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2024-06-11

This is Disha's DBGI daily open-notebook.

Work update from May-June

Doing

  1. #SciComm (Private) In talks with Manuela Dahinden to shape the AGORA grant. Meeting on 17th May with Manuela, Emmanuel and Pierr-Marie.
  2. Start Intro for the paper.
  3. To do still:
  4. Started writing the AGORA grant (Project description - Context).

Done

  1. #VKG (Private) modified TRY-db csv file to include 1 column explaining the data type (one of the folloiwng three values): continuous-trait, discrete-trait, non-trait to distinguish between quuantitative & non-quanititattive trait and non trait data
  2. #VKG (Private) ontop-materialized the vkg (try-db, globi, traits, enpkg). python rdflib used for 'graphfying' and run SPARQL queries (See github repo: https://github.com/digital-botanical-gardens-initiative/integrate_trydb_globi_enpkg)

Todo tomorrow or soon

1.For #VKG (Private) a) Run queries with only plants from ENPKG. Think abut what the user wants.

b) Similarity matrices for traits: scaling followed by euclidean and bray-curtis. how about mixing them (take avg) and then plot node distance based on the avg distance, different edge coloring/width by distance specific to a metric.

c) human-plant interaction. Is there a database which lists plants edible?

d) Manu will provide climate change data from GBIF or from GIFT.

  1. #SciComm (Private) Build a graphical overview of the two ideas discussed with Manuela.
  2. Start writing Introduction and Methods for the paper.

Today I learned that

Paused

  1. Profile article for the DBGI website.
  2. DISPEL conversation.
  3. Looked at PheObs, AusTraits and Globi. AusTraits looks very promising. Have to see how they integrated data.