e-­‐Conference  on  Germplasm  Data  Interoperability,  December  11th  2013.  Dag  Endresen,  GBIF-­‐Norway  (UiO).  

Why  did  we  make  a  germplasm  extension  for  Darwin  Core?  

à Upgrade  germplasm  data  pathways  to  use  web  services  

The  objecNve  was  to  enable  sharing  of  germplasm  informaNon  using  the  standard  web-­‐service  based  biodiversity  data  publishing  toolkits  maintained  by  the  Global  Biodiversity  InformaNon  Facility  (GBIF)  and  the  Biodiversity  InformaNon  Standards  (TDWG).    

   à Upgrade  data  types  to  include  trait  data  The  objecNve  was  to  expand  on  the  germplasm  data  types  published  to  germplasm  data  portal  from  basic  passport  data  to  include  in  parNcular  crop  trait  informaNon.  

2  

The  compaNbility  of  data  standards  between  PGR  and  biodiversity  collecNons  made  it  possible  to  integrate  the  worldwide  germplasm  collecNons  into  the  biodiversity  community  (TDWG,  GBIF).  

PotenNal  of  the  GBIF  technology  

hTp://data.gbif.org/datasets/network/2    hTp://www.gbif.org/network/ae3a42e4-­‐5829-­‐4210-­‐8d8a-­‐84b0cbda47bc      

Using  GBIF/TDWG  technology  (and  contribuNng  to  its  development),  the  PGR  community  can  more  easily  establish  specific  PGR  networks  without  duplicaNng  GBIF's  work.  

2,106,765  records  of  germplasm  data  (status  2013)  

3  

Genebank dataset  

Global Crop Registries  

European EURISCO Catalog  

European Crop Databases  

4  

GBIF  

MulNple-­‐purpose  data  export  services  

genesys-­‐pgr.org  

The  GENESYS  gateway  to  geneNc  resources  provides  access  to  informaNon  on  more  than  2.3  million  genebank  accessions,  hTp://www.genesys-­‐pgr.org/    

2,348,549  records  of  germplasm  accessions    

The  European  GeneNc  Resources  Search  Catalogue  (EURISCO)  receives  data  from  the  NaNonal  Inventories  (NI)  and  provides  access  to  all  ex  situ  PGR  accessions  in  Europe,  hTp://eurisco.ecpgr.org    

1,074,136  records  of  germplasm  accessions    

6  

A  total  of  64  ECPGR  Central  Crop  Databases  have  been  established  by  individual  insNtutes  and  the  ECPGR  Working  Groups.  The  databases  hold  passport  data  and,  to  varying  degrees,  characterizaNon  and  primary  evaluaNon  data  of  the  major  collecNons  of  the  respecNve  crops  in  Europe,  hTp://www.ecpgr.cgiar.org/germplasm_databases/central_crop_databases.html    

(8  databases)  

(10  databases)  

(6  databases)  

(10  databases)  

(8  databases)  

(22  databases)  

7  

Possible  Upgraded  PGR  Network  Model  

8  

v  Each dataset is shared from the holding gene bank.

v  The National Inventory (NI) endorse all national gene banks for EURISCO.

v  ECPGR Crop databases can access passport data from EURISCO and additional crop specific data from the gene bank IPT interface.

v  Standard data sharing tools ensure that the genebank dataset is available to other relevant decentralized thematic, regional or global networks. IllustraNon  from  the  GBIF  

annual  report  2009,  page  47.  

