Formats¶

• Comparison tables
• Darwin Core
  • Darwin Core changes
  • Darwin Core terms
• VegCSV
  • Map refactoring
  • VegCore
    • Combining VegCore and VegBIEN
    • Normalized VegCore to-dos
    • SQL dotpaths
    • Text IDs
      • String IDs
      • U-name
        • C-name
        • Globally unambiguous
    • VegCore refactoring
  • VegCSV-DwC merging
  • VegCSV FAQ
  • VegCSV subfolders
  • VegCSV vision
  • VegCSV vs VegX
  • VegX to VegCSV
• VegX
• XML
  • XPath cleanup
  • XPath reversing

• Table of contents
• Formats
  • Motivation
  • Diagrams
  • Data dictionaries
  • XML schemas
  • Formats
    • VegBank
    • VegX
    • SALVIAS
    • Ecological Metadata Language
    • Darwin Core
    • Turboveg for Windows
    • ABCD: Access to Biological Collections Data
    • TAPIR - TDWG Access Protocol for Information Retrieval: database query protocol
    • TCS: Taxonomic Concept Transfer Schema
    • UBIF: Unified Biosciences Information Framework
    • SDD: Structure of Descriptive Data
    • ESVeg
    • OBOE & semantic annotation — SONet Project
    • Observational data models as a unifying framework for biodiversity information
  • Entities

Motivation¶

• VegX.schematic_diagram.problem_solution.png

Diagrams¶

• BIEN2_ERD.svg, BIEN2_ERD.pdf (source: BIEN2_ERD.mwb, BIEN2_ERD.sql)
  • previous: bien2_core_schema.png
• VegBank entity relationship diagram (2004-2-18)
  • created with Visio
  • uses "custom tool [...] built into VegBranch" (e-mail from Michael Lee on 2011-10-24)
  • vegbank_MySQL.sql (converted from PostgreSQL)
• Veg-X_elements_relationships.png
  • veg_vegX.svg
  • veg-misc_schema.svg
  • veg-organismobservation_schema.svg
  • veg-plot_PlotType.svg
  • veg-plotobservation_schema.svg
  • EML: eml-resource_schema.svg
  • TCS: tcsv101_schema.svg
  • Darwin Core: tdwg_dw_geospatial_schema.svg
• EML diagram
• SALVIAS: salvias_plots_erd.png

Data dictionaries¶

• Darwin Core (schema)
  • TDWG Darwin Core Terms
  • Google Code Darwin Core Terms
    • Occurrence class
• BIEN 2
• VegBank
• SALVIAS

XML schemas¶

• VegBank: Simplified Schema
• VegX: VegX Schema 1.5.3
• NVS->VegX
• EML: EML 2.1.0 ZIP file
• ABCD
• Darwin Core: Simple Darwin Core XML schema., Darwin Core 1.2 (Classic) schema
• Darwin Core->ABCD
• TCS: "v101.xsd":http://www.tdwg.org/uploads/media/v101.xsd
• SDD: "SDD1.1.zip":http://wiki.tdwg.org/twiki/pub/SDD/Version1dot1/SDD1.1.zip

Formats¶

VegBank¶

• Full Interactive entity relationship diagram
  • slightly out of date: "The ERD and data dictionary are up to date except for a very minor change we made in the plant taxonomy and community taxonomy modules, where plantUsage relates to plantStatus instead of directly to plantConcept. This ties the "party perspective" together into one package." (e-mail from Michael Lee on 2011-10-20)
• PowerPoint explaining ERD: peet-vegbank.ppt: p. 18-50
• Data Dictionary

VegX¶

• contact: Nick Spencer
• "contains information on vegetation (ecological) inventories" (e-mail from Brad Boyle on 2011-10-18)
• Veg-X_elements_relationships.png
• Diagram
• VegX paper in Journal of Vegetation Science
  • VegX paper draft in Applied Vegetation Science
• "The standard supports repeated measurements of both individual organisms and plots" (JVS paper abstract)
• "We had considered making DwC a subset of VegX--and may still do so in future versions--but for the moment there is still disjunction between the two schemas" (e-mail from Brad Boyle on 2011-10-18)
• only New Zealand currently stores data in VegX format (uses sparse format)

SALVIAS¶

Ecological Metadata Language¶

• diagram
• EML 2.1.0 Specification
  • diagrams on p. 233-255
• Metacat

Darwin Core¶

• "contains information on individual museum/herbarium specimens" (e-mail from Brad Boyle on 2011-10-18)
• based on DCMI: Dublin Core Metadata Initiative

Turboveg for Windows¶

• mapping to VegBank: DBASEDIC_rkp2011_mtl2011.xlsx
• Export to standard XML file
• designed for tropical data, which uses rélevés

ABCD: Access to Biological Collections Data¶

TAPIR - TDWG Access Protocol for Information Retrieval: database query protocol¶

TCS: Taxonomic Concept Transfer Schema¶

UBIF: Unified Biosciences Information Framework¶

SDD: Structure of Descriptive Data¶

ESVeg¶

• An Exchange Standard for Vegetation Data

OBOE & semantic annotation — SONet Project¶

Observational data models as a unifying framework for biodiversity information¶

Entities¶

• VegBank entity relationship diagram table colors:
  • Party
  • Plant Taxonomy
  • Observation
  • Plot
  • Taxon Observation
  • Community Taxonomy
  • Observation Interpretation
  • Supplemental
  • Reference
  • Method
• VegX diagram entities:
  • Projects
  • Plots
  • Observations
  • Methods
    • Protocol
  • Organisms
    • Individual
    • Aggregated
  • TaxaOccurence
    • TaxonDetermination
• VegX schema veg.xsd <xsd:element>s:
  • LiteratureCitation
  • Party
  • Project
  • Plot
  • PlotObservation
  • TaxonName
  • TaxonConcept
  • TaxonNameUsageConcept
  • TaxonDetermination
  • CommunityDetermination
  • AggregateOrganismObservation
  • Stratum
  • StratumObservation
  • IndividualOrganismObservation
  • IndividualOrganism
  • AbioticObservation
  • ObservationGrouping
  • Attribute
  • Method
  • Protocol
  • Userdefined