
National Standards
Pest Eradication Activities
Laboratory Activities
NPD
Pest Status Records
Post Entry Quarantine
International Standards
Accredited Suppliers
RELATIONAL DATABASE
MANAGEMENT SYSTEM
Pest Keys & Training
Manuals
Multimedia Training Tools
National Legislation
Industry Groups
Scientists,
Research & Training Institutes
 WEB SERVER
Notification of
Non - Compliance and Emergency
Action
 MAIL SERVER
Official Contact Point & Key
Personnel
Regional Offices & Entry/Exit
points
Online Application for
Certification and “Notice Board”
Phytosanitary Capacity
Evaluation Tool
Strategic Plan Building Tool
Components Installed in
Cambodia, Laos, Myanmar,
Vietnam and Bhutan
Can be linked to
other NPD
databases via the
internet or by a
dedicated line or
remote access
facility
E-Commerce Facility
(including payments online)
Next
Components under development by
GBS & Associates, NZ
Data Entry Screen for Pest Status Records
National Phytosanitary
Database
Pest Status Records – Pest Information Screen
National Phytosanitary
Database
Pest Status Records – Host Information Screen
National Phytosanitary
Database
Pest Status Records – Pest Information Source
National Phytosanitary
Database
Pest Status Records – General Surveillance
National Phytosanitary
Database
General Surveillance – Collection Data
National Phytosanitary
Database
General Surveillance – Identification Data
National Phytosanitary
Database
Pest Status Records – Specific Survey Type
National Phytosanitary
Database
Specific Survey – Identification Data
National Phytosanitary
Database
No. of pests recorded by pest category in some major crops
45
40
35
30
25
20
15
10
5
0
National Phytosanitary
Database
Oryza sativa
50
40
No. of Pests
No. of Pests
Citrus reticulata
30
20
10
Bacterium
Fungi
Insecta
Mites
0
Nematode
Fungi
45
40
35
30
25
20
15
10
5
0
Nematode
Malus domestica
60
50
No. of Pests
No. of Pests
Solanum tuberosum
Insecta
40
30
20
10
Bacterium
Fungi
Insecta
Plasmodium
Virus
0
Fungi
Insecta
Mites
Nematode
Overview
• Major development issues
• Pacific Islands Pest List Database
• Three Australian Databases:
– West Australian Department of Agriculture Insect
Collection Database
– Biolink
– KE Emu
• National Phytosanitary Database
– Cambodia, Lao PDR, Myanmar, Vietnam