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Big-Bee-Network / bif

Biodiversity Interaction Finder - using Preston and Elton to detect bee interactions in existing biodiversity data infrastructures like GBIF/iDigBio/ALA etc.
Creative Commons Zero v1.0 Universal
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provide estimate of interaction records in bif #1

Open jhpoelen opened 2 months ago

jhpoelen commented 2 months ago

@seltmann says 2M

@jhpoelen says 2.1M

seltmann commented 1 month ago

Hi @jhpoelen I am wondering if we got the same output from bif. I have 5,446,329 interaction records and it took 5710.24s user 1120.76s system 66% cpu 2:51:39.66 total

jhpoelen commented 1 month ago

@seltmann nice!

Interesting to see that I got a different result . . . with ~16M interaction records after about 5 hours of processing. 10M records remained after removing duplicate datasets (e.g., datasets indexed by both iDigBio and GBIF).

Can you share a list of unique citations to check whether we ended up using the same datasets? 

cat interactions.tsv\
 | mlr --tsvlite cut -f citation\
 | uniq\
 | sort\
 | uniq
seltmann commented 1 month ago

Hi @jhpoelen There were 3,516,157 unique citations. See https://drive.google.com/file/d/1tYp26ZcfUEVDRMa_KUPzgyvwrfnXswQL/view?usp=drive_link

jhpoelen commented 1 month ago

Hey @seltmann - thanks for sharing your list of unique "referenceCitation" values. I was hoping to compare the list of unique "citation" values instead. This list should be in the order of 100k or less. Alternatively, perhaps to save back and forth, please share your interactions.tsv, so I can have a look at your source data instead.

PS Note that referenceCitations are the per-claim citations. "Citation" values refer to the dataset under review.

jhpoelen commented 1 month ago

I do realize that the names "referenceCitation" and "citation" are pretty similar and potentially confusing . Perhaps "claimCitation" and "datasetCitation" would be more intuitive. Open to suggestions. . .

seltmann commented 1 month ago

Here is the interactions.tsv https://drive.google.com/file/d/1qbsnK2_3KPCY7foCPSyO9Ujp661caUPt/view?usp=drive_link

I was looking for similar headers as found in the GloBI interactions.tsv file. Dataset citation/claim citation are more intuitive.

seltmann commented 1 month ago

@jhpoelen Also, would you be able to share your interactions.tsv output

jhpoelen commented 1 month ago

@seltmann for sure! Thought you'd never ask ; ) Here's a temporary download link for my interactions.tsv.gz https://send.tresorit.com/a#2wa6zr8XkuayhqmBV4kFeQ . Please confirm receipt.

jhpoelen commented 1 month ago

I did a mlr --tsvlite mlr cut -f citation | sort | uniq on both our interactions.tsv and attached the results.

citations-uniq.zip

with 

$ wc -l bif-jorrit/citations-uniq.txt
1011 bif-jorrit/citations-uniq.txt

and 

$ wc -l bif-katja/citations-uniq.txt
407 bif-katja/citations-uniq.txt
jhpoelen commented 1 month ago

Hmm. Looks like your run may have been stopped prematurely. Did you perhaps go home after 2.5 hours and close your laptop and stop the process?

Probably a good reason to add some more (automated) info on the origin of the data by documenting what script was executed when, and what output they produced. . .

seltmann commented 1 month ago

@jhpoelen received!

jhpoelen commented 1 month ago

By the way, I am trying to restructure Elton to allow for "streaming" reviews. This way, we can see how many potential interaction records are not included due to unknown interaction types. Hoping to make some progress on this . . .

allowing for workflows like:

preston head\
 | preston cat\
 | elton review\
 > review.tsv

to review the latest version of some Preston archive.

jhpoelen commented 1 month ago

After some hacking . . . I was able to create a first pass at streaming reviews with 

./find-datasets-with-interactions.sh\
 | grep "hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf"\
 | head -1\
 | elton stream --record-type review\
 > review.tsv.txt

producing

review.tsv.txt

with the first bunch of records indicating that UCSB-IZC makes . . . biotic interaction claims . . . how about that!

