Laura Russell Programmer VertNet Buenos Aires (Argentina) 28 September 2011 Training course on biodiversity data publishing and.

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Presentation transcript:

Laura Russell Programmer VertNet Buenos Aires (Argentina) 28 September 2011 Training course on biodiversity data publishing and fitness-for-use in the GBIF Network, 2011 edition How to publish taxonomic data

Data publishing process

What is a checklist? A list containing sets of scientific names that implicitly or explicitly refer to taxa. The set of names may be constrained by: -taxonomic group, -geographic region, -or by a theme, such as invasive Species, -or some combination of all three

Resource Types Name lists Nomenclatural lists (Nomenclators) Taxonomic checklist Annotated checklists Flora or Faunal lists Monographs “Hyam. R., Standardisation of Data Exchange in the Pan-European Species-directories Infrastructure (PESI) Deliverable D 4.1”

Who uses checklists? Taxonomists Catalog of Life (aggregator) Protected area managers Conservation organizations Policy makers Ecologists

Where to find checklists? Currently discoverable in the registry, accessible in the GBIF data portal in 2012.

Using Darwin Core Archive to prepare a checklist Checklist metadata Checklist data – extensions Best practices

Checklist Metadata Documenting the provenance and scope of datasets is required in order to publish checklist data through the GBIF network. Data set documentation enables users to evaluate the fitness-for-use of a dataset.

Checklist data Taxon taxonID | acceptedNameUsageID | acceptedNameUsage | parentNameUsageID | parentNameUsage | originalNameUsageID | originalNameUsage | nameAccordingToID | nameAccordingTo | namePublishedInID | namePublishedIn | taxonConceptID | scientificNameID | scientificName | scientificNameAuthorship | higherClassification | kingdom | phylum | class | order | family | genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank | vernacularName | nomenclaturalCode | taxonomicStatus | nomenclaturalStatus | taxonRemarks | modified | language | rights | rightsHolder | accessRights | bibliographicCitation | informationWithheld | datasetID | datasetName | source

Checklist data: Extensions Vernacular names vernacularName | source | language | temporal | locationID | locality | countryCode | sex | lifeStage | isPlural | isPreferredName | organismPart | taxonRemarks Species descriptions description | type | source | language | creator | contributor | audience | license | rightsHolder Species distributions locationID | locality | countryCode | lifeStage | occurrenceStatus | threatStatus | establishmentMeans | appendixCITES | eventDate | startDayOfYear | endDayOfYear | source | occurrenceRemarks

Checklist data: Extensions References identifier | bibliographicCitation | title | creator | date | source | description | subject | language | rights | taxonRemarks | type Type information bibliographicCitation | occurrenceID | institutionCode | collectionCode | catalogNumber | typeStatus | scientificName | taxonRank | identificationRemarks | locality | sex | recordedBy | source | verbatimEventDate | verbatimLabel | verbatimLongitude | verbatimLatitude

Checklist data: Extensions Links and identifiers – Dynamic links – Alternative identifiers identifier | title | subject | format | – Resource relationship resourceRelationshipID | relatedResourceID | relationshipOfResource | relationshipAccordingTo | relationshipEstablishedDate | relationshipRemarks | scientificName

Checklist best practices Sharing scientific names Publishing classifications Publishing synonymy Metadata citation and attribution

Spreadsheet processor 1.Download the spreadsheet processor/templates/metadata/metadata-1_v1.xls processor/templates/metadata/metadata-1_v1.xls 2.Complete the spreadsheet 3.Transform it using the spreadsheet processor Validate with Darwin Core Archive Validator Publish the checklist to a stable URL.

IPT 1.Create a new resource in the IPT -Include appropriate extensions -Follow best practices 2.Complete the metadata -Consider which metadata will provide the most detail regarding the data set. 3.Publish it -Core data file -Required metadata file -Optional extension files -Data descriptor file

Resources Publishing Species Checklists, Best Practices Publishing Species Checklists, Step-by-Step Guide GBIF GNA Profile Reference Guide for Darwin Core Archive, Core Terms and Extensions

Presenter ( ) Role Organization Buenos Aires (Argentina) 28 September 2011 Training course on biodiversity data publishing and fitness-for-use in the GBIF Network, 2011 edition How to publish taxonomic data