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Transcript of Observational Data Standard, v 1.0 Lynn Kutner, Donna Reynolds, Jennifer Nichols, Kristin Barker,...
Observational Data Standard, v 1.0
Lynn Kutner, Donna Reynolds, Jennifer Nichols, Kristin Barker, Kristin Snow
April 2007
A Provisional Standard to Facilitate Data Sharing and Aggregation
Working GroupNatureServe Lynn Kutner Carol Fogelsong Donna Reynolds Jennifer Nichols Bruce Stein Rickie White Keith Carr Kelly Gravuer Larry Master Kristin Barker
Member Programs Karen Cieminski (MN) Karen Walker (MT) Pete Sorrill (ON) John Fleckenstein (WA) Nicole Firlotte (MB) Jim Morefield (NV) Tim Howard (NY) Melanie Arnett (WY)
Partners Parks Canada Canadian Wildlife Service Cornell Lab of Ornithology Larry Morse
Reviewers Member Programs: Alberta, British Columbia, Connecticut,
Idaho, Maine, Manitoba, Maryland, Massachusetts, Minnesota, Montana, Nevada, New Hampshire, New York, Ontario, Pennsylvania, Saskatchewan, Texas, Vermont, Virginia, Washington, West Virginia, Wyoming
NatureServe Central NatureServe Canada Canadian Wildlife Service Cornell Lab of Ornithology Information Center for the Environment (ICE), University of
California, Davis Parks Canada U.S. National Park Service VegBank Washington Department of Fish and Wildlife
Development of the Standard
Process Funded by the Gordon and Betty Moore Foundation NatureServe is a co-sponsor of the Taxonomic
Databases Working Group (TDWG) Observational Data Subgroup: this is a provisional standard as an input for that group’s work towards an international observational data standard
Multi-institutional Observation Working Group Compared 16 observation databases to identify
breadth and commonalities among attributes: Salvias, ABCD, VegBank, Darwin Core2, Member Program custom databases
Project began mid-2005. Version 1.0 published September 2006
Initial implementation in NatureServe’s Kestrel Revisions expected
What is an Observation?
An observation characterizes evidence for the presence or absence of an organism or set of organisms through a data collection event at a location.
Goals & Requirements Useable—minimal requirements, simple Extensible, e.g., discipline-specific data Universal
core set of concepts, broadly applicable, for data sharing and aggregation
compatible with (and incorporating) existing standards Software-independent
Accommodate: species AND ecological communities (inc. plots) historical data different protocols negative (absence) data data quality and validation attributes monitoring
Overview of the Standard
http://www.natureserve.org/prodServices/obsStandard.jsp
Major Entities
Observation
Observation Grouping
Survey
Species List
Project (group of surveys)
Protocol (methods)
Search Area
External Documentation
Ranking of Attributes
Required – cannot be null, but in some cases can be “unknown”
Priority Core – should always be recorded if possible
Core – important but not required (not always available or applicable)
Additional – supplementary data
Attribute Table
Observation: Required Attributes
1. What: Scientific nameCalypte anna or
Quercus velutina / Ilex opaca Forest or
“a community”
2. Where: GIS shape, coordinates, or text New Mexico: Eddy County, 3 mi S of Artesia along Rt. 285
3. When: Date (to year, at least)
30 November 1978
4. Who: Observer Name(s) or “Unknown”D.J. Davis
Observation: “What” Scientific Name Author – of scientific name
Concept reference & name used in concept ref
Name Type – “taxon” or “ecological community” Identification Confidence – high, medium, low
Concept Fit – extent to which observed community fits with published concept
Secondary Designation – other communities / taxa that this observation may relate to
Verbatim Scientific Name
GUID – global universal identifier of a taxonomic concept
Observation: “Where” Link to GIS feature (point, line, polygon)
Latitude, Longitude, Datum
Location Description (text)
OR
Country
Mapping Accuracy – distance within which the location of the observation has believed to have been captured
Location confidence – high, medium, low
Location fuzzed – indicator and/or description of process if data have been randomized / generalized
Date of the observation – includes either full date, partial date, or range of dates
Date Accuracy – proposed values: accurate within 1 day, 1 week, 1 month, 3 months, 1 year, 3 years, 10 years, >10 years
Observation Start Time and End Time
Observation: “When”
Observer Name – full name(s) of the person(s) who collected data
Observer Affiliation
Observer Postal Address, Phone Number, E-mail Address
Observer Role – primary observer, observer, collector, submitter, verifier
Observation: “Who”
Protocol – protocol used to collect data
Found Indicator – used to indicate negative (absence) data
Confidence – confidence in search result (High, Medium, Low)
Level of Effort – effort expended on a given visit
Additional Inventory Needed – Is additional inventory of the area needed for this element? (Y / N)
Evidence Type – sample values: Specimen, Sighting, Literature, Photograph, Tracks
Evidence Comments
Observation: “How”
Observation: Evidence
Observation: Biology Number of Individuals (species)
Estimated / Observed – whether number is estimate or actual count
Reproductive Evidence – element reproducing at the location? (Y / N)
Condition of Element – description of the quality of element (e.g., health, alive or dead)
Density / Distribution – distribution of the element on the landscape (e.g., solitary individual, patchy, scattered, solid cover)
Strata – vegetation strata in the community
Origin – sample values: Native, Nonindigenous, Unknown/Undetermined
Invasiveness Comments – notes about the degree of invasiveness
Observation: Environment Habitat Description – text description of the local or surrounding
habitat
IUCN Habitat Category – habitat type, selected from a picklist
Condition of Site – condition of the surroundings (e.g., flooded, burned, etc.)
