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Matthew J Collins edited this page Dec 14, 2017 · 6 revisions

Wrapup Notes

Please edit or merge with your group information: https://hackmd.io/MYEwrAzBDsBmCcBaAHAJggNkQFlfAhivGFrMAKb4AMAjLLCBsuUA

Group 1: Environments! And Phenopackets

  • What traits are unique to organisms that live in low-light environments?
  • Deliverable: Best practices for representing phenopackets, try to add it to ENVO
    • Talk to the ENVO people
  • Deliverable: See if we can automatically make a phenopacket

Group 2: Integrating Museum Specimen Data with Phenoscape

Notes from initial pitch

  • Can definitely map ~200 specimens in Phenoscape to iDigBio
  • But linking taxonomy is difficult, but there will be a lot of overlap
  • Look at how morphology maps onto a global map
  • 1.8 million museum records in iDigBio about frogs
  • Records coming from Morphosource, which has manually curated images, hopefully using Uberon terms
  • Look at limb structure of frogs on a latitudinal gradient
  • Selfish reason: museums specimen to phylogenies via phenotypes
  • Open Tree of Life uses GBIF Backbone Taxonomy, so that should be easy to link with iDigBio
  • Ideas for questions they could ask?

Outcomes

Group page with code, notes, and datasets

Group 3: Harnessing Phenoscape infrastructure for other groups

Notes from pitch and ensuing discussion

  • Make a "Plant Phenoscape Lite"
  • How do you move from a model organism like Rhabadopsis, what is the actual process that gets something that can integrate with Phenoscape?
  • What is the process of semnatic annotation?
  • Want something that's reprodible
  • Start within the order Brassicales, focus on one plant family in particular, maybe focus exclusively on floral anatomy
  • Will need someone from Phenoscape to work with.
  • Deliverable: prepare an outline for a paper on this subject
  • iDigBio has a bunch of plants, so include specimen identifiers from the start!
  • Research questions?
    • Identifying and studying trait evolution?
  • Images would be awesome!

Goals

  • Stand up a "Plant Phenoscape Lite"
  • Explore and document how you move from a set of inputs through a processing pipeline to a functioning KB in a reproducible manner:
    • model organism data such as Arabidopsis
    • evolutionary data from the order of Brassicales and floral anatomy as a starting point of focus
    • specimen identifiers to link to iDigBio
    • images?
  • Walk through the process of semantic annotation
  • Paper describing process and outcomes
  • Research questions:
    • Identifying and studying trait evolution

Outcomes

Group 4: NeXML to JSON-LD Conversion

  • https://hackmd.io/CwdgZghhxgjAtMAxgIxIgHATgKzwziAAzwBsAJkQEwixICmRERSQA===#
  • NeXML would have rich expressivity for trait data, including RDFa
  • NeXML in theory has an RDF basis
  • So you could do NeXML -> RDF, and then save that as JSON-LD? (I don't think that would work well)
  • Merged with original idea of Phenoscape talking to RDF
  • Could be a white paper on how those transformations take place
  • Driving use-cases:
    • Adding Phenoscape (or any other semantic) annotations to NeXML may be easier to express in JSON-LD than in meta RDFa.
    • Phenoscape data embedded in NeXML would be easier to mobilize if the entire document was in JSON-LD. (The current strategy extracts only RDFa data, and rest of NeXML is lost. and RDF-XML is still cumbersome)
    • moving annotations round-trip from Phenoscape
  • What is the application? How do you evaluate that the result meets the goal?
    • Looking at what's in the RDF files and seeing what the connections are?
    • Goal: preserving semantics between the various portals

Group 5: PhenoPhylo

  • Shared evolutionary history of a taxa and
  • Better connections between phenotype data and phylogenies
  • How do we interpret changes in the composition of taxonomy (e.g. families).
  • Pasan has software for reconciliating phylogenies from the Open Tree with Phenoscape phenotypes

Group 6: Using Noctua for composing Phenotype

  • Set up an instance of Noctua with all the ontologies we use
  • Maybe write a white paper on how to express complex phenotypes, based on a previous white paper written by them
  • Maybe a demo of Noctua if there is time?

Group 7: Extracting data for comparative trait analysis from Phenoscape

Sponsored by Phenoscape, a project funded by NSF grants DBI-1062404 and DBI-1062542. Phenoscape was incubated and supported by the National Evolutionary Synthesis Center (NESCent), NSF EF-0905606.

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