{"metadata":{"related_identifiers":[{"relation":"isAlternateIdentifier","identifier":"hash://md5/9e3f7e0b37c3873f4763d4dd7304cd47"},{"relation":"isAlternateIdentifier","identifier":"urn:lsid:globalbioticinteractions.org:dataset:globalbioticinteractions/pocock2021"},{"relation":"hasVersion","identifier":"hash://md5/9e3f7e0b37c3873f4763d4dd7304cd47"},{"relation":"isCompiledBy","identifier":"10.5281/zenodo.14927734","resource_type":"software"},{"relation":"isCompiledBy","identifier":"10.5281/zenodo.14893840","resource_type":"software"},{"relation":"isCompiledBy","identifier":"10.5281/zenodo.14662206","resource_type":"software"}],"communities":[{"identifier":"globi-review"}],"upload_type":"publication","creators":[{"name":"Elton"},{"name":"Nomer"},{"name":"Preston"}],"publication_type":"datapaper","title":"A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/pocock2021 hash://md5/9e3f7e0b37c3873f4763d4dd7304cd47","publication_date":"2025-04-13","keywords":["biodiversity informatics","ecology","species interactions","biotic interactions","automated manuscripts","taxonomic names","taxonomic name alignment","biology"],"description":"

Introduction

\n

Data Review and Archive

\n

Data review and archiving can be a time-consuming process, especially\nwhen done manually. This review report aims to help facilitate both\nactivities. It automates the archiving of datasets, including Darwin\nCore archives, and is a citable backup of a version of the dataset.\nAdditionally, an automatic review of species interaction claims made in\nthe dataset is generated and registered with Global Biotic Interactions\n(J. H. Poelen, Simons,\nand Mungall 2014).

\n

This review includes summary statistics about, and observations\nabout, the dataset under review:

\n
\n

Pocock, Michael J.O., Schmucki, Reto, & Bohan, David A. (2020).\nInferring quantitative species interactions of seeds and seed-feeding\ncarabid beetles from ecological survey data [Data set]. Zenodo.\nhttps://doi.org/10.5281/zenodo.4252783\nhttps://github.com/globalbioticinteractions/pocock2021/archive/640388beda95447a7c35fd9e98b9c0faa38028cd.zip\n2025-04-12T10:14:37.030Z hash://md5/9e3f7e0b37c3873f4763d4dd7304cd47

\n
\n

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/pocock2021\nand inspect associated metadata files including, but not limited to,\nREADME.md, eml.xml, and/or globi.json.

\n

Methods

\n

The review is performed through programmatic scripts that leverage\ntools like Preston (Elliott\net al. 2025), Elton (Kuhn, Poelen, and Leinweber 2025), Nomer\n(Salim and Poelen\n2025), globinizer (J. Poelen, Seltmann, and Mietchen 2024)\ncombined with third-party tools like grep, mlr, tail and head.

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Tools used in this review process
tool nameversion
preston0.10.1
elton0.15.9
nomer0.5.13
globinizer0.4.0
mlr6.0.0
jq1.6
yq4.25.3
pandoc3.1.6.1
\n

The review process can be described in the form of the script below\n1.

\n
# get versioned copy of the dataset (size approx. 33.4KiB) under review \nelton pull globalbioticinteractions/pocock2021\n\n# generate review notes\nelton review globalbioticinteractions/pocock2021\\\n > review.tsv\n\n# export indexed interaction records\nelton interactions globalbioticinteractions/pocock2021\\\n > interactions.tsv\n\n# export names and align them with the Catalogue of Life using Nomer \nelton names globalbioticinteractions/pocock2021\\\n | nomer append col\\\n > name-alignment.tsv
\n

or visually, in a process diagram.

\n
\n\"Review\n
Review Process Overview
\n
\n

You can find a copy of the full review script at check-data.sh. See also GitHub\nand Codeberg.

\n

Results

\n

In the following sections, the results of the review are summarized\n2. Then, links to the detailed review\nreports are provided.

