bif

Biodiversity Interaction Finder (pronounced Bifi) - using Preston and Elton to detect bee interactions in existing biodiversity data infrastructures like GBIF/iDigBio/ALA etc. Slight modifications can be done to filter interactions based on any catalog.

Methods

Workflow

0. discover GIB corpus versions [1] using

preston history\
 --remote https://zenodo.org/records/7651831/files,https://linker.bio

1. pick a corpus version (e.g., https://linker.bio/hash://sha256/37bdd8ddb12df4ee02978ca59b695afd651f94398c0fe2e1f8b182849a876bb2, see also https://linker.bio)

1a. Find the most recent preston archive given an older one --preston head --anchor hash://sha256/37bdd8ddb12df4ee02978ca59b695afd651f94398c0fe2e1f8b182849a876bb2 --remote https://linker.bio

preston cat\
 --remote https://zenodo.org/records/7651831/files,https://linker.bio\
 hash://sha256/37bdd8ddb12df4ee02978ca59b695afd651f94398c0fe2e1f8b182849a876bb2

2. list all references to dwc-a content in that version

preston cat\
 --remote https://zenodo.org/records/7651831/files,https://linker.bio\
 hash://sha256/37bdd8ddb12df4ee02978ca59b695afd651f94398c0fe2e1f8b182849a876bb2\
 | grep --after 10 "application/dwca"\
 | grep hasVersion\
 | grep -Eo "hash://[a-z0-9]+/[a-f0-9]+" 

3a. detect interactions: for each dwc-a create a globi.json and do a review

globi.json

{ 
  "format": "dwca",
  "url" : "https://linker.bio/hash://sha256/69c839dc05a1b22d2e1aac1c84dec1cfd7af8425479053c74122e54998a1ddc2",
  "citation" : "hash://sha256/69c839dc05a1b22d2e1aac1c84dec1cfd7af8425479053c74122e54998a1ddc2"
}

3b. detect bees:

For each dwc-a to detect whether there are bee names associated with the dwc-a

preston cat\
 --remote https://zenodo.org/records/7651831/files,https://linker.bio\
 hash://sha256/37bdd8ddb12df4ee02978ca59b695afd651f94398c0fe2e1f8b182849a876bb2\
 | grep --after 10 "application/dwca"\
 | grep hasVersion\
 | preston dwc-stream\
 | jq -c '{ "src": .["http://www.w3.org/ns/prov#wasDerivedFrom"], "name": .["http://rs.tdwg.org/dwc/terms/scientificName"] }'\
 | mlr --ijsonl --otsv cat\
 | nomer append discoverlife\
 | grep -v NONE\
 | grep -Eo "hash://[a-z0-9]+/[a-f0-9]+ 

4. make list of dwca that have at least one interaction (3a) and at least one bee name
5. for this list of dwca candidates, generate full reviews
6. concat the indexed-interactions.tsv.gz to create "BIF" archive.
7. publish the BIF archive indexed-interactions.tsv.gz to Zenodo

References

[1] Poelen, J. H. (2023). A biodiversity dataset graph: GBIF, iDigBio, BioCASe hash://sha256/450deb8ed9092ac9b2f0f31d3dcf4e2b9be003c460df63dd6463d252bff37b55 hash://md5/898a9c02bedccaea5434ee4c6d64b7a2 (0.0.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7651831