EPGRIS EURSICO descriptors

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(No Transcript)
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EPGRIS technical issue
EURISCO descriptor list
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EURISCO descriptor list

• principles
• general format rules
• descriptors
• definition
• coding schemes
• differences EURISCO - MCPD v1 - MCPD v2
• additional requirements
• summary differences
• EURISCO - MCPD v2
• MCPD v2 - MCPDv1

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EURISCO descriptor list

• principles
• data from National Inventory are uploaded to
  EURISCO in a fixed format
• to allow automation
• to allow validation
• descriptor list is only for uploading
• National Inventory descriptors can be different
• scripts for conversion can be necessary

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EURISCO descriptor list

• principles
• the EURISCO descriptor list is an extension of
  the FAO/IPGRI Multi Crop Passport Descriptor List
  version 2 (December 2001)
• the MCPD list v2 is used without changes but with
  six additions
• additions are necessary for
• identification of the data set
• solving problems related to missing FAO
  institution codes
• linking to additional data

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EURISCO descriptor list

• principles
• FAO/IPGRI Multi Crop Passport Descriptor List
• proposed and discussed at the 1996 Budapest
  meeting, published in 1997
• widely adopted
• CGIAR
• ECCDBs
• version 2 appeared in December 2001
• based on feedback from EPGRIS and others

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EURISCO descriptor list

• general format rules
• preferred language English
• multiple values should be separated by a
  semicolon () without space
• in MCDLv1 this was semicolon plus space
• example VorgebirgstraubenEmma
• all dates are recorded as YYYYMMDD
• missing parts with hyphens
• examples 199505031985----

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EURISCO descriptor list

• general format rules
• country codes extended three-letter ISO 3166-1
  codes
• examples DDRNLD
• institute codes FAO Institute Codes
• consist of the 3-letter ISO 3166 country code
  plus a number
• in MCPDv1 acronyms and preliminary codes were
  allowed
• examples NLD037SWE002

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EURISCO descriptor list

• descriptors (0-2/33)
• National Inventory code (NICODE)
• not in MCPD list
• country code of the National Inventory
• example NLD
• institute code (INSTCODE)
• code of the institute where the accession is
  maintained
• example NLD037
• accession number (ACCENUMB)
• example CGN00254

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EURISCO descriptor list

• descriptors (3-4/33)
• collecting number (COLLNUMB)
• original number assigned by the collector(s) of
  the sample
• example FA90-110
• collecting institute code (COLLCODE)
• not in MCPDv1
• code of the Institute collecting the sample
• example NLD037

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EURISCO descriptor list

• descriptors (5-7/33)
• genus (GENUS)
• genus name for taxon, in latin
• example Allium
• species (SPECIES)
• specific epithet portion of the scientific name,
  in latin
• example paniculatum
• species authority (SPAUTHOR)
• was in MCPDv1 combined with SPECIES
• authority for the species name
• example L.

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EURISCO descriptor list

• descriptors (8-9/33)
• subtaxa (SUBTAXA)
• any additional taxonomic identifier, in latin
• allowed abbreviations subsp. convar. var.
  f.
• example subsp. Fuscum
• subtaxa authority (SUBTAUTHOR)
• was in MCPDv1 combined with SUBTAXA
• subtaxa authority at the most detailed taxonomic
  level
• example (Waldst. et Kit.) Arc.

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EURISCO descriptor list

• descriptors (10-11/33)
• common crop name (CROPNAME)
• not in MCPDv1
• colloquial name of the crop
• examples malting barley
• cauliflower
• accession name (ACCENAME)
• either a registered or other formal designation
  given to the accession
• first letter uppercase
• example VorgebirgstraubenEmma

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EURISCO descriptor list

• descriptors (12-13/33)
• acquisition date (ACQDATE)
• not in MCPDv1
• date on which the accession entered the
  collection
• example 1968----
• country of origin (ORIGCTY)
• code of the country in which the sample was
  originally collected
• example NLD

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EURISCO descriptor list

• descriptors (14-15/33)
• location of collecting site (COLLSITE)
• location where the accession was collected
• example
• 7 km south of Curitiba in the state of Parana
• latitude of collecting site (LATITUDE)
• degree (2 digits) minutes (2 digits), and seconds
  (2 digits) followed by N (North) or S (South)
• missing digit should be indicated with a hyphen
• example 10----S011530N

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EURISCO descriptor list

• descriptors (16-17/33)
• longitude of collecting site (LONGITUDE)
• degree (3 digits), minutes (2 digits), and
  seconds (2 digits) followed by E (East) or W
  (West)
• missing digits should be indicated with hyphens
• examples 0762510W076----W
• elevation of collecting site (ELEVATION)
• expressed in meters above sea level
• example 763

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EURISCO descriptor list

• descriptors (18-19/33)
• collecting date of sample (COLLDATE)
• example 1968----
• breeding institute code (BREDCODE)
• not in MCPDv1
• code of institute that has bred the material

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EURISCO descriptor list

• descriptors (20/33)
• biological status of accession (SAMPSTAT)
• 100) Wild
• 110) Natural
• 120) Semi-natural/wild
• 200) Weedy
• 300) Traditional cultivar/landrace
• 400) Breeding/research material
• 410) Breeder's line
• 411) Synthetic population
• 412) Hybrid
• 413) Founder stock/base population
• 414) Inbred line (parent of hybrid cultivar)
• 415) Segregating population
• 420) Mutant/genetic stock
• 500) Advanced/improved cultivar
• 999) Other (Elaborate in REMARKS field)