\n

Files

\n

The following files are produced in this review:

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
filenamedescription
biblio.biblist of bibliographic reference of this review
check-dataset.shdata review workflow/process as expressed in a bash script
data.zipa versioned Preston (Elliott et al. 2025) archive of the data\nunder review
HEADthe digital signature of the data under review
index.docxreview in MS Word format
index.htmlreview in HTML format
index.mdreview in Pandoc markdown format
index.pdfreview in PDF format
indexed-citations.csv.gzlist of distinct reference citations for reviewed species\ninteraction claims in gzipped comma-separated values file format
indexed-citations.html.gzlist of distinct reference citations for reviewed species\ninteractions claims in gzipped html file format
indexed-citations.tsv.gzlist of distinct reference citations for reviewed species\ninteraction claims in gzipped tab-separated values format
indexed-interactions-col-family-col-family.svgnetwork diagram showing the taxon family to taxon family interaction\nclaims in the dataset under review as interpreted by the Catalogue of\nLife via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024)
indexed-interactions-col-kingdom-col-kingdom.svgnetwork diagram showing the taxon kingdom to taxon kingom\ninteraction claims in the dataset under review as interpreted by the\nCatalogue of Life via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen\n2024)
indexed-interactions.csv.gzspecies interaction claims indexed from the dataset under review in\ngzipped comma-separated values format
indexed-interactions.html.gzspecies interaction claims indexed from the dataset under review in\ngzipped html format
indexed-interactions.tsv.gzspecies interaction claims indexed from the dataset under review in\ngzipped tab-separated values format
indexed-interactions-sample.csvlist of species interaction claims indexed from the dataset under\nreview in gzipped comma-separated values format
indexed-interactions-sample.htmlfirst 500 species interaction claims indexed from the dataset under\nreview in html format
indexed-interactions-sample.tsvfirst 500 species interaction claims indexed from the dataset under\nreview in tab-separated values format
indexed-names.csv.gztaxonomic names indexed from the dataset under review in gzipped\ncomma-separated values format
indexed-names.html.gztaxonomic names found in the dataset under review in gzipped html\nformat
indexed-names.tsv.gztaxonomic names found in the dataset under review in gzipped\ntab-separated values format
indexed-names-resolved-col.csv.gztaxonomic names found in the dataset under review aligned with the\nCatalogue of Life as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped comma-separated values format
indexed-names-resolved-col.html.gztaxonomic names found in the dataset under review aligned with the\nCatalogue of Life as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped html format
indexed-names-resolved-col.tsv.gztaxonomic names found in the dataset under review aligned with the\nCatalogue of Life as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped tab-separated values format
indexed-names-resolved-discoverlife.csv.gztaxonomic names found in the dataset under review aligned with\nDiscover Life bee species checklist as accessed through the Nomer Corpus\nof Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ncomma-separated values format
indexed-names-resolved-discoverlife.html.gztaxonomic names found in the dataset under review aligned with\nDiscover Life bee species checklist as accessed through the Nomer Corpus\nof Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\nhtml format
indexed-names-resolved-discoverlife.tsv.gztaxonomic names found in the dataset under review aligned with\nDiscover Life bee species checklist as accessed through the Nomer Corpus\nof Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ntab-separated values format
indexed-names-resolved-gbif.csv.gztaxonomic names found in the dataset under review aligned with GBIF\nBackbone Taxonomy as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped comma-separated values format
indexed-names-resolved-gbif.html.gztaxonomic names found in the dataset under review aligned with GBIF\nBackbone Taxonomy as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped html format
indexed-names-resolved-gbif.tsv.gztaxonomic names found in the dataset under review aligned with GBIF\nBackbone Taxonomy as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped tab-separated values format
indexed-names-resolved-itis.csv.gztaxonomic names found in the dataset under review aligned with\nIntegrated Taxonomic Information System (ITIS) as accessed through the\nNomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ncomma-separated values format
indexed-names-resolved-itis.html.gztaxonomic names found in the dataset under review aligned with\nIntegrated Taxonomic Information System (ITIS) as accessed through the\nNomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\nhtml format
indexed-names-resolved-itis.tsv.gztaxonomic names found in the dataset under review aligned with\nIntegrated Taxonomic Information System (ITIS) as accessed through the\nNomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ntab-separated values format
indexed-names-resolved-mdd.csv.gztaxonomic names found in the dataset under review aligned with the\nMammal Diversity Database as accessed through the Nomer Corpus of\nTaxonomic Resources (J.\nH. (ed. ). Poelen 2024) in gzipped comma-separated values\nformat