9  

Background  and  context  

10  

MCPD  revisions  

 1997  2001  2012  

11  

May  2009  

Some  of  the  data  publishing  toolkits  ICIS  (Java,  1996  à)  

BioMOBY  (Perl,  2001  à)  

EURISCO  (tab-­‐delimited,  2003  à)    

DiGIR  (PHP,  2001  -­‐  2006)  

TapirLink  (PHP,  2007  à)  

BioCASE  (Python,  2001  à)  

TAPIR  PyWrapper3  (Python,  2006  –  2008)  

GBIF  IPT  (Java,  2009  à)  

2  

12  

Demo  project  in  2005  using  BioCASE  

13  

Mapping  of  MCPD  à  ABCD  v2.06    was  required  before  using  BioCASE  

National Inventory Code Institute Code Accession Number

Collecting Number Collecting Institute Code

Genus Species

Species Authority „Subtaxa“

„Subtaxa“ Authority Common Crop Name Accession Name Acquisition Date

Country of Origin Location of Collection Site Latitude of CS Longitude of CS Elevation of CS Collecting Date of Sample Breeding Institute Code Biological Status of Accession Ancestral Data Collecting/Acquisition Source

Donor Institute Code Donor Accession Number Other Identification (Number) associated

with the accession Location of Safety Duplicates Type of Germplasm Storage Remarks Decoded Collecting Institute Decoded Breeding Institute Decoded Donor Institute Decoded Safety Duplication Location Accession URL

Helmut  Knüpffer  IPK  Gatersleben  

Walter  Berendsohn  BGBM,  Berlin  

Berendsohn,  W.  and  H.  Knüpffer  (2004  -­‐  2006).  Dral  mapping  of  Eurisco  descriptors  to  ABCD  2.06.  Available  at  hTp://www.bgbm.org/tdwg/codata/Schema/Mappings/EURISCO-­‐2-­‐ABCD.pdf  

14  

Highlight in green good match, orange acceptable match, red no match (was included as PGR extension in ABCD v2.06).  

2005  :  BioCASE  demo  

Genebank/germplasm  extension  to  the  ABCD  v2.06  15  

Demo  project  in  2010  using  the  GBIF  IPT  

16  

The  Darwin  Core  germplasm  extension  was  required  for  meaningful  descripNon  of  germplasm  data  sets  using  Darwin  Core  and  the  GBIF  IPT.      A  mapping  of  MCPD  terms  to  Darwin  Core.  

Plus  some  addiGonal  terms  to  describe  germplasm:  •   breeding/culNvaNon  event  (source:  MCPD),  •   crop  trait  experiments  (source:  EPGRIS3/ECPGR),  •   and  internaNonal  crop  treaty  regulaNons.  

   The  first  DRAFT  version  was  released  in  August  2009.  

17  

Mapping  of  MCPD  à  Darwin  Core  was  required  before  using  the  GBIF  IPT  

v  EURISCO v  NordGen (Nordic countries) v  Bioversity-Montpellier (France) v  IPK Gatersleben (Germany) v  BLE (Germany) v  WUR CGN (The Netherlands) v  CRI (Czech Republic) v  VIR (Russian Federation) v  SeedNET (Balkan) v  Baltic (Estonia, Latvia, Lithuania)

2010  :  IPT  installaNons  for  EURISCO  

18  

Darwin  Core  “The  Darwin  Core  is  primarily  based  on  taxa,  their  occurrence  in  nature  as  documented  by  observa;ons,  specimens,  and  samples,  and  related  informa;on.”    •     a  well-­‐defined  standard  core  vocabulary  •     a  flexible  framework  to  maximize  re-­‐usability    •     approved  as  TDWG  standard  2009    hTp://rs.tdwg.org/dwc/      Wieczorek  J.,  D.  Bloom,  R.  Guralnick,  S.  Blum,  M.  Döring,  R.  Giovanni,  T.  Robertson,  D.  Vieglais  (2012).  Darwin  Core:  An  Evolving  Community-­‐Developed  Biodiversity  Data  Standard.  PLoS  ONE  7(1):  e29715.    doi:10.1371/journal.pone.0029715   19  

Darwin  Core  star  schema  

Germplasm  Breeder  Trait  

Audubon  core  

Can relate elements one-to-one or one-to-many.

