Links

Links to Internet biodiversity information resources

Biodiversity Information Systems (Aggregators)

Australia

• ALA - Atlas of living Australia http://www.ala.org.au/
  • Centre for Plant Biodiversity Research Programs: ALA (NCRIS) project http://www.anbg.gov.au/cpbr/program/hb/hb-atlas-living-aust.html
  • TDWG Atlas of Living Australa page http://www.tdwg.org/biodiv-projects/projects-database/view-project/119/
• AVH - Australia's Virtual Herbarium http://www.anbg.gov.au/chah/avh/index.html
• IBIS - Integrated Botanical Information System http://www.cpbr.gov.au/ibis/
• OZCAM - Online Zoological Collections of Australian Museums http://www.ozcam.gov.au/

Rest of the World

• ATRIUM - Botanical Research Institute of Texas: http://atrium.andesamazon.org/index.php
• EoL - Encyclopedia of Life http://www.eol.org/
• FishNet2 http://www.fishnet2.net/portal-presentation/fishnet2portal?action=home
• GBIF - Global biodiversity Information Facility http://www.gbif.org/
• HerpNET http://www.herpnet.org/
• MaNIS - Mammal Networked Information System http://manisnet.org/
• ORNIS http://olla.berkeley.edu/ornisnet/

Collections and their databases

• ANFC - Australina National Fish Collection http://www.pi.csiro.au/aus_biological_collections/anfc.html
• ANIC - Australian National Insect Collection http://www.csiro.au/places/ANIC.html
• ANWC - Australian National Wildlife Collection http://www.csiro.au/places/anwc.html
• Biodiverstiy and Biological Collections http://www.biocollections.org/
• CPBR & ANH - Centre for Plant Biodiversity Research and Australian National Herbarium http://www.anbg.gov.au/cpbr/
  • Botanical databases http://www.cpbr.gov.au/cpbr/databases/index.html

Collections Councils

• CHAEC - Council of Heads of Australasian Entomological Collections http://flyaqis.museum.vic.gov.au/chaec/index.html
• CHAFC - Council of Heads of Australasian Faunal Collections (no website - see OZCAM aggregator website above)
  • FCIG - Faunal Collection Information Group
• CHAH - Council of Heads of Australasiian Herbaria http://www.anbg.gov.au/chah/index.html
  • HISCOM - Herbarium Information Systems Committee http://plantnet.rbgsyd.nsw.gov.au/HISCOM/
  • APC - Australian Plant Census http://www.anbg.gov.au/apni/index-APC.html
• CHABG - Council of Heads of Australian Botanic Gardens http://www.anbg.gov.au/chabg/
• BGANZ - Botanic Gardens Australia and New Zealand http://www.bganz.org.au/

Taxonomic Resources

• Collecting

  • EDIT (European Distributed Institute of taxonomy) Report: Modelling Report and Bottleneck Analysis.

• Specimen Curation

  • .. to come

• Collections Curation

  • .. to come

• Research

  • Phylogeny

    • http://evolution.genetics.washington.edu/phylip.html - a free package of programs for inferring phylogenies.

• Publishing

  • .. to come

• Maintenance

  • .. to come

• Information Services

  • e-Science

    • Cloud computing for eScience? . There are some interesting models from other areas of science with possible applications in taxonomy.
    • Hadoop - http://hadoop.apache.org/core/ and their Wiki at http://en.wikipedia.org/wiki/Hadoop

    • e-Taxonomy

      • CATE - Creating a Taxonomic e-Science http://www.cate-project.org/
      • EDIT European Distributed Institute of Taxonomy http://www.e-taxonomy.eu/
      • EDIT scratchpads http://www.editwebrevisions.info/scratchpads Hadoop - Wiki http://mantis.cs.umb.edu/wiki/index.php/Main_Page

    • project management

      • Why Most IT Projects Fail. And How Agile Principles Help. http://www.agile-software-development.com/2007/08/why-most-it-projects-fail-and-how-agile.html?gclid=CLbGsJXK65ICFST2YAodBVZ7yA

      workflow

      • Kepler Project;
        • Scientific workflow http://kepler-project.org/ and http://seek.ecoinformatics.org/Wiki.jsp?page=Kepler

  Keys

  Existing tools

  • EFG - Electronic Field Guides (open source) from University of Massachusetts, funded by the National Science Foundation]
  • http://www.navikey.net/ - a web tool for descriptive DELTA data. java applet.
  • http://delta-intkey.com/www/comparison.htm#Programs_compared Compares tools for keys and description ( unbiased?)

