CalBug: Databasing, Georeferencing, and Related Information

Web Resources:

• Darwin Core
• MaNIS/HerpNet/ORNIS Georeferencing Guidelines: http://manisnet.org/GeorefGuide.html
• Essential Attributes of Coordinate Data: http://manisnet.org/GeorefGuide.html#essential_attributes

• UC Berkeley Essig database:
  • Screen shot of Essig specimen entry form
  • Essig specimen table schema
  • Essig batch specimen upload form (via Excel)
  • Essig specimen database search: long form; short form
  • Essig database home page
  • Data Entry Procedures for Essig Web Data Portal

• Data summary for participating collections. (google doc)

• Transcribing from labels: Sample labels, fields to database, and issues from the Essig database. Also see additional sample labels.

• Bug OCR blog: Kai Wang, grad student at UCSD, and Phuc Nguyen are working with CalBug to help digitize specimens using OCR.

• Citizen Science: Notes from Nature -- start transcribing!

• Video: Global Change and CalBug

---

Three sets of overlapping fields are important to CalBug:

1. Fields an institution needs for populating its own database. Decisions about exactly what fields should be captured are up to each institution, but from this data CalBug needs to extract certain fields for its cache and for georeferencing.
2. Fields for the CalBug cache, to be used for: spatial analysis, cross-institutional web searches and mapping, searching across arthropod/plant/vertebrate collections.
3. Fields to be used during georeferencing. Some of these fields will be in the cache at the end of the project, but some will only be stored in individual institution databases.

Field required for cache

Field required for georeferencing

Field recommended for populating while digitizing specimens

 

Darwin Core field name	other field names	comments	links to description and information
catalogNumber	Unique coden		http://rs.tdwg.org/dwc/terms/index.htm#catalogNumber
institutionCode	Source institution coden (EMEC, CSCA, UCD,etc.)		http://rs.tdwg.org/dwc/terms/index.htm#institutionCode
Taxonomy and Identification
kingdom			http://rs.tdwg.org/dwc/terms/index.htm#kingdom
phylum			http://rs.tdwg.org/dwc/terms/index.htm#phylum
class			http://rs.tdwg.org/dwc/terms/index.htm#class
order			http://rs.tdwg.org/dwc/terms/index.htm#order
family			http://rs.tdwg.org/dwc/terms/index.htm#family
genus			http://rs.tdwg.org/dwc/terms/index.htm#genus
specificEpithet			http://rs.tdwg.org/dwc/terms/index.htm#specificEpithet
	subspecies	this is infraspecificEpithet in DC, but not the same -- see links	http://rs.tdwg.org/dwc/terms/index.htm#infraspecificEpithet http://code.google.com/p/darwincore/wiki/Taxon
	TaxonIDCertainty
scientificNameAuthorship			http://rs.tdwg.org/dwc/terms/index.htm#scientificNameAuthorship
identifiedBy	Identifier		http://rs.tdwg.org/dwc/terms/index.htm#identifiedBy
dateIdentified	Date Identified		http://rs.tdwg.org/dwc/terms/index.htm#dateIdentified
Geography
country			http://rs.tdwg.org/dwc/terms/index.htm#country
stateProvince			http://rs.tdwg.org/dwc/terms/index.htm#stateProvince
county			http://rs.tdwg.org/dwc/terms/index.htm#county
locality			http://rs.tdwg.org/dwc/terms/index.htm#locality
minimumElevationInMeters			http://rs.tdwg.org/dwc/terms/index.htm#minimumElevationInMeters
maximumElevationInMeters			http://rs.tdwg.org/dwc/terms/index.htm#maximumElevationInMeters
Fields to fill during georeferencing
decimalLatitude	also required for cache		http://rs.tdwg.org/dwc/terms/index.htm#decimalLatitude
decimalLongitude	also required for cache		http://rs.tdwg.org/dwc/terms/index.htm#decimalLongitude
coordinateUncertaintyInMeters	also required for cache Error radius in meters		http://rs.tdwg.org/dwc/terms/index.htm#coordinateUncertaintyInMeters
geodeticDatum	also required for cache Datum		http://rs.tdwg.org/dwc/terms/index.htm#geodeticDatum
verbatimCoordinateSystem	Original_Coord_System		http://rs.tdwg.org/dwc/terms/index.htm#verbatimCoordinateSystem
georeferenceSources	Reference		http://rs.tdwg.org/dwc/terms/index.htm#georeferenceSources
georeferencedBy	Lat_Long_Determined_By		http://rs.tdwg.org/dwc/terms/index.htm#georeferencedBy
	Lat_Long_Determined_Date
georeferenceRemarks			http://rs.tdwg.org/dwc/terms/index.htm#georeferenceRemarks
Other
	collectionBeginDate: Begin date of collection 2009-06-14	DC has several options for date formats now. I would like a begin and and end date in the form 1987-05-13 but that doesn't seem to be an option ?	http://rs.tdwg.org/dwc/terms/index.htm#eventDate
	collectionEndDate: End date of collection (in case of date ranges) 2009-06-30	see above
recordedBy	Collector(s)		http://rs.tdwg.org/dwc/terms/index.htm#recordedBy
samplingProtocol	Collection type, Collection_Method		http://rs.tdwg.org/dwc/terms/index.htm#samplingProtocol (see also http://rs.tdwg.org/dwc/terms/index.htm#samplingEffort)
associatedTaxa ?	Plant association		http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
associatedTaxa ?	Host association		http://rs.tdwg.org/dwc/terms/index.htm#associatedTaxa
	Associated materials
sex?	No. males	Counts: Darwin Core doesn't split counts by sex	http://rs.tdwg.org/dwc/terms/index.htm#sex
sex ?	No. females	Counts: Darwin Core doesn't split counts by sex	http://rs.tdwg.org/dwc/terms/index.htm#sex
sex ?	No. other	Counts: Darwin Core doesn't split counts by sex	http://rs.tdwg.org/dwc/terms/index.htm#sex
individualCount	Total specimens		http://rs.tdwg.org/dwc/terms/index.htm#individualCount
	Comments	Darwin Core has several "Remarks" fields: occurrenceRemarks, eventRemarks, locationRemarks, georeferenceRemarks, taxonRemarks, identificationRemarks, etc