indexed-names-resolved-mdd.html.gztaxonomic names found in the dataset under review aligned with\nMammal Diversity Database as accessed through the Nomer Corpus of\nTaxonomic Resources (J.\nH. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-mdd.tsv.gztaxonomic names found in the dataset under review aligned with\nMammal Diversity Database as accessed through the Nomer Corpus of\nTaxonomic Resources (J.\nH. (ed. ). Poelen 2024) in gzipped tab-separated values\nformat
indexed-names-resolved-ncbi.csv.gztaxonomic names found in the dataset under review aligned with the\nNCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped comma-separated values format
indexed-names-resolved-ncbi.html.gztaxonomic names found in the dataset under review aligned with the\nNCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped html format
indexed-names-resolved-ncbi.tsv.gztaxonomic names found in the dataset under review aligned with the\nNCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped tab-separated values format
indexed-names-resolved-pbdb.csv.gztaxonomic names found in the dataset under review aligned with the\nPaleobiology Database as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped comma-separated values format
indexed-names-resolved-pbdb.html.gztaxonomic names found in the dataset under review aligned with\nPaleobiology Database as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped html format
indexed-names-resolved-pbdb.tsv.gztaxonomic names found in the dataset under review aligned with\nPaleobiology Database as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped tab-separated values format
indexed-names-resolved-tpt.csv.gztaxonomic names found in the dataset under review aligned with the\nTerrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed\nthrough the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ncomma-separated values format
indexed-names-resolved-tpt.html.gztaxonomic names found in the dataset under review aligned with the\nTerrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed\nthrough the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\nhtml format
indexed-names-resolved-tpt.tsv.gztaxonomic names found in the dataset under review aligned with the\nTerrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed\nthrough the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ntab-separated values format
indexed-names-resolved-wfo.csv.gztaxonomic names found in the dataset under review aligned with the\nWorld of Flora Online as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped comma-separated values format
indexed-names-resolved-wfo.html.gztaxonomic names found in the dataset under review aligned with the\nWorld of Flora Online as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped html format
indexed-names-resolved-wfo.tsv.gztaxonomic names found in the dataset under review aligned with the\nWorld of Flora Online as accessed through the Nomer Corpus of Taxonomic\nResources (J. H. (ed. ).\nPoelen 2024) in gzipped tab-separated values format
indexed-names-resolved-worms.csv.gztaxonomic names found in the dataset under review aligned with the\nWorld Register of Marine Species (WoRMS) as accessed through the Nomer\nCorpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ncomma-separated values format
indexed-names-resolved-worms.html.gztaxonomic names found in the dataset under review aligned with the\nWorld Register of Marine Species (WoRMS) as accessed through the Nomer\nCorpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\nhtml format
indexed-names-resolved-worms.tsv.gztaxonomic names found in the dataset under review aligned with the\nWorld Register of Marine Species (WoRMS) as accessed through the Nomer\nCorpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped\ntab-separated values format
indexed-names-sample.csvfirst 500 taxonomic names found in the dataset under review in\ncomma-separated values format
indexed-names-sample.htmlfirst 500 taxonomic names found in the dataset under review in html\nformat
indexed-names-sample.tsvfirst 500 taxonomic names found in the dataset under review in\ntab-separated values format
interaction.svgdiagram summarizing the data model used to index species interaction\nclaims
nanopub-sample.trigfirst 500 species interaction claims as expressed in the nanopub\nformat (Kuhn and Dumontier\n2014)
nanopub.trig.gzspecies interaction claims as expressed in the nanopub format (Kuhn and Dumontier\n2014)
process.svgdiagram summarizing the data review processing workflow
prov.nqorigin of the dataset under review as expressed in rdf/nquads
review.csv.gzreview notes associated with the dataset under review in gzipped\ncomma-separated values format
review.html.gzreview notes associated with the dataset under review in gzipped\nhtml format
review.tsv.gzreview notes associated with the dataset under review in gzipped\ntab-separated values format
review-sample.csvfirst 500 review notes associated with the dataset under review in\ncomma-separated values format
review-sample.htmlfirst 500 review notes associated with the dataset under review in\nhtml format
review-sample.tsvfirst 500 review notes associated with the dataset under review in\ntab-separated values format
review.svga review badge generated as part of the dataset review process
zenodo.jsonmetadata of this review expressed in Zenodo record metadata
\n

