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Home » Database development » Meetings » 2011-10-24 to 28 working group »

2011 working group Th Summary of subgroups

Data

  • work with VegBank, DwC
    • make adjustments
  • static db?
  • central core db
  • analysis db vs growing db like what we have now but with ability to import datasets
  • db where individual users can upload data on own, and edit/update data
  • internal prioritization, question of how much can be done
  • full-blown UI w/ users editing/uploading data out of scope
  • ingest new data using protocols for getting/refreshing new data
  • other people building universal data entry tool that outputs VegX -> upload to BIEN
  • outside person to develop data entry tool
  • hierarchical list of things to build
  • definitely building core db
  • users entering data much smaller than users taking data out but # users entering will grow
  • data load process
  • BIEN 3 workflow
    • core db
    • loading modules
    • validation
    • derived data products: range maps, etc.
    • public access point: UI, APIs
    • versioning
  • goal for 1 year: mech for loading data (not necessarily UI)
  • who could load data
  • any VegX/DwC data can go in directly
  • Aaron responsible for scripting suiting domain: loading scripts
  • map specific datasets to VegX
  • views with validated data (TNRS, geoscrubbing)
  • data discovery and downloads
  • data upload, entry, editing
  • queries exposed on WordPress site in CSV download interface
  • DBI: advances in biological informatics
    • Peter McCartney, Ann are program directors
  • limited subset of people who can grow db
  • end products
  • 6 use cases
  • add derived analysis products that can be added back to repo
  • short term outputs this afternoon
  • phylogenetics: scope of iPToL: link to BIEN
  • produce data w/ lat/long
  • taxa submitting to iPToL: what are they returning to end user?
  • store taxon metrics in BIEN
  • iPToL contact: Nain
  • data assembly: big tree
  • algorithms scaled up to very large trees
  • iPlant/iPToL traits group has software more than traits data
  • external to BIEN:
    • climate/geospatial info
    • traits
    • phylogenies/systematics
  • open pipeline between BIEN, trait values
    • needed for endpoint
  • recent article: Earth losing species rapidly
    • food, fiber, fuel
    • see Plone site
  • writing requirements document
    • already have detailed schema: extending VegBank schema

Science

  • 5 papers

Range methods

  • expert ranges not always best
  • bounding box/convex hull good
  • difficult to quantify range

Relationship abundance and range size

  • conservation, red list comparison
  • map of threatened species
  • correlates of highly threatened species
  • richness driven by what range size?

Commonness/rarity

  • a lot of very rare species in BIEN
  • trace whether rare or just taxonomic mass
  • rarity, plot map
  • gaps: geographic, climate space, taxonomic undersampling, habit undersampling
  • map of intensity, holes
  • goal of white paper: statement of BIEN's existence, purpose
  • 2:30pm: iPlant geospatial discussion in room 222 (2nd floor; small room)
  • comments on paper: editing, method, citations
  • get feedback from each author? difficult to consolidate
  • who to include in paper?
    • how many meetings attended, contributed? 2
    • or more likely recent participants?
    • active paper participants?
    • data contributors?

Afternoon:

  • 2:30pm: iPlant geospatial discussiong
  • 1:30pm: data committee conference call with Mike Lee
  • will BIEN meet next year?
  • 6:30pm: dinner