Data Standards for Pest Records and Lists

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Data Standards for Pest Records and Lists

• Dr Ian Naumann,
• Office of the Chief Plant Protection Officer

Pest Lists Workshop Kuala Lumpur,
Malaysia August 2005
2
Overview

• International Standards for Phytosanitary
  Measures (ISPMs)
• Other international standards

3
International Standards for Phytosanitary
Measures (ISPMs)
ISPM 3. Code of Conduct for the Import and
Release of Exotic Biological Control Agents ISPM
6. Guidelines for Surveillance ISPM 8.
Determination of Pest Status in an Area ISPM 11.
Pest Risk Analysis for Quarantine Pests
4
ISPM 8. Determination of Pest Status in an Area
PEST RECORD

• Scientific name of pest
• Classification
• Life stage
• Identification method
• Date of record
• Locality, including site particulars
• Name of host
• Host damage or method of collection
• Prevalence
• Bibliographical references

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ISPM 8. Determination of Pest Status in an Area
RELIABILITY OF A RECORD
1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
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ISPM 8. Determination of Pest Status in an Area

• 1. Collectors
• Taxonomic specialist
• Professional diagnostician
• Scientist
• Technician
• Expert amateur
• Non-specialist
• Collector/identifier

1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
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ISPM 8. Determination of Pest Status in an Area

• 2. Technical Identification
• Biochemical or molecular diagnosis
• Specimen or culture in official collection,
  taxonomic description by specialist
• Specimen in general collection
• Description and photograph
• Visual description only
• Method of identification not known

1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
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ISPM 8. Determination of Pest Status in an Area

• 3. Location and date
• Delimiting or detection surveys
• Other field or production surveys
• Casual or incidental field observation, possibly
  with no defined location/date
• Observation with/in products or by-products
  interception
• Precise location and date not known

1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
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ISPM 8. Determination of Pest Status in an Area

• 4. Recording and publication
• NPPO record/RPPO publication (where refereed)
• Scientific or technical journal (refereed)
• Official historical record
• Scientific or technical journal (not refereed)
• Specialist amateur publication
• Unpublished scientific or technical document
• Non-technical publication, periodical, newspaper
• Personal communication, unpublished

1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
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Pest Information Sources
Unpublished information (letters, unpublished
documents)
Grey Literature (conference proceedings
pamphlets, PRAs)
Primary Literature (research papers, specialist
texts)
Listservers
Newspapers
Secondary Literature (encyclopaedias)
Electronic sources
Specimen information
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Pest Information Sources
Primary Literature (research papers, specialist
texts)
1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
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Pest Information Sources
Grey Literature (conference proceedings
pamphlets, PRAs)
3. Location
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Pest Information Sources
3. Location
4. Recording and publication
Secondary Literature (encyclopaedias)
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Pest Information Sources
2. Technical Identification
3. Location
Electronic sources
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Pest Information Sources
Unpublished information (letters, unpublished
documents)
1. Collectors
Listservers
Newspapers
2. Technical Identification
3. Location
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Pest Information Sources
1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
Specimen information
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Pest Information Sources
1. Collectors
2. Technical Identification
3. Location
4. Recording and publication
Specimen information
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Beyond the ISPMs TDWG

• International Taxonomic Data Working Group
  meets approximately annually with work continuing
  throughout year
• Develops and promotes use of standards
• Standards for use in local databases
• Standards facilitating exchange and pooling of
  data globally
• Currently developing ABCD Schema next version
  to be endorsed in St Petersburg, Russia in
  September 2005
• http//www.tdwg.org/

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TDWG Standards

• Authors of plant names
• Economic botany data collection standards
  standards
• Floristic regions of the world
• Herbaria of the world
• Plant occurrence and status scheme
• Taxonomic literature
• World geographical scheme for recording
  distribution
• Darwin core / ABCD Schema

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TDWG Standards

• Plant occurrence and status scheme
• compiled by World Conservation Monitoring Centre
• http//www.tdwg.org/poss_standard.html
• e.g. Native status
• Native
• Assumed to be native
• Doubtfully native
• Formerly native (i.e. now extinct)
• Recorded as native in error
• No information