reviewId reviewDate reviewer namespace reviewCommentType reviewComment archiveURI referenceUrl institutionCode collectionCode collectionId catalogNumber occurrenceId sourceCitation dataContext
fece06c8-512d-47ad-8dc4-a6974ee0755b 2024-08-01T20:49:13Z GloBI automated reviewer (elton-0.13.7-SNAPSHOT) hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf info [https://linker.bio/hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf]: indexing interaction records
fece06c8-512d-47ad-8dc4-a6974ee0755b 2024-08-01T20:49:16Z GloBI automated reviewer (elton-0.13.7-SNAPSHOT) hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf info biotic interaction found https://linker.bio/hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf https://ecdysis.org/collections/individual/index.php?occid=881445 UCSB IZC b03a3f0c-bfa5-4e02-b5d3-56ff38626302 UCSB-IZC00038170 3faf957a-ae15-4fda-b597-79489f23dac9 hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf. Accessed at https://linker.bio/hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf on 01 Aug 2024. {"reviewId":"fece06c8-512d-47ad-8dc4-a6974ee0755b","reviewDate":"2024-08-01T20:49:16Z","reviewerName":"GloBI automated reviewer (elton-0.13.7-SNAPSHOT)","reviewCommentType":"info","reviewComment":"biotic interaction 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fece06c8-512d-47ad-8dc4-a6974ee0755b 2024-08-01T20:49:16Z GloBI automated reviewer (elton-0.13.7-SNAPSHOT) hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf info biotic interaction found https://linker.bio/hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf https://ecdysis.org/collections/individual/index.php?occid=881446 UCSB IZC b03a3f0c-bfa5-4e02-b5d3-56ff38626302 UCSB-IZC00038207 463f1784-1b1f-4368-a441-8a5732a46512 hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf. Accessed at https://linker.bio/hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf on 01 Aug 2024. {"reviewId":"fece06c8-512d-47ad-8dc4-a6974ee0755b","reviewDate":"2024-08-01T20:49:16Z","reviewerName":"GloBI automated reviewer (elton-0.13.7-SNAPSHOT)","reviewCommentType":"info","reviewComment":"biotic interaction found","namespace":"hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf","context":{"archiveURI":"https://linker.bio/hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf","basisOfRecordName":"PreservedSpecimen","contentHash":"9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf","decimalLatitude":"34.42174","decimalLongitude":"-119.87186","dwc:coreid":"881446","http://purl.org/dc/elements/1.1/rights":"http://creativecommons.org/publicdomain/zero/1.0/","http://purl.org/dc/terms/accessRights":"https://www.ccber.ucsb.edu/collections/databases-searching-specimen-data-and-images","http://purl.org/dc/terms/language":null,"http://purl.org/dc/terms/modified":"2023-06-23 13:11:01","http://purl.org/dc/terms/references":"https://ecdysis.org/collections/individual/index.php?occid=881446","http://purl.org/dc/terms/rightsHolder":"The Regents of the University of California","http://rs.tdwg.org/dwc/terms/associatedOccurrences":null,"http://rs.tdwg.org/dwc/terms/associatedSequences":null,"http://rs.tdwg.org/dwc/terms/associatedTaxa":"on flower of Mimulus auranticus","http://rs.tdwg.org/dwc/terms/basisOfRecord":"PreservedSpecimen","http://rs.tdwg.org/dwc/terms/catalogNumber":"UCSB-IZC00038207","http://rs.tdwg.org/dwc/terms/class":"Insecta","http://rs.tdwg.org/dwc/terms/collectionCode":"IZC","http://rs.tdwg.org/dwc/terms/collectionID":"b03a3f0c-bfa5-4e02-b5d3-56ff38626302","http://rs.tdwg.org/dwc/terms/continent":null,"http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters":"10","http://rs.tdwg.org/dwc/terms/country":"United