Datasources¶

• VegBIEN contents

• CTFS
• Historical BIEN
  • BIEN1
  • BIEN2
    • Data loading scripts
    • ViewFullOccurrence
  • BIEN2 5
• Mappings
• SALVIAS
• TEAM
• Tropicos

• Table of contents
• Datasources
  • BIEN3 data
  • BIEN2 data
  • Comparison
    • BIEN 2 datasources
    • Observations
  • References
  • Traits
  • Taxonomic name resolution

BIEN3 data¶

• Available on vegbiendev in /home/bien/
• Datasources are available on vegbiendev in /home/bien/inputs/

BIEN2 data¶

Available on nimoy in /home/bien_shared/raw_data/

Comparison¶

Legend: (e-mail from Brad Boyle on 2011-10-14)

• specimens: "verifiable georeferenced point observations"
• species locations: "assertions of presence within political divisions or other polygon-type localities"

See Data loading scripts for locations of BIEN2 input data

Databank	Available	Type	Aggregator/Primary	Format	Taxonomy	In BIEN2	In VegBIEN
BIEN 2	phpMyAdmin	plots	aggregator	MySQL	TNRS	-	Y1
VegBank	exportable	plots	aggregator	Access, XML	Plant Search	Y	Y
GBIF	exportable	specimens (DwC)	aggregator	web service, XML, CSV, Excel, maps	GNA	Y	Y
NVS	data request form	plots	primary	VegX, Access, XML, ASCII, Excel	NVS Names	Y	Y2
CTFS	some	plots	primary	MySQL clone, HTML tables, Excel, Google maps	-	Y	Y
SALVIAS	exportable clone	plots	aggregator	MySQL clone, CSV	TaxonScrubber	Y	Y
CVS	viewable	plots	primary	HTML tables, Google maps, links to VegBank plots	US Southeast flora atlas		Y
KNB	downloadable	plots	aggregator	CSV, EML metadata	-	N
Atlas of Living Australia	downloadable	species locations + observations	aggregator+primary	CSV	IBIS TaxonName	N
Australia’s Virtual Herbarium	exportable	specimens	aggregator	CSV	-	N
PLANTS	viewable maps	species locations	primary	maps	PLANTS Checklist	N
Forest Plots Database	requires login	plots	primary	unknown	-	Y
FIA	downloadable	plots	primary	CSV	-	Y	Y
SEINET	downloadable	specimens	aggregator	CSV	PLANTS Checklist	N
U. Arizona Herbarium	downloadable	specimens	primary	CSV	PLANTS Checklist	Y	Y
MO Bot. Garden	downloadable, large downloads by request	specimens	primary	web service, HTML tables, CSV by request	Tropicos	Y	Y
TEAM	downloadable	specimens?	primary	CSV	-	N	Y
TRY	data request form	species traits	primary	CSV	-	N
REMIB	exportable	specimens	aggregator	CSV	-	Y	Y
REMIB nodes	exportable (REMIB Server column)	specimens	primary	DiGIR	-	N

¹ raw data used for BIEN2, rather than BIEN2 itself

² sample project
.

BIEN 2 datasources¶

Datasource	In VegBIEN
ARIZ	Y
SpeciesLink	Y
GBIF	Y
MO	Y
NCU-NCSC	Y
NY	Y
REMIB	Y
U	Y
UNCC	Y
CTFS	Y
CVS	Y
FIA	Y
Madidi	Y
SALVIAS	Y
TEAM	Y
VegBank	Y

Observations¶

• Most databanks do not make their data available in a unified, exportable format.

References¶

• VegBank
  • contacts: Mike Lee (manager), Bob Peet (designed UI), ESA
  • vegbankvm and vegbankdev servers
    • install dir: /var/lib/tomcat6/webapps/vegbank
    • database access: become postgres user and run psql -d vegbank
    • databaseConnectString: jdbc:postgresql://localhost/vegbank
    • source code (also in svn below): /home/lee/
    • XSLTs for importing/exporting XML: /var/lib/tomcat6/webapps/vegbank/xsl/*.xsl
  • vegbank svn repository
    • Java class for importing XML
    • class-action mapping XML
  • vegbank_erd.pdf
  • VegBank XML
  • VegBank Data Dictionary: Menu
    • /src/sql/createdb.sh: creates VegBank database
    • /REINSTALL_NEW_SERVER.txt: reinstalling VegBank on VegBankVM
  • VegBranch: VegBranch, version 1.7, VegBank Module database
  • VegBranch tools : Normalizer
  • Bugzilla
• GBIF: Global Biodiversity Information Facility
  • Data Portal
  • can export as Darwin Core
  • has TAPIR, ABCD web service
• New York Botanical Garden: Index Herbariorum
  • has coordinates of herbaria for determining if plots are cultivated
• SALVIAS
  • contacts: Brad Boyle, Brian Enquist
  • DATA DICTIONARY
  • clone on nimoy in salvias_plots MySQL database
  • data: CSV
  • requires login to access data
• CVS: Carolina Vegetation Survey
• KNB: The Knowledge Network for Biocomplexity
  • EML: Ecological Metadata Language
  • data: plain text tables
• Atlas of Living Australia: species locations; CSV
  • Contributors: pulls data from other databases, such as Australia’s Virtual Herbarium
  • How to Share Datasets | Atlas of Living Australia
• AVH: Australia’s Virtual Herbarium: species locations; CSV
• NVS: The National Vegetation Survey Databank (New Zealand)
  • Requesting data
  • has SQL Server schema
  • sample VegX and raw XML data in nimoy:/home/bien_shared/raw_data/nvs/
• CTFS: Center for Tropical Forest Science
  • data: HTML tables, Excel spreadsheets, Google maps
• RAINFOR
• TEAM
  • contact: Eric Fegraus
  • wants to produce VegX output
• Dashboard - iPlant Collaborative Wiki
• Home - iPToL - iPlant Collaborative Wiki
• PLANTS: species locations in U.S. and Canada; map images
  • search
• Forest Plots Database
  • requires login to access data
• JEDI: Jellyfish Database Initiative
  • contact: Jim Regetz (updated by Mark)
• Nutrient Network
  • "a network of small experiments [...] designed to answer a broad set of questions about how grasslands respond to global change"

Traits¶

• TRY Initiative on Plant Traits
  • requires application to access data
• TraitNet

Taxonomic name resolution¶

• TNRS: Taxonomic Name Resolution Service
  • reference taxonomy: Tropicos
• Tropicos
• Global Names Index
• GNA: Global Names Architecture
  • GBIF work
• TAXAMATCH/IRMNG
• Plantminer
  • reference taxonomy: The Plant List, Tropicos
• uBio
• VegBank Plant Search
• SALVIAS TaxonScrubber
• GRIN TAXONOMY
  • format: dbase; use *nix dbfdump (or Perl dbfdump, Shapefile C library) to export to CSV
• US Southeast flora atlas
• Name Resolution Service | Atlas of Living Australia
  • NSL Services
  • biodiversity.org.au taxonomic repository services
  • uses Taxon Concept Schema (TCS)
• PLANTS Checklist
• TNC: Taxonomic Names and Concepts Group