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TDWG Standards

• Economic Botany Data Standards
• compiled by Royal Botanic Gardens, Kew, United
  Kingdom
• http//www.rbgkew.org.uk/tdwguses/
• e.g. Master list for plant parts
• Galls
• Leaf galls
• Root galls
• Stem galls
• Fruit galls
• Other galls

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TDWG Standards

• Economic Botany Data Standards
• compiled by Royal Botanic Gardens, Kew, United
  Kingdom
• http//www.rbgkew.org.uk/tdwguses/
• e.g. Master list for plant parts
• Infructescences
• Fruits
• Entire immature fruits
• Entire mature fruits
• Deseeded fruits
• Fruit pulp
• Fruit juice
• Epicarp
• Other parts

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ABCD Schema

• Access to Biological Collection Data
• Content Definition

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ABCD Schema
Purpose of ABCD Schema

• A common data specification for biological
  collection units
• primary occurrence data
• living and preserved specimens as well as field
  observations
• Intended to support the exchange and integration
  of detailed primary data

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• Darwin Core / ABCD Standard (1)
• Global Unique Identifier
• Date Last Modified
• Basis Of Record
• Institution Code
• Collection Code
• Catalog Number

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• Darwin Core / ABCD Standard (2)
• Global Unique Identifier
• Date Last Modified
• Basis Of Record
• A descriptive term indicating whether the record
  represents a preserved specimen, a living
  culture, an observation etc.
• Institution Code
• Collection Code
• Catalog Number

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• Darwin Core / ABCD Standard (2)
• Global Unique Identifier
• Date Last Modified
• Basis Of Record
• A descriptive term indicating whether the record
  represents a preserved specimen, a living
  culture, an observation etc.
• Institution Code
• Collection Code
• Catalog Number

ISPM 8 Elements 4, 10
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• Darwin Core / ABCD Standard (3)
• Global Unique Identifier
• Date Last Modified
• Basis Of Record
• Institution Code
• The code or acronym identifying the institution
  or collection holding the record, e.g MZB for
  Museum Zoologicum Bogoriense in Indonesia IRRI
  for the International Rice Research Institute in
  The Philippines.
• Collection Code
• Catalog Number

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• Darwin Core / ABCD Standard (4)
• Scientific Name
• Higher Taxon
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus bacterial, botanical, virus, zoological
  genus or single name
• Specific Epithet bacterial, botanical,
  zoological species name
• Infraspecific name - bacterial, botanical,
  zoological subspecies etc, including names of
  viruses, breeds, cultivars.
• Scientific Name Author
• Identification qualifier
• Method of identification

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• Darwin Core / ABCD Standard (4)
• Scientific Name
• Higher Taxon
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus bacterial, botanical, virus, zoological
  genus or single name
• Specific Epithet bacterial, botanical,
  zoological species name
• Infraspecific name - bacterial, botanical,
  zoological subspecies etc, including names of
  viruses, breeds, cultivars.
• Scientific Name Author
• Identification qualifier
• Method of identification

ISPM 8 Elements 1 and 2
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• Darwin Core / ABCD Standard (4)
• Scientific Name
• Higher Taxon
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus bacterial, botanical, virus, zoological
  genus or single name
• Specific Epithet bacterial, botanical,
  zoological species name
• Infraspecific name - bacterial, botanical,
  zoological subspecies etc, including names of
  viruses, breeds, cultivars.
• Scientific Name Author
• Identification qualifier
• Method of identification

ISPM 8 Element 4
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• Darwin Core / ABCD Standard (5)
• Scientific Name
• Higher Taxon
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus bacterial, botanical, virus, zoological
  genus or single name
• Specific Epithet bacterial, botanical,
  zoological species name
• Infraspecific name - bacterial, botanical,
  zoological subspecies etc, including names of
  viruses, breeds, cultivars.
• Scientific Name Author
• Identification qualifier
• Method of identification

International Code of Zoological Nomenclature
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• Darwin Core / ABCD Standard (6)
• Scientific Name
• Higher Taxon
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus bacterial, botanical, virus, zoological
  genus or single name
• Specific Epithet bacterial, botanical,
  zoological species name
• Infraspecific name - bacterial, botanical,
  zoological subspecies etc, including names of
  viruses, breeds, cultivars.
• Scientific Name Author
• Identification qualifier
• Method of identification