Archived Dataset

\n

Note that data.zip file in this\narchive contains the complete, unmodified archived dataset under\nreview.

\n

Biotic Interactions

\n
\n\"Biotic\n
Biotic Interaction Data\nModel
\n
\n

In this review, biotic interactions (or biotic associations) are\nmodeled as a primary (aka subject, source) organism interacting with an\nassociate (aka object, target) organism. The dataset under review\nclassified the primary/associate organisms with specific taxa. The\nprimary and associate organisms The kind of interaction is documented as\nan interaction type.

\n

The dataset under review, named globalbioticinteractions/pocock2021,\nhas fingerprint hash://md5/9e3f7e0b37c3873f4763d4dd7304cd47, is 33.4KiB\nin size and contains 180 interactions with 1 unique type of association\n(e.g., eatenBy) between 68 primary taxa (e.g., Capsella bursa-pastoris)\nand 5 associated taxa (e.g., Harpalus rufipes).

\n

An exhaustive list of indexed interaction claims can be found in\ngzipped csv and tsv archives. To facilitate\ndiscovery, a preview of claims available in the gzipped html page at indexed-interactions.html.gz are\nshown below.

\n

The exhaustive list was used to create the following data summaries\nbelow.

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Sample of Indexed Interaction Claims
sourceTaxonNameinteractionTypeNametargetTaxonNamereferenceCitation
Rumex acetosaeatenByHarpalus rufipesHonek et al 2003
Achillea millefoliumeatenByHarpalus rufipesHonek et al 2003
Alliaria petiolataeatenByHarpalus rufipesHonek et al 2003
Amaranthus retroflexuseatenByHarpalus rufipesHonek et al 2003
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Most Frequently Mentioned Interaction Types (up to 20 most\nfrequent)
interactionTypeNamecount
eatenBy180
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Most Frequently Mentioned Primary Taxa (up to 20 most\nfrequent)
sourceTaxonNamecount
Capsella bursa-pastoris7
Cirsium arvense7
Fallopia convolvulus7
Fumaria officinalis7
Galium aparine7
Taraxacum officinale7
Viola arvensis7
Veronica hederaefolia5
Alopecurus myosuroides5
Senecio vulgaris5
Rumex acetosa2
Achillea millefolium2
Alliaria petiolata2
Amaranthus retroflexus2
Anagallis arvensis2
Arctium lappa2
Arenaria serpyllifolia2
Ballota nigra2
Bellis perennis2
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Most Frequently Mentioned Associate Taxa (up to 20 most\nfrequent)
targetTaxonNamecount
Harpalus rufipes75
Harpalus affinis75
Pterostichus melanarius10
Poecilus cupreus10
Amara conularis10
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Most Frequent Interactions between Primary and Associate Taxa\n(up to 20 most frequent)
sourceTaxonNameinteractionTypeNametargetTaxonNamecount
Capsella bursa-pastoriseatenByHarpalus rufipes2
Cirsium arvenseeatenByHarpalus rufipes2
Fallopia convolvuluseatenByHarpalus rufipes2
Fumaria officinaliseatenByHarpalus rufipes2
Galium aparineeatenByHarpalus rufipes2
Taraxacum officinaleeatenByHarpalus rufipes2
Viola arvensiseatenByHarpalus rufipes2
Capsella bursa-pastoriseatenByHarpalus affinis2
Cirsium arvenseeatenByHarpalus affinis2
Fallopia convolvuluseatenByHarpalus affinis2
Fumaria officinaliseatenByHarpalus affinis2
Galium aparineeatenByHarpalus affinis2
Taraxacum officinaleeatenByHarpalus affinis2
Viola arvensiseatenByHarpalus affinis2
Rumex acetosaeatenByHarpalus rufipes1
Achillea millefoliumeatenByHarpalus rufipes1
Alliaria petiolataeatenByHarpalus rufipes1
Amaranthus retroflexuseatenByHarpalus rufipes1
Anagallis arvensiseatenByHarpalus rufipes1
\n