1:1  

1:many  1:many  

1:many   1:many  

20  

Darwin  Core  Archive  (DwC-­‐A)  v  DwC-A publish Darwin Core records including extensions v  Simple text based format v  Zipped single file archive

Germplasm.txt  

21  

22  

The  Darwin  Core  extension  for  genebanks  is  an  extension  to  the  Darwin  Core  standard.    Provides  a  mapping  of  MCPD  terms  and  Darwin  Core  terms.    And  it  includes  addiNonal  terms  required  for  describing  germplasm  resources  that  were  missing  in  Darwin  Core.  

•  Endresen,  D.,  S.  Gaiji,  and  T.  Robertson  (2009).  Darwin  Core  Germplasm  extension  and  deployment  in  the  GBIF  infrastructure.  Proceedings  of  TDWG  2009,  Montpellier,  France.  Bioversity  InformaNon  Standards  (TDWG).  

•  Endresen,  D.T.F.  and  H.  Knüpffer  (2012).  The  Darwin  Core  extension  for  genebanks  opens  up  new  opportuniNes  for  sharing  genebank  data  sets.  Biodiversity  InformaNcs  8:11-­‐29.  

Darwin  Core  extension  for  genebanks  

Namespace (SKOS/RDF) (stable version) hTp://purl.org/germplasm/germplasmTerm#       Code repository (stable version)hTp://code.google.com/p/darwincore-­‐germplasm   Community discussion (development version) hTp://terms.tdwg.org/wiki/Germplasm    

Darwin  Core  extension  for  genebanks  

23  

MCPD  (2012)   Darwin  Core   MCPD  (2012)   Darwin  Core  

(missing)   dwc.datasetID   15.5   COORDUNCERT   dwc.coordinateUncertaintyInMeters  

(missing)   dwc.occurrenceID   15.6   COORDDATUM   dwc.geodeNc.Datum  

1   INSTCODE   dwc.insNtuNonCode   15.7   GEOREFMETH   dwc.georeferenceSources  

2   ACCENUMB   dwc.catalogNumber   16   ELEVATION   dwc.minimumElevaNonInMeters  

3   COLLNUMB   dwc.recordNumber   17   COLLDATE   dwc.eventDate  

4   COLLCODE   g.collecNngInsNtuteCode   18   BREDCODE   g.breederInsNtuteID  

4.1   COLLNAME   dwc.recordedBy   18.1   BREDNAME   g.breedingInsNtute  

4.1.1   COLLINSTADDRESS   (dwc.recordedBy)   19   SAMPSTAT   g.biologicalStatus  

4.2   COLLMISSID   dwc.collecNonCode   20   ANCEST   g.ancestralData,  g.purdyPedigree  

5   GENUS   dwc.genus   21   COLLSRC   g.acquisiNonSource  

6   SPECIES   dwc.specificEpithet   22   DONORCODE   g.donorInsNtuteID  

7   SPAUTHOR   dwc.scienNficNameAuthorship   22.1   DONORNAME   g.donorInsNtute  

8   SUBTAXA   dwc.infraspecificEpithet   23   DONORNUMB   g.donorsIdenNfier  

9   SUBTAUTHOR   (dwc.scienNficNameAuthorship)   24   OTHERNUMB   dwc.otherCatalogNumbers  

10   CROPNAME   dwc.vernacularName   25   DUPLSITE   g.safetyDuplicaNonInsNtuteID  

11   ACCENAME   g.breedingIdenNfier   25.1   DUPLINSTNAME   g.safetyDuplicaNonInsNtute  

12   ACQDATE   g.acquisiNonDate   26   STORAGE   g.storageCondiNon  

13   ORIGCTY   dwc.countryCode   27   MLSSTAT   g.mlsStatus  

14   COLLSITE   dwc.locality   28   REMARKS   dwc.occurrenceRemarks  

15.1   DECLATITUDE   dwc.decimalLaNtude  

15.2   LATITUDE   dwc.verbaNmLaNtude  

15.3   DECLONGITUDE   dwc.decimalLongitude  

15.4   LONGITUDE   dwc.verbaNmLongitude  24  

Mapping  of  DwC  to  to  MCPD  

Data  set  

dcmitype:Dataset  (Darwin  Core:  Record-­‐level  terms)  

