Releases: globalbioticinteractions/elton
0.16.9
Features
n/a
Improvements
n/a
Bugs
- enable checklistbank datasets to be used in preston/elton streaming workflows:
e.g.,
elton track --algo md5 urn:lsid:checklistbank.org:dataset:265709 --prov-mode \
| elton tee --algo md5 \
| elton stream --algo md5 --data-dir data --prov-dir data
where elton tee transforms the elton resource graph to one compatible with preston.
For first record produced by workflow see, example xtab formatted record below
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId
sourceCatalogNumber
sourceCollectionCode
sourceCollectionId
sourceInstitutionCode
sourceTaxonId 7
sourceTaxonName Abantiades argentata
sourceTaxonRank species
sourceTaxonPathIds
sourceTaxonPath Animalia | Arthropoda | Insecta | Lepidoptera | Hepialidae | Abantiades | Abantiades argentata
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002470
interactionTypeName eats
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Myrtaceae (Eucalyptus camaldulensis)
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName
http://rs.tdwg.org/dwc/terms/eventDate
decimalLatitude
decimalLongitude
localityId
localityName
referenceDoi
referenceUrl https://doi.org/10.5281/zenodo.8292448
referenceCitation Grehan, J.R., Mielke, C.G.C., Turner, J.R.G. & Nielsen, J.E.,, 2023b. A revised world catalogue of Ghost Moths (Lepidoptera: Hepialidae) with taxonomic and biological annotations.. ZooNova, 28. https://doi.org/10.5281/zenodo.8292448
namespace urn:lsid:checklistbank.org:dataset:265709
citation @misc{ChecklistBankDatasetHepialidae, version = {1.0.4}, url = {https://doi.org/10.5281/zenodo.8292448}, title = {A Revised World Catalogue of Ghost Moths (Lepidoptera: Hepialidae)}, author = {{Grehan}, {John R.} and {Mielke}, {Carlos G.C.} and {Turner}, {John R.G.} and {Nielsen}, {John E.}}, year = 2025, month = 10}
archiveURI hash://md5/30a5abf7c337f606e030e5b73dbaa7d6
lastSeenAt 2026-04-01T15:56:39.364Z
contentHash urn:uuid:0659a54f-b713-4f86-a917-5be166a14110
eltonVersion 0.16.9
0.16.8
Features
- towards support for indexing checklistbank datasets with interaction …
…claims; related to globalbioticinteractions/globalbioticinteractions#753
ChecklistBank uses Catalogue of Life Data Packages (coldp). These coldp's include a table SpeciesInteraction.csv (or similar) that resemble the DwC's ResourceRelations extension in which a resource can be related to another resource.
Here's an example of the first two lines of a speciesinteractions.csv as expressed in XTAB: pretty-printed transposed tabular via unzip -p ~/Downloads/dataset-2017.zip speciesinteractions.csv | head -2 | mlr --icsv --oxtab cat [1]
taxonID S100010010
relatedTaxonID
relatedTaxonScientificName Mesocomys pulchriceps Cameron
type has parasite
referenceID 6968
remarks
This record documents a claim made in reference 6968 in which an individual of taxon with ID S100010010 has a parasite of individual classified as taxon with name Mesocomys pulchriceps Cameron . With this elton release, this records is combined with other tables in the CoLDP archive via:
elton track urn:lsid:checklistbank.org:dataset:2017
elton interactions urn:lsid:checklistbank.org:dataset:2017 \
mlr --itsvlite --oxtab filter '$sourceTaxonId == "S100010010" && $interactionTypeName == "hasParasite" && $targetTaxonName == "Mesocomys pulchriceps Cameron"'to produce:
argumentTypeId https://en.wiktionary.org/wiki/support
[...]
sourceTaxonId S100010010
sourceTaxonName Agrionympha capensis
[...]
interactionTypeId http://purl.obolibrary.org/obo/RO_0002445
interactionTypeName hasParasite
[...]