States","http://rs.tdwg.org/dwc/terms/county":"Santa Barbara","http://rs.tdwg.org/dwc/terms/dataGeneralizations":null,"http://rs.tdwg.org/dwc/terms/dateIdentified":"24-May-2022","http://rs.tdwg.org/dwc/terms/day":"26","http://rs.tdwg.org/dwc/terms/decimalLatitude":"34.42174","http://rs.tdwg.org/dwc/terms/decimalLongitude":"-119.87186","http://rs.tdwg.org/dwc/terms/disposition":null,"http://rs.tdwg.org/dwc/terms/dynamicProperties":null,"http://rs.tdwg.org/dwc/terms/endDayOfYear":null,"http://rs.tdwg.org/dwc/terms/establishmentMeans":null,"http://rs.tdwg.org/dwc/terms/eventDate":"2022-04-26","http://rs.tdwg.org/dwc/terms/eventID":null,"http://rs.tdwg.org/dwc/terms/family":null,"http://rs.tdwg.org/dwc/terms/fieldNumber":"PAN2","http://rs.tdwg.org/dwc/terms/genus":null,"http://rs.tdwg.org/dwc/terms/geodeticDatum":"WGS84","http://rs.tdwg.org/dwc/terms/georeferenceProtocol":null,"http://rs.tdwg.org/dwc/terms/georeferenceRemarks":null,"http://rs.tdwg.org/dwc/terms/georeferenceSources":"GPS","http://rs.tdwg.org/dwc/terms/georeferenceVerificationStatus":null,"http://rs.tdwg.org/dwc/terms/georeferencedBy":null,"http://rs.tdwg.org/dwc/terms/habitat":"Newly restored salt marsh","http://rs.tdwg.org/dwc/terms/higherClassification":"Animalia\|Arthropoda\|Hexapoda\|Insecta\|Pterygota\|Neoptera","http://rs.tdwg.org/dwc/terms/identificationQualifier":null,"http://rs.tdwg.org/dwc/terms/identificationReferences":null,"http://rs.tdwg.org/dwc/terms/identificationRemarks":null,"http://rs.tdwg.org/dwc/terms/identifiedBy":"Katja Seltmann","http://rs.tdwg.org/dwc/terms/individualCount":"1","http://rs.tdwg.org/dwc/terms/informationWithheld":null,"http://rs.tdwg.org/dwc/terms/infraspecificEpithet":null,"http://rs.tdwg.org/dwc/terms/institutionCode":"UCSB","http://rs.tdwg.org/dwc/terms/island":null,"http://rs.tdwg.org/dwc/terms/islandGroup":null,"http://rs.tdwg.org/dwc/terms/kingdom":"Animalia","http://rs.tdwg.org/dwc/terms/lifeStage":"Adult","http://rs.tdwg.org/dwc/terms/locality":"University of California Santa Barbara North Campus Open Space - 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fece06c8-512d-47ad-8dc4-a6974ee0755b 2024-08-01T20:49:16Z GloBI automated reviewer (elton-0.13.7-SNAPSHOT) hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf info biotic interaction found https://linker.bio/hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf https://ecdysis.org/collections/individual/index.php?occid=881447 UCSB IZC b03a3f0c-bfa5-4e02-b5d3-56ff38626302 UCSB-IZC00038169 786ac5ea-d21b-4b78-911a-2db3f7ae5c94 hash://sha256/9cd053d40ef148e16389982ea16d724063b82567f7ba1799962670fc97876fbf. 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jhpoelen commented 1 month ago

A current review of candidate interaction record can be found in

Seltmann, K., Poelen, J. H., & Augusto Salim, J. (2024). A Review of Candidate Interaction Records in Biodiversity Datasets registered with GBIF and iDigBio as seen via Biodiversity Interaction Finder (BIF) hash://sha256/56ce90e39c2f3a038d577faad70b65573e7ab2e0e69f735f14d71cf4b3b0966b hash://md5/6c497d45da7f79d054d8a5203bd439c0 (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.13272096

See also https://github.com/globalbioticinteractions/globalbioticinteractions/issues/999#issuecomment-2276061193 .

jhpoelen commented 1 month ago

fyi @zedomel @seltmann