dwc:datasetID   (missing  in  MCPD)  

dwc:datasetName   (eurisco:  NICODE)  

dwc:collecNonID  

dwc:collecNonCode   mcpd:  COLLMISSID  

dwc:insNtuNonID  

dwc:insNtuNonCode   mcpd:  INSTCODE  

25  

dwc  =   hTp://rs.tdwg.org/dwc/terms/  

g  =   hTp://purl.org/germplasm/germplasmTerm#  

dcmitype  =   hTp://purl.org/dc/dcmitype/  

dsw  =   hTp://purl.org/dsw/  

mcpd  =   hTp://www.bioversityinternaNonal.org/index.php?id=244&tx_news_pi1%5Bnews%5D=1350&cHash=d953e45ada3ab285d635593b5068a38f  

epgris3  =   hTp://www.epgris3.eu/docs/acNviNes/2-­‐05/Inclusion%20of%20C&E%20data.pdf  

Nomenclature  

dwctype:Taxon  dwc:taxonID   (missing  in  MCPD)  

dwc:scienNficNameID  

dwc:scienNficName  

dwc:genus   mcpd:  GENUS  

dwc:specificEpithet   mcpd:  SPECIES  

dwc:scienNficNameAuthorship   mcpd:  SPAUTHOR, SUBTAUTHOR  

dwc:vernacularName   mcpd:  CROPNAME  

26  

Germplasm  accession  

g:GermplasmAccession  (see  also:  dsw:Specimen)  

dwc:occurrenceID   (missing  in  MCPD)  

g:germplasmID   (epgris3:  GENOTYPE_NUMBER)  

dwc:catalogNumber   mcpd:  ACCENUMB  

g:germplasmIdenNfier   mcpd:  ACCENAME  

g:biologicalStatus   mcpd:  SAMPSTAT  

g:storageCondiNon   mcpd:  STORAGE  

dwc:otherCatalogNumbers   mcpd:  OTHERNUMB  

dwc:occurrenceDetails   (eurisco:  ACCEURL)  

dwc:occurrenceRemarks   mcpd:  REMARKS  

27  

CollecNng  event  g:CollecGngEvent  (dwc.Event,  dcmitype:Event)  

dwc:eventID  

dwc:recordNumber   mcpd:  COLLNUMB  

dwc:decimalLaNtude   mcpd:  DECLATITUDE     [geo:lat]  

dwc:decimalLongitude   mcpd:  DECLONGITUDE     [geo:long]  

dwc:geodeNcDatum   mcpd:  COORDDATUM  

dwc:minimumElevaNonInMeters   mcpd:  ELEVATION     [geo:alt]    

dwc:eventDate   mcpd:  COLLDATE  

dwc:locality   mcpd:  COLLSITE   [geo:locaNon]  

dwc:countryCode   mcpd:  ORIGCTY     [mcpd:  ISO  3166-­‐1  alpha-­‐3]  

dwc:verbaNmLaNtude   mcpd:  LATITUDE  

dwc:verbaNmLongitude   mcpd:  LONGITUDE  

dwc:georeferenceSources   mcpd:  GEOREFMETH  

g:collecNngInsNtuteID   mcpd:  COLLCODE  

dwc:recordedBy   mcpd:  COLLNAME  

dwc:eventRemarks  

28  

Breeding  event  

g:BreedingEvent  (see  also  dcmitype:Event)  

g:breedingID  

g:breedingIdenNfier     mcpd:  ACCENAME  

g:breedingYear  

g:breedingCountry  

g:breedingCountryCode  

g:breedingInsNtuteID     mcpd:  BREDCODE  

g:breedingInsNtute   mcpd:  BREDNAME  

g:breedingPerson  

g:ancestralData     mcpd:  ANCEST  

g:purdyPedigree   (mcpd:  ANCEST)  

