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Standards and tools for publishing biodiversity data
Yu-Huang WangJune 25, 2012
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GBIF informatics infrastructure
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GBIF biodiversity data resources• Resource =
Meta data + Dataset• A dataset is a collection of data
records.• Metadata describe datasets.
In context of GBIF, metadata provide information about the suppliers of biodiversity data and about the origins and purpose of those data.
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GBIF biodiversity data resources• A data record is a collection of record
elements or properties. An example data record may describe a museum specimen. One of the data elements would almost certainly be a scientific name element.
• A record element contains the data values (i.e., the data). An example value in a scientific name record element would be Abies kawakamii.
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Three core data types• Primary biodiversity data or occurrence data,
e.g., a dataset of bird observation data records, specimen data records from a natural history museum, etc.
• Taxonomic data, e.g., a dataset of an annotated checklist of bird species
• Resource metadata, data records that provide descriptive information about datasets.
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Data publishing workflow
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Publishing options in the GBIF Network
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Standards for publishing data• Darwin Core
- occurrence- check list
• EML metadata• Darwin Core Archive
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Darwin core terms
• Record-level • Occurrence • Event • GeologicalContext • Location
• Identification• Taxon• ResourceRelationship • MeasurementOrFact• Type Vocabulary
http://code.google.com/p/darwincore/
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Darwin core & extensions definitions
http://tools.gbif.org/resource-browser/
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EML• GBIF metadata profile is primarily based on
the Ecological Metadata Language (EML).• Currently, GBIF refers to KNB EML 2.1.0
specification (http://knb.ecoinformatics.org/software/eml/)
• GBIF profile utilizes a subset of EML and extends it to include additional requirements that are not accommodated in the EML specification.
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12 forms for metadata in IPT2
• Basic Metadata• Geographic Coverage• Taxonomic Coverage• Temporal Coverage• Other Keywords• Associated Parties• Project Data
• Sampling Methods• Citations• Collection Data• Physical Data• Additional Metadata
12
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Darwin core archive (DwC-A) component
• Core data file
• Optional extension file
scientificName
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Darwin core archive (DwC-A) component
• Metafile
• Resource metadata
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Darwin core archive (DwC-A)• Core data file• Extension files• Metafile• Metadata file
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Tools • Excel templates• Spreadsheet processor• IPT2
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Data publishing mechanism
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Excel template & spreadsheet processor
http://tools.gbif.org/spreadsheet-processor/
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Metadata template• Readme
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Metadata template• Metadata
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Occurrence template• Readme
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Occurrence template
• Metadata• Occurrence
- 45 terms (columns)
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Check list 1 template• Readme
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Check list 1 template• Classification “Nomalized”
- 14 terms (columns)
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Check list 2 template• Readme
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Check list 2 template• Higher Classification in unranked columns
- 19 terms (columns)
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Check list 3 template• Readme
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Check list 3 template• Standard Linnaean Classification
- 18 terms (columns)
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Upload your excel template
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Publish data via IPT2
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Document map for publishing data
http://www.gbif.org/informatics/discoverymetadata/publishing/
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Thank You!
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