New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.
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New Frontiers in Mapping Biodiversity Specimen Data
Gail E. KampmeierIllinois Natural History Survey
Institute of Natural Resource SustainabilityUniversity of Illinois at Urbana-Champaign
7th International Congress of Dipterology
Symposium: Getting Diptera taxonomy up-to-date: New frontiers & the Web
What Does this Mean for Dipterists?
Short-term goals Publication Looking for trends Where do species exist relative to one
another? In geologic time Finding outliers in your data (data cleaning) Planning collecting expeditions for fresh
specimens Providing checklists of species Meeting the terms of a grant or project
Long-term Goals Synergy of combining your data with that of others Analyze trends with diverse & more comprehensive
data sets Reveal how species respond to environmental
changes Contributes to land management decisions Indicators of environmental health Range expansion or extinction Potential for invasive species Google, LifeMapper, DesktopGARP, OpenModeler, &
Spire: ELVIS
Many other uses http://www.biogeomancer.org/bg_library/references/uses/ Improve the ease of sharing data
Ratified in October 2009, the DwC includes not only descriptive political & geographical terms, but extensive ability to record georeferencing terms
Verbatim Interpreted Datum Uncertainty Precision Protocol Sources Status
Standards: Darwin Core (DwC)
Fitness-for-Use For some applications, data
quality may be low (e.g., accurate to the county/province level) but adequate for the scale of the question being asked: Does this species occur in Costa Rica?
However, Does this species occur with this soil type or habitat type? will require more accurate & precise data
http://en.wikipedia.org/wiki/Accuracy_and_precision
Data Cleaning Services to Detect, Flag, & Correct Where Initial data not accurate and/or precise
Misspellings/non-standard abbreviations Incomplete/ambiguous locality/collecting event
descriptions Errors introduced during data entry
Decimal point misplaced Wrong hemisphere or doesn’t match locality string Latitude/Longitude values flipped
Errors converting to decimal lat/long http://biodivertido.blogspot.com/2009/02/grid-data-shared-as-point-data-errors.html
Geodetic datum unspecified or incorrect from GPS
measurements (see why this is important: http://zistmz.blogspot.com/2009/05/gps-coordinate-systems-google-earth.html
)
Why Should We Care? The Issues: Errors erode confidence in user community
Data errors cause misinterpretation of results when used in analyses
Duplication of effort Lack of awareness/coordination of efforts Territoriality of politically-based funding sources
Beta, Demo, Proposed… Ephemerality of politically-based funding sources
Multistep process Detecting anomalous data by expanding
• Temporal coverage• Species distribution models; checklists• Languages of existing tools, (oeste = west = W = O)
Reporting errors to data provider Resolving/correcting errors at source
Early Tools for Retrospective Georeferencing
Paper gazetteers & maps Helpful for legacy datasets particularly
where political boundaries have changed or entities are not well documented
Require expert knowledge to interpret
Desktop gazetteers – Microsoft Encarta (late 1990’s only) (PC only)
Fuzzy spelling accepted Would measure displacements
Current Tools for Georeferencing Online Gazetteers
Getty Thesaurus of Geographic Names (TGN) http://www.getty.edu/research/conducting_research/vocabularies/tgn/
Annotated lists of gazetteers• http://www.inhs.illinois.edu/research/mandala/geocoding.html
• http://www.herpnet.org/Gazetteer/GeorefResources.htm
Online Mapping Google Maps http://maps.google.com/maps?hl=en&tab=wl Google Earth http://earth.google.com/intl/en/ DiscoverLife.org – create albums with photos
http://pick14.pick.uga.edu/pa/ph/ Automated Georeferencing
BioGeoMancer Classic & Workbench
GEOLocate
Parque Nacional Santa Rosa, Liberia, Stor Santa Rosa
Georeferencing - Prospective GPS (Global Positioning System) unit or mobile
phone Taken to the field – calibration errors possible;
geodetic datum not set or noted Single reading taken at start, while collector roams
wide area Specimens mobile or collected in flight Precision & uncertainty of measurement
• 30 m uncertainty is considered normal for GPS reading http://rs.tdwg.org/dwc/terms/index.htm#coordinateUncertaintyInMeters
• GPS precision for decimal degrees, 0.00001 Logging into your database on the go
From iPhone to Filemaker Go http://www.supportgroup.com/explore/geolocation-with-filemaker-go/
GBIF (Global Biodiversity Information Facility)
Best known Provides
leadership & some seed funding to support
Standards development
Global catalog of taxonomic names
Biodiversity data mobilization
Label data
Record provenance & Taxonomic Name
AntWeb in Google Earth
•Community showcase
•Only ants
Atlas of Living Australia (ALA)
Public launch of their geospatial portal planned for October 2010 http://www.ala.org.au/
Environmental & contextual data linked to georeferenced specimens & observations
• 250 layers from the Australian Environmental GIS library
• Partnering with ERIN (Environmental Resources Information Network) http://www.environment.gov.au/erin/
• Australia was pioneer in digitizing its collections, convincing politicians of the economic sense of linking the museum holdings
Audience for ALA is very broad, hope to answer• Where is this thing?• What things occur in this area – with 6 different ways
to define “area” Will exist in the cloud Will include links to
• Biodiversity Heritage Library (BHL)• Citizen science• Video images• Keys
• DNA – Dan Faith’s phylogenetic diversity http://en.scientificcommons.org/daniel_p_faith
Will have Creative Commons licensingFrom Skype with Lee Belbin, ALA Geospatial Team Leader; misinterpretations derived are my own. --gk
Is the Future in the Cloud?
J.A. Olson (2010) Data as a Service: Are we in the clouds?