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EURISCO descriptor list

• descriptors (21/33)
• ancestral data (ANCEST)
• not in MCPDv1
• either pedigree or other description of ancestral
  information
• examples Hanna/7Atlas//Turk/8Atlas
• mutation found in Hanna
• selection from Irene
• cross involving a/o Hanna and Irene

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EURISCO descriptor list

• descriptors (22/33)
• collecting/acquisition source (COLLSRC)
• 10) Wild habitat 30) Market or shop
• 11) Forest/woodland 40) Institute, Experimental
  station,
• 12) Shrubland Research organization,
  Genebank
• 13) Grassland 50) Seed company
• 14) Desert/tundra 60) Weedy, disturbed or
  ruderal habitat
• 15) Aquatic habitat 61) Roadside
• 20) Farm or cultivated habitat 62) Field margin
• 21) Field 99) Other (Elaborate in REMARKS
  field)
• 22) Orchard
• 23) Backyard, kitchen or home garden (urban,
  peri-urban or rural)
• 24) Fallow land
• 25) Pasture
• 26) Farm store
• 27) Threshing floor
• 28) Park

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EURISCO descriptor list

• descriptors (23-24/33)
• donor institute code (DONORCODE)
• FAO Institute Code for the donor institute
• donor accession number (DONORNUMB)
• number assigned to an accession by the donor
• example NGB1912

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EURISCO descriptor list

• descriptors (25/33)
• other identification (numbers) associated with
  the accession (OTHERNUMB)
• any other identification (numbers) known to exist
  in other collections for this accession
• format INSTCODEACCENUMB
• if the institute is not known, the number should
  be preceded by a colon
• example NLD037CGN00254Bra2343

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EURISCO descriptor list

• descriptors (26/33)
• location of safety duplicates (DUPLSITE)
• not in MCPDv1
• FAO Institute Code of the institute where a
  safety duplicate of the accession is maintained

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EURISCO descriptor list

• descriptors (27/33)
• type of germplasm storage (STORAGE)
• not in MCPDv1
• multiple choices are allowed
• 10) Seed collection
• 11) Short term
• 12) Medium term
• 13) Long term
• 20) Field collection
• 30) In vitro collection (Slow growth)
• 40) Cryopreserved collection
• 99) Other (elaborate in REMARKS field)

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EURISCO descriptor list

• descriptors (28/33)
• remarks (REMARKS)
• notes or elaboration on descriptors with value 99
  or 999 (Other)
• prefix with the field name they refer to and a
  colon
• example COLLSRCroadside

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EURISCO descriptor list

• descriptors (29/33)
• decoded collecting institute (COLLDESCR)
• not in MCPD list
• brief name and location of the collecting
  institute
• only to be used if COLLCODE can not be used since
  the FAO Institution Code for this institute is
  not (yet) available
• example Jan Zomeren, Arnhem, The Netherlands

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EURISCO descriptor list

• descriptors (30-32/33)
• decoded breeding institute (BREDDESCR)
• decoded donor institute (DONORDESCR)
• decoded safety duplication location (DUPLDESCR)
• not in MCPD list
• same principle as COLLDESCR

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EURISCO descriptor list

• descriptors (33/33)
• accession URL (ACCEURL)
• not in MCPD list
• URL linking to additional data about the
  accession either in the holding genebank or from
  another source
• example
• www.cgn.wageningen-ur.nl/pgr/collections/passdeta
  .asp?accenumbCGN04848

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EURISCO descriptor list

• additional requirements
• the fields identifying the accession are
  mandatory, all other fields are optional
• mandatory NICODE, INSTCODE, ACCENUMB, GENUS
• the combination of mandatory fields has to be
  unique

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EURISCO descriptor list

• additional requirements
• order of the fields
• as presented
• first NICODE
• next all MCPDL descriptors in order as listed
• after final MCPDL descriptor (REMARKS) COLLDESCR,
  BREDDESCR, DONORDESCR, DUPLDESCR, ACCEURL

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EURISCO descriptor list

• differences EURISCO - MCPD v2
• six additional fields
• NICODE for identification data set
• COLLDESCR, BREDDESCR, DONORDESCR, DUPLDESCR for
  solving institution code problem
• ACCEURL to link to additional data

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EURISCO descriptor list

• summary differences MCPD v2 - MCDLv1
• format separator multiple values
• was but is now (without a space)
• format LONGITUDE and LATITUDE
• was for example 07625W is now 0762510W
  (including the minutes)
• no acronyms for institution codes
• NLDCGN was allowed, but no longer
• no preliminary institution codes
• NLDZANDSTR5 was allowed, but no longer

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EURISCO descriptor list

• summary differences MCPD v2 - MCDLv1
• authorities SPECIES and SUBTAXA are split off in
  separate fields SPAUTHOR and SUBTAUTHOR
• SPECIES was for example sativa L. is now
  sativa and SPAUTHOR is L.
• coding systems of SAMPSTAT, COLLSRC and STORAGE
  have changed (see tables)
• new fields COLLCODE, CROPNAME, ACQDATE, BREDCODE
  and ANCEST