map ffbi to https://github.com/edamontology/edam-bioimaging, particularly for "microscopy" concepts

[lubianat]

I am happy to take that on

[lubianat]

proposal:

create a SSSOM table, say on Google Sheet with the microscopy terms from FBBI and match to EDAM

[JSDLacoste]

Please add the term "Widefield fluorescence microscopy" to fbbi. That term is already in EDAM BioImaging. Please note that in the OME.xml, the term "Wide-field Fluorescence" is part of a list of accepted values for modalities.

[strambc]

@lubianat regarding "microscopy" some of the proposed mapping between EDAM and fbbi terms was already done at the foundingGIDE hackaton in Kope in November 2024.
Judith and I will meet tomorrow and post here information regarding what was done and the consensus decision that emerged from that discussion.

[gouttegd]

@lubianat : The infrastructure is already in place to have SSSOM mappings maintained within FBbi. :) We have a SSSOM table (with for now one poor lone mapping!) here: https://github.com/foundingGIDE/fbbi/blob/master/src/mappings/main.sssom.tsv

[strambc]

@lubianat I also found this from the 2024 Kobe hackathon

https://github.com/foundingGIDE/hackathon_2024_metadata_ontologies/tree/main/fbbi_edam_mapper

[strambc]

This is also summarized here:
https://www.figma.com/board/Q474eTKax8T3S8UZYx6QcM/QUAREP_Proposal-for-Imaging-Modality-Data-Model?node-id=549-648&t=sJfD1FNaAEtjU8MK-1

and here:

https://imagesc.zulipchat.com/#narrow/channel/466189-Zzz.3A-.5B2024-11.5D-FoundingGIDE-Bioimage-Hackathon/topic/Ontology.20Deep.20Dive.3A.20FBbi.20or.20EDAM.3F/with/481067815

[lubianat]

@strambc thank you so much!

https://github.com/foundingGIDE/hackathon_2024_metadata_ontologies/tree/main/fbbi_edam_mapper looks very relevant

One "todo" now for us would be converting some of these into the SSSOM mapping file that Damien shared above

[strambc]

@lubianat agreed.
One question: when I go to the SSSOM mapping link I do not find the actual tsv (it gives me 404). Where do I find it?

[strambc]

@lubianat @gouttegd
You can find the work Judith and I made to map EDAM to FBbi here

https://docs.google.com/spreadsheets/d/1RREAbMbqCGjSUiwQ9wsnRN-EniE6A0Vr/edit?usp=sharing&ouid=101141664079197066125&rtpof=true&sd=true

Also same information can be found in graphical format here:
https://www.figma.com/board/Q474eTKax8T3S8UZYx6QcM/QUAREP_Proposal-for-Imaging-Modality-Data-Model?node-id=0-1&t=rajldZRrAJNeWiZK-1