Transformation of ENVO terms to their respective URLs

[laurianvm]

for sediment, water and armsdata columns with ENVO terms are the same:

• /*_observatory.csv
  • env_broad_biome
  • env_local
• /*_sampling.csv
  • env_material

values appear to be always lists of structure

term[ENVO:code] ; ...

and this should become

http://purl.obolibrary.org/obo/ENVO_{code}

[laurianvm]

@bulricht please let me know if this is something I can do :)

[bulricht]

new data rule for envo terms has been implemented

[laurianvm]

https://github.com/emo-bon/observatory-bpns-crate/blob/218de52ff20a8147a6174a1ba6330f306b76b39a/sediment/sampling/EMOBON_BPNS_So_1#L42
--> latest update still shows statement with "[ENVO ...]"

but not sure if this is because workflow, implementing these action rules, is being worked on atm?

[laurianvm]

need to update input files to be standardized (e.g. occurrence of "ENVO:00000447" and "ENVO_01000024" in https://github.com/emo-bon/observatory-bpns-crate/blob/main/logsheets/raw/sediment_observatory.csv) --> code expects all to be ":"
@kmexter can we take this up with Ioulia and Christina (or quickly change ourselves)?

[kmexter]

is that not a QC issue?