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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




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

• International Standards for Phytosanitary Measures
  (ISPMs)
• Other international standards
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
ISPM 8. Determination of Pest Status in an Area


          PEST RECORD
    1.Scientific name of pest
    2.Classification
    3.Life stage
    4.Identification method
    5.Date of record
    6.Locality, including site particulars
    7.Name of host
    8.Host damage or method of collection
    9.Prevalence
    10. Bibliographical references
ISPM 8. Determination of Pest Status in an Area

          RELIABILITY OF A RECORD

  1. Collectors

  2. Technical
      Identification

  3. Location

  4. Recording and publication
ISPM 8. Determination of Pest Status in an Area

                       1.   Collectors
                       a.    Taxonomic specialist
                       b.    Professional diagnostician
  1. Collectors
                       c.    Scientist
                       d.    Technician
  2. Technical         e.    Expert amateur
      Identification   f.    Non-specialist
                       g.    Collector/identifier

  3. Location

  4. Recording and publication
ISPM 8. Determination of Pest Status in an Area

                       2. Technical Identification
                     a. Biochemical or
                         molecular diagnosis
  1. Collectors
                     b. Specimen or culture in
                         official collection,
  2. Technical           taxonomic description
      Identification     by specialist
                     c. Specimen in general
                         collection
  3. Location        d. Description and
                         photograph
                     e. Visual
  4. Recording and publication description only
                     f. Method of identification
                         not known
ISPM 8. Determination of Pest Status in an Area

                         3. Location and date
                         a. Delimiting or detection
                            surveys
  1. Collectors          b. Other field or
                            production surveys
  2. Technical           c. Casual or incidental
      Identification        field observation,
                            possibly with no
                            defined location/date
  3. Location            d. Observation with/in
                            products or by-
                            products; interception
  4. Recording and publication
                         e. Precise location and
                            date not known
   ISPM 8. Determination of Pest Status in an Area

                               4. Recording and publication
                               a. NPPO record/RPPO
     1. Collectors                 publication (where
                                   refereed)
                               b. Scientific or technical
     2. Technical                  journal (refereed)
         Identification        c. Official historical record
                               d. Scientific or technical
                                   journal (not refereed)
     3. Location               e. Specialist amateur
                                   publication
                               f. Unpublished scientific or
4. Recording and publication       technical document
                               g. Non-technical publication,
                                   periodical, newspaper
                               h. Personal communication,
                                   unpublished
Pest Information Sources
                                       Unpublished information
                                    (letters, unpublished documents)
Primary Literature (research                          Grey Literature
papers, specialist texts)                                  (conference
                          Listservers                    proceedings;
                                                    pamphlets, PRA’s)
                                      Newspapers



Secondary Literature
 (“encyclopaedias”)
                        Specimen information     Electronic sources
   Pest Information Sources

Primary Literature (research
papers, specialist texts)
                            1. Collectors

                         2. Technical
                             Identification


                          3. Location

     4. Recording and publication
Pest Information Sources

                            Grey Literature
                                (conference
                               proceedings;
                           pamphlets, PRA’s)




 3. Location
   Pest Information Sources




                       3. Location

                       4. Recording and publication
Secondary Literature
 (“encyclopaedias”)
Pest Information Sources




 2. Technical
     Identification

 3. Location

                           Electronic sources
 Pest Information Sources

                                  Unpublished information
                               (letters, unpublished documents)
1. Collectors        Listservers
                                   Newspapers



2. Technical
    Identification

3. Location
Pest Information Sources




 1. Collectors

 2. Technical
     Identification

 3. Location        4. Recording and publication

                 Specimen information
Pest Information Sources




 1. Collectors

 2. Technical
     Identification

 3. Location        4. Recording and publication

                 Specimen information
       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/
             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
• ……
• ……
                 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
               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
                   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
        ABCD Schema

Access to Biological Collection Data
Content Definition
 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
Darwin Core” / ABCD Standard (1)

•Global Unique Identifier
•Date Last Modified
•Basis Of Record
•Institution Code
•Collection Code
•Catalog Number
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
Darwin Core” / ABCD Standard
(2)

•Global Unique Identifier
•Date Last Modified     ISPM 8 Elements 4, 10
•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
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
   “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
   “Darwin Core” / ABCD Standard (4)
•Scientific Name
•Higher Taxon
•Kingdom                      ISPM 8 Elements 1 and 2
•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
   “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       ISPM 8 Element 4
•Method of identification
   “Darwin Core” / ABCD Standard (5)
•Scientific Name
•Higher Taxon
•Kingdom
               International Code of
•Phylum
•Class       Zoological Nomenclature
•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
   “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
                                         Coccus cambodiensis Takahashi
                                              NOMENCLATURE:

  Coccus 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].
   “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
   “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
  “Darwin Core” / ABCD Standard (9)

•Higher Geography
•Continent                          ISPM 8 Element 6
•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
•Coordinate Uncertainty In Meters
“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
“Darwin Core” / ABCD Standard (10)

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

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

•Year Collected
•Month Collected     ISPM 8 Elements 7, 8 , 9
•Day Collected
•Time Collected
•Julian Day
•Collector
•Method of collection
•Sex - including mycological sexual stage
•Life Stage
•Image URL
•Related Information
          “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
                       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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