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2024-04-15

This is Disha's DBGI daily open-notebook.

Work update from April first-half

Doing

  1. #VKG (Private) For scaling the VKG of trydb/GLOBI/enpkg so that the full tables (some of them upto 7 GB) can be integrated, I applied for an account on CCFS UniNe. But it is taking a lot of time to get this done. So, I decided to use databricks community edition to run simple workflows which require upto 15GB RAM (https://community.cloud.databricks.com/). I made an account, now working on technical aspects to make R and bash scripts work.
  2. #VKG (Private) Integrating data from GLOBI. Filtering interactions specific to plant species in TRY-db (Of all the interaction tuples, I will extract the ones which have atleast one component matching the Plant species NCBI name from gLOBI)
  3. #VKG (Private) Perform extensive tests with integrate_trydb VKG. Check at all levels with SPARQL. Validate the results.

Done

  1. #VKG (Private) Modified ontologies for connecting information from enpkg, traits metadata, trydb observation data, taxonomic ids. However, there are inconsistencies in the results obtained from SPARQL query.

  2. #SciComm (Private) As suggested by Philipp from Science-et-cite, I had a meeting with Manuela from Zurich-Basel Plant Science centre. We did some brainstorming around how best to proceed with the AGORA project. Important points discussed: a) Two main ideas: Make a video of informal interviews with researchers and PI who are deeply involved in this project, Design a SciComm project around data literacy (a topic rarely touched upon while comunicating with general public from non-Science background) b) Combination of both digital and physical components. e.g: A screen-panel with virtual safaris, where people can click a location on a word map and see what plants exist where, maybe try to convert this into a game with a reward. Note: Idea not discussed with Manuela: Virtual exhibition using https://v21artspace.com/virtual-exhibitions or https://www.artsteps.com/ c) Fund-raising and SciComm are different projects. Try not to mix them. d) Apply for the big grant with a deadline in Sept rather than the rolling call. Set aside salary % (upto 40%) for Science communication expert. e) Check eligibility to appy for AGORA : citizenship criteria, research employment criteria (if I can show an employment contract with salary covered for the period of the employment, I can apply for AGORA individually, otherwise I can ask Emmanuel to apply).

I talked to Emmanuel about this and we discussed the following: a) He will contact directors of botanical garden in Neuchatel if they would like to have a panel with virtual components. b) Making a video is a good idea. I will contact a professional to help us with that. c) Data literacy sounds great, but the implementation is tricky and needs efforts.

Notes

Todo tomorrow or soon

  1. #SciComm (Private) Philipp gave contacts for people who can help with making videos.

From Philip:

Daniel Saraga:

https://www.saraga.ch/

Mirko Bischofberger (also a film maker):

https://www.science-studios.ch/

  1. #VKG (Private) Put the new ontologies to the github account. Transfer the integrate_trydb from my github account to DBGI's.
  2. #VKG (Private) Incorporate ttl files for traits on the ontop VKG for coherence.
  3. #SciComm (Private) Build a graphical overview of the two ideas discussed with Manuela.

Today I learned that

  1. Ontop with duckdb https://www..com/pulse/scaling-sparql-querying-billion-observations-ontop-duckdb-gschwend-myghf/

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.