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Coccus cambodiensis Takahashi NOMENCLATURECoccu
s cambodiensis Takahashi, 1942b 17. Type data
CAMBODIA Angkor, on Ficus sp. Syntypes, female.
Type depository Taichung Taiwan Agricultural
Research Institute, Entomology Collection,
Taiwan.HOSTS Moraceae Ficus Takaha1942a,
Ali1971, Ficus retusa Tang1991.DISTRIBUTION
Oriental Kampuchea (Cambodia)
Ali1971.GENERAL REMARKS Good description and
illustration of the adult female given by Tang
(1991).KEYS Tang 1991 76 (female)
China.CITATIONS Ali1971 host, distribution
22 BenDov1993 catalogue 68 Takaha1942b
taxonomy, description, illustration, host,
distribution 17-19 Tang1991 taxonomy,
description, illustration, host, distribution
79-80 Tao1999 taxonomy, host, distribution
53.
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• Darwin Core / ABCD Standard (7)
• Scientific Name
• Higher Taxon
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus bacterial, botanical, virus, zoological
  genus or single name
• Specific Epithet bacterial, botanical,
  zoological species name
• Infraspecific name - bacterial, botanical,
  zoological subspecies etc, including names of
  viruses, breeds, cultivars.
• Scientific Name Author
• Identification qualifier
• Method of identification

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• Darwin Core / ABCD Standard (8)
• Scientific Name
• Higher Taxon
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus bacterial, botanical, virus, zoological
  genus or single name
• Specific Epithet bacterial, botanical,
  zoological species name
• Infraspecific name - bacterial, botanical,
  zoological subspecies etc, including names of
  viruses, breeds, cultivars.
• Scientific Name Author
• Identification qualifier
• Method of identification

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• Darwin Core / ABCD Standard (9)
• Higher Geography
• Continent
• Water Body
• Island Group
• Island
• Country
• State Province
• County
• Locality
• Minimum Elevation In Meters
• Maximum Elevation In Meters
• Minimum Depth In Meters
• Maximum Depth In Meters
• Decimal Latitude
• Decimal Longitude
• Geodetic Datum

ISPM 8 Element 6
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• Darwin Core / ABCD Standard (10)
• Year Collected
• Month Collected
• Day Collected
• Time Collected
• Julian Day
• Collector
• Method of collection
• Sex - including mycological sexual stage
• Life Stage
• Image URL
• Related Information

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• Darwin Core / ABCD Standard (10)
• Year Collected
• Month Collected
• Day Collected
• Time Collected
• Julian Day
• Collector
• Method of collection
• Sex - including mycological sexual stage
• Life Stage
• Image URL
• Related Information

ISPM 8 Element 5
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• Darwin Core / ABCD Standard (10)
• Year Collected
• Month Collected
• Day Collected
• Time Collected
• Julian Day
• Collector
• Method of collection
• Sex - including mycological sexual stage
• Life Stage
• Image URL
• Related Information

ISPM 8 Element 3
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• Darwin Core / ABCD Standard (10)
• Year Collected
• Month Collected
• Day Collected
• Time Collected
• Julian Day
• Collector
• Method of collection
• Sex - including mycological sexual stage
• Life Stage
• Image URL
• Related Information

ISPM 8 Elements 7, 8 , 9
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Darwin Core / ABCD Standard (10)

• This standard provides a basic and exhaustive
  data format for specimen-based records.
• It is compatible with the definition of a pest
  record in ISPM 8.

International Standards for Phytosanitary
Measures (ISPMs)
ISPM 3. Code of Conduct for the Import and
Release of Exotic Biological Control Agents ISPM
6. Guidelines for Surveillance ISPM 8.
Determination of Pest Status in an Area ISPM 11.
Pest Risk Analysis for Quarantine Pests
44
Overview

• International Standards for Phytosanitary
  Measures (ISPMs)
• Other international standards
• Standards for primary data, biological and
  physical
• Standards for records based on specimens,
  observations, literature citations

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