targetTaxonId
targetTaxonName Mesocomys pulchriceps Cameron
[...]
referenceCitation Prinsloo G. L. & Uys V. M. (Eds.), 2015, Insects of cultivated plants and natural pastures in Southern Africa. vol issue pages i–xiv, 1–785
namespace urn:lsid:checklistbank.org:dataset:2017
citation @misc{ChecklistBankDataset2017, publisher = {Belgian Biodiversity Platform, Belspo}, address = {Brussels, Belgium}, version = {2026-03-01}, url = {https://www.afromoths.net/}, title = {Afromoths, online database of Afrotropical moth species (Lepidoptera)}, author = {{De Prins}, {Jurate} and {De Prins}, {Willy}}, year = 2026, month = 3}
archiveURI https://api.checklistbank.org/dataset/2017/archive.zip
lastSeenAt 2026-03-31T13:59:37.121Z
contentHash dd778e9038f87067815f9c7afdec1286db2e4cc08a298cbab27fe23dba2e1b44
eltonVersion 0.16.8
Note that the sourceTaxonName and referenceCitation were expanded and provenance information was added to help document the context in which the claim was made.
Thanks for @mdoering 's tip globalbioticinteractions/globalbioticinteractions#753 to list checklistbank datasets with species interaction claims in them.
Example use:
# list known checklistbank datasets with species interaction claims
elton ls --online --registry checklistbank
which produced, at time of writing 2026-03-31:
urn:lsid:checklistbank.org:dataset:1049
urn:lsid:checklistbank.org:dataset:1061
urn:lsid:checklistbank.org:dataset:1133
urn:lsid:checklistbank.org:dataset:1166
urn:lsid:checklistbank.org:dataset:1199
urn:lsid:checklistbank.org:dataset:2017
urn:lsid:checklistbank.org:dataset:2207
urn:lsid:checklistbank.org:dataset:2317
urn:lsid:checklistbank.org:dataset:2362
urn:lsid:checklistbank.org:dataset:124661
urn:lsid:checklistbank.org:dataset:265709
These lsids can then be used for tracking, review and listing interactions and/or names:
# create a local snapshot version of the remote dataset
elton track urn:lsid:checklistbank.org:dataset:2017
# list interactions of a version snapshot
elton interactions urn:lsid:checklistbank.org:dataset:2017
# do a review of a local version snapshot
elton review urn:lsid:checklistbank.org:dataset:2017
Improvements
- upgrade to globi libs v0.28.17
- support event-based resource relations suppo… - …rt; related to globalbioticinteractions/globalbioticinteractions#1150
Bugs
References
[1] De Prins, J., & De Prins, W. (2026). Afromoths, online database of Afrotropical moth species (Lepidoptera) (Version 2026-03-01). Belgian Biodiversity Platform, Belspo, Brussels, Belgium. https://www.afromoths.net/ https://doi.org/10.48580/d4fl.v123 https://www.checklistbank.org/dataset/2017
Contributors
Assets 7
0.16.7
0.16.6
Features
n/a
Improvements
- add more contextual information when unable to process a dataset; rel…
…ated to #75 ; fyi @zedomel - upgrade to globi libs v0.28.12
Bugs
n/a
Contributors
Assets 7
0.16.5
0.16.4
0.16.3
0.16.2
Features
n/a
Improvements
- upgrade to preston v0.11.4 to support anchored data streams bio-guoda/preston#356
- register IRI converter for provenance anchor option
Bugs
n/a
0.16.1
Features
n/a
Improvements
- add brew install instruction
- support auto-detection of semicolon delimited data; #73
- upgrade to globi-lib v0.28.9
Bugs
n/a
0.16.0
Features
n/a
Improvements
- include elton-bin.zip and elton-bin.tar.gz to help facilitate support for Homebrew installer/formula. See bio-guoda/preston#348
- generate man pages for subcommands also
Bugs
n/a