Background reading and skills development for advanced Arctos use

Biodiversity Informatics

• Introduction to Biodiverity Informatics
  • Wikipedia
  • 2009 review of the field
  • A recent review
• Data objects:
  • Specimens
    • The extended specimen
  • Observations
  • DNA data
  • Media
  • Phenotype (characters, measurements)
  • Literature
• Biological taxonomy:
  • Names
  • Accepted names and synonymy
  • Taxonomic concepts
  • Classification
  • GlobalNames
• Standards:
  • TDWG
  • Darwin Core
• Aggregators:
  • GBIF
  • Data quality issues
• Other specimen platforms:
  • Symbiota
  • Specify
  • K-EMU
  • TaxonWorks
• Annual meetings:
  • iDigBio
  • TDWG
• Journals and Blogs:
  • Biodiverity Informatics
  • iPhylo
• Small and standardized data vs. ‘Big Data’
• Uses of biodiversity data
  • Inventories and checklists
  • Endangered species and conservation
  • Basic taxonomic research
  • Ecological niche modeling
  • Evolutionary studies of ecological niche, morphology, distribution

Hacking skills

• SQL (PostgreSQL flavor)
• Handling CSV, JSON and XML
• Git
• GitHub
• Data processing scripting (Python, Perl or Awk)