  Translators and projects

  • http://www.diversitycampus.net/Projects/TDWG-SDD/Docs/SDD_DELTA.html]] Gregor Hagedorn compares SDD and Delta
  • http://webdelta.infobio.net/

    " a free Web-based DELTA editor written in Perl, developed n Italy ten years ago by Claudio Rivetti and Riccardo Percudani University of Parma). At least since 2002 it has no longer been available, but I retrieved a copy of the last version (WebDelta? 1.2) and from July 30, 2008 I will start distributing it from " July 31, 2008. ... allows editing of delta websites over the internet. " modifications " welcome as distributor is " not a perl programmer ".. contact: Dr. Mauro J. Cavalcanti. Dr. Mauro J. Cavalcanti, Separtamento de Zoologia, Universidade do Estado do Rio de Janeiro Rua São Francisco Xavier, 524, CEP 20559-900 Rio de Janeiro, RJ, BRASIL, maurobio@gmail.com Web: http://maurobio.infobio.net

  • IdentifyLife
    • http://www.identifylife.org/
    • http://wiki.identifylife.org/

Images

• "One button" specimen imaging and data capture http://www.herbis.org/
• Geocoded images.
  • Two projects show what is possible with a well defined interface and geocoded photos WHICH OVERLAP.
    • Panaramio (Google). Simpler (& less computer intensive design).
      http://nv0.panoramio.com/navigate.php?id=6587448
      http://nv0.panoramio.com/navigate.php?id=6587457
    • Photosynth (Microsoft). More beautiful.
      http://www.ted.com/index.php/talks/blaise_aguera_y_arcas_demos_photosynth.html
      http://tinyurl.com/6999xr
  • [ of relevance to our project is the development of platforms and well defined interfaces for overlapping goecoded images]

Names

• AFD Australian Faunal Directory http://www.environment.gov.au/biodiversity/abrs/online-resources/fauna/afd/
• APNI Australian Plant Name Index http://www.anbg.gov.au/apni/index.html
• Flora of Australia Online

Research and Information Networks

Australia

• ALA - Atlas of Living Australia http://www.ala.org.au/
• TRIN - Taxonomy Reseach and Information Network http://www.taxonomy.org.au/

Rest of the World

• CollectionsWeb - Research Coordination Network (RCN) for Building a National Community of Natural History Collections http://www.collectionsweb.org/

Framework Development and Collaboration

• A Taxonomy of Diagram Taxonomies http://www.cl.cam.ac.uk/~afb21/publications/TwD98.html
• Biodiversity and Ecosystem Informatics Lab (check out EFG and the Wiki - see also under interactive keys)
• Creative Synthesis Collaborative http://www.creativesynthesis.net/blog/education/introduction-to-creative-synthesis/

Standards

Biodiversity information standards

• Atlas of living Australia; preferred data standards http://www.ala.org.au/datastandards.htm
• HISPID Herbarium Information Standards and Protocols for Interchange of Data http://plantnet.rbgsyd.nsw.gov.au/HISCOM/HISPID/HISPID3/hispidright.html
• TDWG - Biodiversity Information Standards http://www.tdwg.org/
  • TDWG standards http://www.tdwg.org/standards/
  • TDWG Atlas of Living Australa(ALA) page http://www.tdwg.org/biodiv-projects/projects-database/view-project/119/
  • Darwin Core Wiki site http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome
    • Darwin Core Concept List http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreDraftStandard
  • ABCD http://www.tdwg.org/activities/abcd/
  • Taxon Occurrence Ontology http://rs.tdwg.org/ontology/voc/TaxonOccurrence
  • Observational data http://www.tdwg.org/activities/osr/
  • SDD (Structured Descriptive Data)
    • Standard Primer http://wiki.tdwg.org/twiki/bin/view/SDD/Primer/WebHome
    • SDD Wiki http://wiki.tdwg.org/SDD
  • Species Profile Model (based on DwC and ABCDE) http://wiki.tdwg.org/SPM/

Georeferencing standards

• BioGeomancer? Library for georeferencing resources http://www.biogeomancer.org/library.html
• GBIF Guide to Best Practices for Georeferencing http://www.gbif.org/prog/digit/Georeferencing
• 1/5/2008 Editorial in Nature on calling for georeferenced data PRIOR to acceptance for publication.
  http://www.nature.com/nature/journal/v453/n7191/full/453002a.html

Web standards

• Semantic Web
  • http://www.w3.org/2001/sw/
  • This is a Wiki which discusses Ontologies and Tools for the Semantic Web
  • Wikipedia http://en.wikipedia.org/wiki/Semantic_Web
• W3C - World Wide Web Consortium http://www.w3c.org/
  • Wikipedia http://en.wikipedia.org/wiki/World_Wide_Web_Consortium

Wikis for taxonomy and biodiversity informatics

• EFG Electronic Field Guide Wiki site - has a Wiki web on Ants; does not accept registrations.

-- Updated 29 Jul 2008