g:breedingRemarks    

29  

AcquisiNon  event  

g:AcquisiGonEvent  (see  also  dcmitype:Event)  

g:acquisiNonID  

g:donorsID  

g:donorsIdenNfier     mcpd:  DONORNUMB  

g:donorInsNtuteID     mcpd:  DONORCODE  

g:donorInsNtute     mcpd:  DONORNAME  

g:acquisiNonDate     mcpd:  ACQDATE  

g:acquisiNonSource     mcpd:  COLLSRC  

g:acquisiNonRemarks    

30  

Safety  duplicaNon  

g:SafetyDuplicaGon  (see  also  dcmitype:Event)  

g:safetyDuplicaNonID  

g:safetyDuplicaNonDate  

g:safetyDuplicaNonInsNtuteID     mcpd:DUPLSITE  

g:safetyDuplicaNonInsNtute   mcpd:  DUPLINSTNAME  

g:safetyDuplicaNonRemarks    

31  

Treaty  or  legislaNon  

g:TreatyOrRegulaGon  (see  also  dcmitype:Text,  foaf:Document)  

g:treatyOrRegulaNonID  

g:treatyOrRegulaNonName  

g:treatyOrRegulaNonGoverningBody  

g:mlsStatus     mcpd:  MLSSTAT  

32  

Measurement  method  (trait)  

g:MeasurementMethod  (see  also  dwc:MeasurementOrFact)  

g:measurementMethodID     epgris3:  TRAIT_NUMBER  

g:measurementMethodName     epgris3:  TRAIT_NAME  

g:measurementMethodCategory  

g:measurementMethodScale  

g:measurementMethodSource  

g:measurementMethodRemarks     epgris3:  TRAIT_REMARK  

dwc:measurementType  

dwc:measurementMethod    

33  

Measurement  experiment  

g:MeasurementExperiment  (see  also  dcmitype:Event)  

g:measurementEperimentID  

g:measurementExperimentIdenNfier  

g:measurementExperimentYear  

g:measurementExperimentReport  

g:measurementExperimentRemarks    

34  

Measurement  or  fact  

dwc:MeasurementOrFact  dwc:measurementID  

dwc:measurementValue  

dwc:measurementUnit  

dwc:measurementAccuracy  

dwc:measurementDeterminedDate  

dwc:measurementDeterminedBy  

g:measurementByInsNtuteID  

g:measurementGrowthStage    

35  

Controlled  value  vocabulary  Biological  status  type  wild  (100)  |  natural  (110)  |  semiNaturalWild  (120)  |  semiNaturalSown  (130)  |  weedy  (200)  |  landrace  (300)  |  breedingResearchMaterial  (400)  |  breedersLine  (410)  |  syntheNcPopulaNon  (411)  |  hybrid  (412)  |  founderStock  (413)  |  inbredLine  (414)  |  segregaNngPopulaNon  (415)  |  clonalSelecNon  (416)  |  geneNcStock  (420)  |  mutant  (421)  |  cytogeneNcStock  (422)  otherGeneNcStock  (423)  |  advancedCulNvar  (500)  |  GMO  (600)  |  otherBiologicalStatus  (999)    Acquisi1on  type  wildHabitat  (10)  |  forest  (11)  |  shrubland  (12)  |  grassland  (13)  |  desertOrTundra  (14)  |  aquaNcHabitat  (15)  |  culNvatedHabitat  (20)  |  field  (21)  |  orchard  (22)  |  backyard  (23)  |  fallowLand  (24)  |  pasture  (25)  |  farmStore  (26)  |  threshingFloor  (27)  |  park  (28)  |  marketOrShop  (30)  |  insNtuteOrGenebank  (40)  |  seedCompany  (50)  |  ruderalHabitat  (60)  |  roadside  (61)  |  fieldMargin  (62)  |  otherAcquisiNon  (99)  [Most  of  these  could  perhaps  be  replaced  by  their  respec;ve  term  from  the  Environmental  Ontology  (EnvO).]    Storage  type  seedCollecNon  (10)  |  shortTerm  (11)  |  mediumTerm  (12)  |  longTerm  (13)  |  fieldCollecNon  (20)  |  inVitro  (30)  |  cryopreserved  (40)  |  DNA  (50)  |  otherStorage  (99)    