Interaction Networks

\n

The figures below provide a graph view on the dataset under review.\nThe first shows a summary network on the kingdom level, and the second\nshows how interactions on the family level. It is important to note that\nboth network graphs were first aligned taxonomically using the Catalogue\nof Life. Please refer to the original (or verbatim) taxonomic names for\na more original view on the interaction data.

\n
\n\n
Interactions on taxonomic kingdom rank as\ninterpreted by the Catalogue of Life download\nsvg
\n
\n
\n\n
Interactions on the taxonomic family rank\nas interpreted by the Catalogue of Life. download\nsvg
\n
\n

You can download the indexed dataset under review at indexed-interactions.csv.gz. A\ntab-separated file can be found at indexed-interactions.tsv.gz

\n

Learn more about the structure of this download at GloBI website, by\nopening a GitHub\nissue, or by sending an email.

\n

Another way to discover the dataset under review is by searching for\nit on the GloBI\nwebsite.

\n

Taxonomic Alignment

\n

As part of the review, all names are aligned against various name\ncatalogs (e.g., col, ncbi, discoverlife, gbif, itis, wfo, mdd, tpt,\npbdb, and worms). These alignments can help review name usage or aid in\nselecting of a suitable taxonomic name resource.

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Sample of Name Alignments
providedNamerelationNameresolvedCatalogNameresolvedName
Achillea millefoliumSYNONYM_OFcolAchillea aspleniifolia
Achillea millefoliumHAS_ACCEPTED_NAMEcolAchillea millefolium
Alliaria petiolataHAS_ACCEPTED_NAMEcolAlliaria petiolata
Alopecurus myosuroidesHAS_ACCEPTED_NAMEcolAlopecurus myosuroides
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Distribution of Taxonomic Ranks of Aligned Names by Catalog.\nNames that were not aligned with a catalog are counted as NAs. So, the\ntotal number of unaligned names for a catalog will be listed in their NA\nrow.
resolvedCatalogNameresolvedRankcount
colNA6
colspecies64
colsubspecies10
colvariety1
discoverlifeNA73
gbifNA6
gbifspecies65
gbifsubspecies8
gbifvariety2
itisNA8
itisspecies63
itissubspecies2
mddNA73
ncbiNA9
ncbispecies63
ncbisubspecies1
pbdbNA70
pbdbspecies3
tptNA73
wfoNA10
wfospecies62
wfosubspecies5
wormsNA38
wormsspecies35
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Name relationship types per catalog. Name relationship type\n“NONE” means that a name was not recognized by the associated catalog.\n“SAME_AS” indicates either a “HAS_ACCEPTED_NAME” or “SYNONYM_OF” name\nrelationship type. We recognize that “SYNONYM_OF” encompasses many types\nof nomenclatural synonymies (ICZN 1999) (e.g., junior synonym, senior\nsynonyms).
resolvedCatalogNamerelationNamecount
colSYNONYM_OF41
colHAS_ACCEPTED_NAME62
colNONE6
discoverlifeNONE74
gbifHAS_ACCEPTED_NAME80
gbifSYNONYM_OF65
gbifNONE6
itisHAS_ACCEPTED_NAME63
itisNONE8
itisSYNONYM_OF5
mddNONE74
ncbiSAME_AS63
ncbiNONE9
ncbiSYNONYM_OF2
pbdbNONE71
pbdbHAS_ACCEPTED_NAME3
tptNONE74
wfoHAS_ACCEPTED_NAME58
wfoNONE10
wfoSYNONYM_OF21
wfoHAS_UNCHECKED_NAME6
wormsHAS_ACCEPTED_NAME46
wormsNONE39
wormsSYNONYM_OF4
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
List of Available Name Alignment Reports
catalog namealignment results
colassociated names alignments report in gzipped html, csv, and tsv)
ncbiassociated names alignments report in gzipped html, csv, and tsv)
discoverlifeassociated names alignments report in gzipped html, csv, and tsv)
gbifassociated names alignments report in gzipped html, csv, and tsv)
itisassociated names alignments report in gzipped html, csv, and tsv)
wfoassociated names alignments report in gzipped html, csv, and tsv)
mddassociated names alignments report in gzipped html, csv, and tsv)
tptassociated names alignments report in gzipped html, csv, and tsv)
pbdbassociated names alignments report in gzipped html, csv, and tsv)
wormsassociated names alignments report in gzipped html, csv, and tsv)
\n

