TDWG Spatial Data Standards_25_October_2003

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• NotesFromGroup1
• NotesFromGroup2
• NotesFromGroup3
• NotesFromGroup4
• NotesFromGroup5
• NotesFromGroup6

Lunchtime Challenge: Spatial Query, Spatial Response

Assumptions Data sources in heterogeneous frames of reference Data providers are incapable of data transformations

Requirements Arbitrary spatial bound as query condition Results in any spatial reference system Operable via DiGIR/BioCASE

Actions Go to lunch Identify resources needed to fulfill this challenge Post your responses here

Notes From Goup 1

Assisting data providers to georeference their data

• http://www.biogeomancer.com
• http://www.alexandria.ucsb.edu Alexandria digital library
• http://www.museum.tulane.edu/geolocate/contact.aspx GeoLocator - stand alone georeferencer
• http://www.kew.org Kew Botanical locations gazateer

• http://www.ga.gov.au/ Geosciences Australia
• http://www.nima.mil - geonet name server

GBIF portal and other presentation services data discovery should include spatial queries including eg buffering currently assume that most analysis will be carried out locally eg on gis software establish framework of services for generalised species modeling using bioclimatic techniques for example, this would entail distributed sources of variables, range of processing sites and modelling allgorithms, GBIF should only be for data discovery and a centralised registry of available services

Provide feature data (e.g., polygons) for named geospatial entities

• http://www.lpi.nsw.gov.au/ Land and Property Information - NSW topographic
• http://www.CANRI.nsw.gov.au - NSW data

Raster data resources for given map extents

• http://www.ga.gov.au Geoscience Australia
• http://www.canri.nsw.gov.au Community Access to Natural Resource Information - NSW
• http://www.lpi.nsw.go.au Land and Property Information

Specimen point data on maps

• http://www.faunanet.gov.au/
• http://www.ozcam.gov.au
• http://www.kew.org/giswww/herbcatdist.html
• http://www.rbgsyd.nsw.gov.au
• http://map2.eea.eu.int/help/
• http://www.kew.org/gis

Spatial queries for taxa (what's in my backyard)

• http://www.faunanet.gov.au/
• http://secure.bionet.nsw.gov.au

Other ideas

Notes From Goup 2

Assisting data providers to georeference their data http://mapstedi.colorado.edu/geocoding-howto.html GBIF portal and other presentation services Hijmans, R.J., Schreuder, J. De la Cruz, J. and Guarino, L. (1999). Using GIS to check coordinates of genebank accessions. Genetic Resources and Crop Evolution 46: 291-296. Hijmans, R.J., Guarino, L., Bussink, C., Barrentes, I. and Rojas, E. (2003) DIVA-GIS Version 3. A geographic information system for the analysis of biodiversity data. http://www.diva-gis.org. Peterson, A.T., Navarro-Siguenza, A.G. and Benitez-Diaz, H. (1998). The need for continued scientific collecting: A geographic analysis of Mexican bird specimens. Ibis 140: 288-294. Peterson, A.T., Navarro-Siguenza, A.G. and Scachetti-Pereira, R. (in press). Detecting Errors in Biodiversity: Collector’s Itineraries Flag Mislabeled Specimens. Submitted to Bulletin of the British Ornithologists' Club. University of Colorado Regents (2003). mapstedi. Geocoding. Denver: University of Colorado MaPSTeDI project. http://mapstedi.colorado.edu/geocoding.html. Provide feature data (e.g., polygons) for named geospatial entities Shattuck, S.O. (1997). eGaz, The Electronic Gazetteer. ANIC News 11: 9 http://www.ento.csiro.au/research/natres/anicnews/anicnews11_09.html. Chapman, A.D. (1992). Quality Control and Validation of Environmental Resource Data in Data Quality and Standards: Proceedings of a Seminar Organised by the Commonwealth Land Information Forum, Canberra, 5 December 1991. Canberra: Commonwealth land Information Forum. Chapman, A.D. (1999). Quality Control and Validation of Point-Sourced Environmental Resource Data pp. 409-418 in Lowell, K. and Jaton, A. eds. Spatial accuracy assessment: Land information uncertainty in natural resources. Chelsea, MI: Ann Arbor Press. Chapman, A.D. (2002). Risk assessment and uncertainty in mapped and modelled distributions of threatened species in Australia. pp. 31-40 in Hunter, G. and Lowell, K. (eds). Accuracy 2002. 5th International Symposium on Spatial Accuracy Assessment in Natural Resources and Environmental Sciences. Melbourne: RMIT. http://www.biolink.csiro.au/gazfiles.html

Raster data resources for given map extents

Specimen point data on maps
http://www.searchnbn.net
http://www.cbif.gc.ca/mc/index_e.php
http://www.museumsalberta.ab.ca/network/resource.html
http://www.chah.gov.au/avh/avh.html
http://www.biocase.org

Spatial queries for taxa (what's in my backyard)
http://www.searchnbn.net
http://www.br.fgov.be/BIODIV/
http://www.geomuse.org
http://www.deh.gov.au/epbc/
CRIA (2002). SpeciesLink. Campinas: Centro de Referência em Informação Ambiental.
http://splink.cria.org.br/
REMIB Global Biodiversity Information Network www.conabio.gob.mx

Other:
NGDC (2000). Global Land One-kilometer Base Elevation (GLOBE) Digital Elevation Data Version 1.0.
http://www.ngdc.noaa.gov/seg/fliers/globedem.shtml.
TDWG Subgroup on Biological Collection Data - Software for Biological Collection Management
http://www.bgbm.org/TDWG/acc/Software.htm
http://www.google.com
http://mario.lancashire.gov.uk/