36  

Some  proposed  addiNons  

In situ conservation (proposed) IUCNCategory, numberOfSeeds, bioRegion, inSituCountry, inSituRecoveryDateStarted, inSituRecoveryInstitute, inSituRecoveryRemarks Germplasm distribution Perhaps add new terms to facilitate the reporting of germplasm distribution and standards material transfer (SMTA) agreements for the International Treaty for Genetic Resources for Food and Agriculture (ITPGRFA). Germplasm management The Millennium Seed Bank (Kew) contributed feedback to the DwC-G modeling and proposed to include terminology for seed management.

•  Seed processing terms •  Seed cleaning •  Seed germination testing

 

37  

38  

Germplasm  vocabulary  of  terms  (RDF/SKOS)  …  

…  hTp://purl.org/germplasm/germplasmTerm#    

39  

Darwin  Core  Archive  extension  for  IPT  

…  

hTp://rs.gbif.org/extension/germplasm/20120911/GermplasmAccession.xml    

Term  Wiki  

hTp://terms.tdwg.org/wiki/    40  

Concept  Vocabulary    (rdf,  skos)  

Term  Wiki    For  vocabulary  development  

Resources    Repository  

1.  Mint  and  maintain  concepts  and  terms,  in  domain-­‐expert  working  groups.  2.  Release  final  version  as  a  Concept  Vocabulary.    3.  Publish  at  the  GBIF  Resources  Repository.    REUSE  terms  from  published  concept  vocabularies  and  ontologies  when  designing  new  applicaNon  schema  such  as  DwC-­‐A  controlled  term  and  value  vocabularies.  

2  

1  

3  

Work-­‐flow  for  Vocabulary  management  

hTp://rs.gbif.org/terms/  hTp://terms.tdwg.org/wiki/  

41  

Concept  Vocabulary    (rdf,  skos)  

Ontologies  (rdf,  owl)  

Biodiversity  ontology  development  

REUSE  terms  from  concept  vocabularies  whenever  possible.    

Biodiversity  ontology  repository  

hTp://bis.bioportal.bioontology.org/ontologies?filter=BIS  

42  

Example:  master  SKOS/RDF  resource    

hTp://rs.gbif.org/terms/dwc/dwc_translaNons.rdf      

[  [  [  [  en  

es  

zh  

ja  

43  

• Provide  a  shared  understanding  of  what  we  mean  when  describing  biodiversity  enNNes.  

• What  kind  of  thing  or  property.  • A  list  of  things  we  as  a  community  can  agree  upon  the  meaning  of.  

• “Concept  repository”  with  terms  idenNfied  by  URIs.  

Vocabularies/ontologies  

TDWG  Technical  Roadmap  2008  (convened  by  Roger  Hyam).    Photo  CC-­‐by-­‐3.0  by  Hannes  Grobe/AWI.  Palaeoclimate  archives.  

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• Vocabularies/ontologies  are  one  of  the  three  core  components  in  the  TDWG  technical  architecture.  

Vocabulary  management  

Hyam,  R  (2006).  A  technical  architecture  for  TDWG  standards.   45  

GBIF, Global Biodiversity Information Facility http://www.gbif.org

TDWG, Biodiversity Information Standards http://www.tdwg.org BioCASE, The Biological Collection Access Service for Europe

http://www.biocase.org Bioversity International

http://www.bioversityinternational.org NordGen, The Nordic Genetic Resources Center

http://www.nordgen.org

“Things  can  happen  in  a  band,  or  any  type  of  collabora;on,  that  would  not  otherwise  happen”  (Jim  Coleman,  Jazz-­‐musician).  

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