Daas (Data as a Service) Clearinghouse style environment –
remote data storage & maintenance usually provided by companies – generally less useful to biodiversity community except for archiving
Biodiversity community might use US Geological Survey & statewide GIS clearinghouses that provide downloadable mapping layers
Crowd Sourcing in the Cloud
Collaborative projects where all participants can see, use, & contribute data
“Most crowd-based projects are more likely to be locally created and have details and features that commercial data sets do not have. They can be created by groups within a government agency, or groups of researchers, or even a combination of these from around the world working on a project together. Large or small, I believe that crowd sourcing will become the mainstream of scholarship in the near future.” J.A. Olson
Caveat: What happens when it rains?
VertNet: Vertebrate Biodiversity Data in the Cloud Combines global networked information systems for
Mammals - MaNIS Birds – ORNIS Amphibians & Reptiles – HerpNET Fishes – FishNet 2
Working with GBIF to enhance biodiversity data mobilization
Seen a shift from skepticism to enthusiasm for data sharing
Networks facilitate access & sharing of data contributors, who are the primary & authoritative source for information over which they have custody
Incentives:• Improve data quality• Sharing the task of converting textual locality descriptions
into formats for mapping
http://vertnet.org/index.php
VertNet: A New Model in the Cloud Consolidating services
utilizing Google App Engine
Contributors will use a web-based administrative interface to create a provider in the cloud
More scalable, responsive, & sustainable than traditionally maintained contributor server installations
Estimated 16-fold reduction in annual operating costs
Not yet live
DiscoverLife: Operates as a Cloud John Pickering asks “Why try to get taxonomists
to spend their time conforming to standards?” Artificial Language processor has “standards” ~40 routines run on data, including language
recognition Upload a file, send a CD or an email attachment
or point to access your data as Excel® ASCII, tab-delimited text, UTF-8, or with entity codes
Will work with data providers to improve accuracy
Will send data to GBIF at request of provider already maps all of GBIF’s data through an MOU*)
Funded in part through NBII** Maps 22K points/sec; tested with >3M points
* Memorandum of Understanding; ** National Biological Information Infrastructure
Mapping Multiple Species
Access to Specific Records
Using Discover Life’s Albums
Map your records & see details
Techie Solutions for Mapping
Using Google Spreadsheets with Google Maps for Flash (via Yahoo Pipes http://pipes.yahoo.com/pipes/ ) http://biodivertido.blogspot.com/2009/06/using-google-spreadsheets-with-google.html
Google Earth Spreadsheet Mapper http://earth.google.com/outreach/tutorial_spreadsheet.html
DIVA-GIS http://www.diva-gis.org/ FOSS4G (Free & Open Source Software for Geospatial)
conference – resources, talks, etc. from 2009 http://2009.foss4g.org/presentations/
ArcGIS Online http://www.esri.com/software/arcgis/arcgisonline/ World Wind Java SDK http://worldwind.arc.nasa.gov/java/ Comparison of selected web map services
http://en.wikipedia.org/wiki/Comparison_of_Web_Map_Services
Biodivertido http://biodivertido.blogspot.com/
In Which Direction Should the Diptera Community Head? Assume that the following are desired:
Sharing • Able to map multiple taxa
• Restrict datasets mapped
Ease of use Data cleaning & reporting Attribution of data provenance Links to community assets such as keys,
photos/images Speed of access
References & Resources Chapman, A.D. & J. Wieczorek, eds. (2006) Guide to
practices for georeferencing http://www2.gbif.org/BioGeomancerGuide.pdf Georeferencing & GIS Resources
http://www.herpnet.org/Gazetteer/GeorefResources.htm
BioGeomancer http://www.biogeomancer.org/
Constable, et al. (2010) VertNet: A new model for biodiversity data sharing. PLoS Biology 8(2):e1000309 http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000309
GBIF.org Integrated Publishing Toolkit (IPT) http://www.gbif.org/informatics/standards-and-tools/publishing-data/publishing-software/ipt/
DiscoverLife http://www.discoverlife.org/ Boakes, E.H. et al. (2010). Distorted views of biodiversity:
Spatial and temporal bias in species occurrence data. PLoS Biology 8(6):e1000385
European Commission INSPIRE Geoportal http://www.inspire-geoportal.eu/index.cfm/pageid/341
References & Resources Hill A.W., J. Otegui, A.H. Ariño, & R.P Guralnick (2010).
Future directions and recommendations for enhancing fitness-for-use across the GBIF network. Copenhagen: Global Biodiversity Information Facility. 29 pp. anticipated http://www.gbif.org/communications/resources/print-and-online-resources/download-publications/bookelets/
Georeferencing Workshops (presentations, videos, exercises) http://www.gbif.es/formaciondetalles.php?IDForm=39
Chapman, A.D. (2005). Principles of Data Quality, version 1. Copenhagen: Global Biodiversity Information Facility. 58 pp. http://www2.gbif.org/DataQuality.pdf
Olson (2010) Data as a service: Are we in the clouds? Journal of Map & Geography Libraries, 6(1): 76-78. http://www.informaworld.com/smpp/content~db=all~content=a918167873~tab=linking
Hutchison, R.L. (2008) Table of lat/long equivalents in km & miles http://www.zodiacal.com/tools/lat_table.php
Muchissimas Gracias a…
Arturo Ariño, GBIF DIGIT Work Area Chair, for permitting me to view a late draft of a GBIF position paper on fitness-for-use
Lee Belbin, ALA Geospatial Team Leader, for sharing insights into directions for the Atlas of Living Australia
John Pickering, of DiscoverLife.org, for providing a renegade perspective for getting the job done
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