Additional Reviews

\n

Elton, Nomer, and other tools may have difficulties interpreting\nexisting species interaction datasets. Or, they may misbehave, or\notherwise show unexpected behavior. As part of the review process,\ndetailed review notes are kept that document possibly misbehaving, or\nconfused, review bots. An sample of review notes associated with this\nreview can be found below.

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
First few lines in the review notes.
reviewDatereviewCommentTypereviewComment
2025-04-13T04:47:33Zsummaryhttps://github.com/globalbioticinteractions/pocock2021/archive/640388beda95447a7c35fd9e98b9c0faa38028cd.zip
2025-04-13T04:47:33Zsummary180 interaction(s)
2025-04-13T04:47:33Zsummary0 note(s)
2025-04-13T04:47:33Zsummary180 info(s)
\n

In addition, you can find the most frequently occurring notes in the\ntable below.

\n

: Most frequently occurring review notes, if any.

\n

For additional information on review notes, please have a look at the\nfirst 500 Review Notes in html format\nor the download full gzipped csv or tsv archives.

\n

GloBI Review Badge

\n

As part of the review, a review badge is generated. This review badge\ncan be included in webpages to indicate the review status of the dataset\nunder review.

\n
\n\"Picture\n
Picture of a GloBI Review Badge 3
\n
\n

Note that if the badge is green, no review notes were generated. If\nthe badge is yellow, the review bots may need some help with\ninterpreting the species interaction data.

\n

GloBI Index Badge

\n

If the dataset under review has been registered with\nGloBI, and has been succesfully indexed by GloBI, the GloBI Index\nStatus Badge will turn green. This means that the dataset under review\nwas indexed by GloBI and is available through GloBI services and derived\ndata products.

\n
\n\n
Picture of a GloBI Index Badge 4
\n
\n

If you’d like to keep track of reviews or index status of the dataset\nunder review, please visit GloBI’s dataset index 5 for\nbadge examples.

\n

Discussion

\n

This review and archive provides a means of creating citable versions\nof datasets that change frequently. This may be useful for dataset\nmanagers, including natural history collection data managers, as a\nbackup archive of a shared Darwin Core archive. It also serves as a\nmeans of creating a trackable citation for the dataset in an automated\nway, while also including some information about the contents of the\ndataset.

\n

This review aims to provide a perspective on the dataset to aid in\nunderstanding of species interaction claims discovered. However, it is\nimportant to note that this review does not assess the quality\nof the dataset. Instead, it serves as an indication of the open-ness6 and FAIRness (Wilkinson et\nal. 2016; Trekels et al. 2023) of the dataset: to perform this\nreview, the data was likely openly available, Findable,\nAccessible, Interoperable and\nReusable. The current Open-FAIR assessment is\nqualitative, and a more quantitative approach can be implemented with\nspecified measurement units.