Weather – description of the weather conditions at the time of the visit
IUCN Threat Category – primary threat, selected from a picklist
Threat Comments – notes about primary or other threats
Management Activities – activities conducted during a particular visit (e.g., pulling or pesticides applied to invasives)
Management Needs – most important management needs (for enhancement or control) at this observation site
Data Sensitive – Is the observation information sensitive? (Y / N)
Reason Data Sensitive – primary reason why data are sensitive
General Comments – notes about observation not addressed elsewhere
Internal Notes – comments or issues about the observation that are internal to the organization that created the record
Associated Element Scientific Name
Associated Element Origin sample values: Native, Nonindigenous, Unknown/Undetermined
Associated Element Relationship Comments
Other Information
Associated Elements
Major Entities
Observation
Observation Grouping
Survey
Species List
Project (group of surveys)
Search Area (inc. plot) - GIS Shape
Protocol (methods)
Documentation
Observation Grouping
Name of Grouping
Criteria – the common characteristic or other criteria used to group the observations (same element, same location, or any other criteria)
Owner – the person who created the observation grouping
Monitoring Comments – changes over time and trends within the grouping
Species List For community plot data
observation ID search area ID (plot) scientific name / concept stratum cover class percent cover number (per species)
May make an observation record for each species, but not required
Next Steps Current and future software development
projects at NatureServe:
Kestrel
Handheld field data collection tool - funding received from NSF
XML schema, mapping to existing TDWG standards
TDWG Observational Data Subgroup
Kestrel NatureServe’s Web Application for
Observations Data Management
XML-based Web interface Extensible: Data model is dynamically generated
Libraries and Templates Open Source
Kestrel Architecture
KestrelXML Web Service
KestrelXML Web Service
KestrelWeb User Interface
KestrelWeb User Interface
OracleDatabase
Internet
BrowserBrowser
AggregationPortal
AggregationPortal
DesktopApplication
DesktopApplication
Field DeviceField Device
XMLHTML
Application Framework
KestrelXML Web Service
KestrelXML Web Service
KestrelWeb User Interface
KestrelWeb User Interface
OracleDatabase
IDDSpecies Web Service
IDDSpecies Web Service
BioticsDatabase
SecurityXML Web Service
SecurityXML Web Service
Users & Permissions
Database
ArcGIS ServerXML Web Service
ArcGIS ServerXML Web Service
SDEDatabase
Observation Standard Support
Core Attributes Who, what, where, when Managed as relational fields
Extended Attributes Managed as XML
Attribute Extensibility
Individual Attributes defined in XML Help to describe observation or survey Non-trivial effort Signed by author,
optionally by organization
Exam
ple
Att
ribu
te:
Obse
rvati
onTyp
e
Exam
ple
Att
ribu
te:
Aci
dit
y
Attribute Collection
Group of Extended Attributes Strongly associated with observation or survey
Signed by author/organization “Work together” Ad-hoc OR Protocol support, e.g.
Heritage Methodology CI Rapid Assessment Citizen Bird Survey
Timeline
Parks Canada: June 2007 – very basic functionality
NSF Handheld Data Collection Tool: June 2009 – accommodate plots, multivalued data, etc.
Questions / Discussion