Notes From Goup 2

Assisting data providers to georeference their data

• http://unstats.un.org/unsd/geoinfo/Websites-links.htm
• MaNIS
• MaPSTeDI
• INRAM
• http://www.calacademy.org/research/informatics/georef/

GBIF portal and other presentation services

• http://www.biogis.huji.ac.il
• http://digir.net

Provide feature data (e.g., polygons) for named geospatial entities

• ADL
• GNIS
• USGS
• NIMA
• Atlas of Canada
• http://ogcengine.digest.org/

Raster data resources for given map extents

• http://www.biogis.huji.ac.il * [http://viewer.digitalearth.gov * [http://www.lib.ed.ac.uk/resbysub/maps.shtml Specimen point data on maps * [http://www.biogis.huji.ac.il
• http://www.dorsa.de
• http://www.dorsa.de/
• http://mapserver.gis.umn.edu/
• http://deegree.sourceforge.net/
• http://134.197.55.92:8080/

Spatial queries for taxa (what's in my backyard)

• http://www.calflora.org/
• http://lifemapper.org

Resource Lists

• http://opensourcegis.org/
• http://freegis.org
• http://www.fgdc.gov/
• http://www.isotc211.org/
• http://www.remotesensing.org/proj/
• http://www.noaa.gov/
• http://www.fgdc.gov/clearinghouse/clearinghouse.html
• http://gsdi.org/
• http://www.geographynetwork.com/

More... http://www.unep-wcmc.org/: UNEP World Conservation Monitoring Center has ESRI based interactive maps with basic ArcIMS functionality.

http://beta.lifemapper.org/: The user can choose species, find and map units and perform GARP analysis (in cases where enough distinct sites are found). The user interface is poor and slow. We did not succeed in running a GARP analysis.

http://biodi.sdsc.edu/ww_home.html: The WhyWhere site has its own data and analysis tools. Allows selection of location and data, and creates predictive maps and input data to COTS GIS.

http://www.kgs.ukans.edu/Hexacoral/: Biogeoinformatics of hexacorallia has attribute query and map browsing with identify. Uses ESRI's ArcIMS.

http://www.elzaresearch.com/landv/axiomap_ie5.html: AxioMap: XML based GIS. Limited capabilities - works fast.

http://www.ebird.org/eBirdReports: Provides bird observations per species, and allows users to add observations. The interface is simple and slow. No analysis or query; just display by species.

http://elib.cs.berkeley.edu/matrix.html: Points to many data sources and includes a non-COTS viewer. Not easy to use.

http://www.ento.csiro.au/biolink/software.html: BioLink is a taxon- and specimen-based desktop software system. It is not yet fully operational. Provides a built-in mapping tool allowing display of geocoded records. It can produce distribution maps of taxa. The Mapping tool uses ESRI shape files, which will allow users to add their own maps, and maps layers.

http://www.globalforestwatch.org/english/index.htm: Global Forest Watch uses basic ArcIMS capabilities

http://habanero.nhm.ukans.edu/zportal/tsasimple.asp: This is the Species Analyst site for accessing distributed heterogeneous databases using ISO 23950 and XML technology. The main species analyst site is http://tsadev.speciesanalyst.net/

The user interface is nice and it works fast. Output files are XML, Excel or ESRI's shapefile. Currently there is no Internet geographic viewer. Alternative tools are being developed that permit direct access to these data by using Excel and ESRI's ArcView, which are in development, but beta versions may be retrieved from Z.X.

http://www.nationalgeographic.com/wildworld/: National Geographic was one of the first ArcIMS users. The Wild World has interactive maps for conservation and ecoregions.

http://usobi.org/specify/: Specify is a Microsoft Windows database application for entry, management and retrieval of data from biological collections. The databse includes morphological attributes, geospatial coordinates, taxonomic determinations and the ecological data associated with specimen vouchers. Specify is available at no charge. Soon, Specify will use DIGIR serve XML-encoded specimen data to an international network of collaborating museum data servers. We did not download the software yet.

http://www.bdworld.org/: Biodiversity World is a project to create a GRID-based problem solving environment, planned for collaborative exploration and analysis of global biodiversity. The site is not yet operative. A typical workflow will involve:

1. Using the Species 2000 to specify the organisms under study
2. Combine relevant data from rich data sources around the world
3. Use an array of analytical tools for analysis

http://www.searchnbn.net/; Has incomprehensible interactive maps - all specimens at the same points!

http://beta.lifemapper.org/desktopgarp/: Desktop Garp is a software package for biodiversity that allows the user to predict and analyze wild species distributions.

http://www.calacademy.org/research/informatics/georef/: Includes a software tool to help determine the geographic area where a unit (specimen / observation) was found from a text description.

http://www.ramas.com/: Ramas is a commercial Bioinformatics GIS software package.

http://www.bgbm.org/TDWG/acc/Software.htm: A list of resources.

http://www.calacademy.org/research/informatics/sblum/pub/biodiv_informatics.html: An overview of biodiversity informatics that points to a number of sources

http://digir.sourceforge.net/: An organization establishing a standard for a federated heterogeneous biodiversity databases.

http://www.iobis.org/tools.shtml: This is a list of Ocean Biogeographic Information System (OBIS) tools. Most of them are relevant to all biodiversity and are discussed separately in this list.

http://149.170.199.144/new_gis/sitemap.htm: Notes for a course on GIS and conservation biology research and management. Contains a great deal of information and links.

http://www.npaci.edu/online/v5.11/esri-lsi_3.0.html: Announces SDSC / ESRI Collaboration on XML standards.

http://www.sdnp.undp.org/biod/bio.html: A very long, but old (1996) list of biodiversity software tools.

http://sourceforge.net/projects/digir: DGIR standards site

http://www.natureserve.org/prodServices/heritagemethodology.jsp Links at the bottom.