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New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University of Illinois at Urbana- Champaign 7th International Congress of Dipterology Symposium: Getting Diptera taxonomy up-to-date: New frontiers & the Web
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New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

Apr 01, 2015

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Page 1: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 2: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 3: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 4: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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)

Page 5: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 6: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

)

Page 7: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 8: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 9: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 10: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

GEOLocate

Parque Nacional Santa Rosa, Liberia, Stor Santa Rosa

Page 11: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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/

Page 12: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

GBIF (Global Biodiversity Information Facility)

Best known Provides

leadership & some seed funding to support

Standards development

Global catalog of taxonomic names

Biodiversity data mobilization

Page 13: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

Label data

Record provenance & Taxonomic Name

Page 14: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

AntWeb in Google Earth

•Community showcase

•Only ants

Page 15: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 16: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 17: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 18: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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?

Page 19: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 20: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 21: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 22: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

Mapping Multiple Species

Page 23: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

Access to Specific Records

Page 24: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

Using Discover Life’s Albums

Page 25: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

Map your records & see details

Page 26: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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/

Page 27: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 28: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 29: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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

Page 30: New Frontiers in Mapping Biodiversity Specimen Data Gail E. Kampmeier Illinois Natural History Survey Institute of Natural Resource Sustainability University.

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