\n

This report also showcases the reuse of machine-actionable\n(meta)data, something highly recommended by the FAIR Data Principles\n(Wilkinson et al.\n2016). Making (meta)data machine-actionable enables more precise\nprocesing by computers, enabling even naive review bots like Nomer and\nElton to interpret the data effectively. This capability is crucial for\nnot just automating the generation of reports, but also for facilitating\nseamless data exchanges, promoting interoperability.

\n

Acknowledgements

\n

We thank the many humans that created us and those who created and\nmaintained the data, software and other intellectual resources that were\nused for producing this review. In addition, we are grateful for the\nnatural resources providing the basis for these human and bot\nactivities. Also, thanks to https://github.com/zygoballus for helping\nimprove the layout of the review tables.

\n

Author contributions

\n

Nomer was responsible for name alignments. Elton carried out dataset\nextraction, and generated the review notes. Preston tracked, versioned,\nand packaged, the dataset under review.

\n

References

\n
\n
\nElliott, Michael, Jorrit Poelen, Icaro Alzuru, Emilio Berti, and\npartha04patel. 2025. “Bio-Guoda/Preston: 0.10.5.” Zenodo.\nhttps://doi.org/10.5281/zenodo.14662206.\n
\n
\nICZN. 1999. “International Code of Zoological\nNomenclature.” The International Trust for Zoological\nNomenclature, London, UK. https://www.iczn.org/the-code/the-code-online/.\n
\n
\nKuhn, Tobias, and Michel Dumontier. 2014. “Trusty URIs:\nVerifiable, Immutable, and Permanent Digital Artifacts for Linked\nData.” In The Semantic Web: Trends and Challenges,\nedited by Valentina Presutti, Claudia d’Amato, Fabien Gandon, Mathieu\nd’Aquin, Steffen Staab, and Anna Tordai, 395–410. Cham: Springer\nInternational Publishing.\n
\n
\nKuhn, Tobias, Jorrit Poelen, and Katrin Leinweber. 2025.\n“Globalbioticinteractions/Elton: 0.15.1.” Zenodo. https://doi.org/10.5281/zenodo.14927734.\n
\n
\nPoelen, Jorrit H. (ed.). 2024. “Nomer Corpus of Taxonomic\nResources Hash://Sha256/\nB60c0d25a16ae77b24305782017b1a270b79b5d1746f832650 F2027ba536e276\nHash://Md5/17f1363a277ee0e4ecaf1b91c665e47e.” Zenodo. https://doi.org/10.5281/zenodo.12695629.\n
\n
\nPoelen, Jorrit H., James D. Simons, and Chris J. Mungall. 2014.\n“Global Biotic Interactions: An Open Infrastructure to Share and\nAnalyze Species-Interaction Datasets.” Ecological\nInformatics 24 (November): 148–59. https://doi.org/10.1016/j.ecoinf.2014.08.005.\n
\n
\nPoelen, Jorrit, Katja Seltmann, and Daniel Mietchen. 2024.\n“Globalbioticinteractions/Globinizer: 0.4.0.” Zenodo. https://doi.org/10.5281/zenodo.10647565.\n
\n
\nSalim, José Augusto, and Jorrit Poelen. 2025.\n“Globalbioticinteractions/Nomer: 0.5.15.” Zenodo. https://doi.org/10.5281/zenodo.14893840.\n
\n
\nTrekels, Maarten, Debora Pignatari Drucker, José Augusto Salim, Jeff\nOllerton, Jorrit Poelen, Filipi Miranda Soares, Max Rünzel, Muo Kasina,\nQuentin Groom, and Mariano Devoto. 2023. “WorldFAIR Project (D10.1) Agriculture-related pollinator\ndata standards use cases report.” Zenodo. https://doi.org/10.5281/zenodo.8176978.\n
\n
\nWilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg,\nGabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al.\n2016. “The FAIR Guiding Principles for Scientific\nData Management and Stewardship.” Scientific Data 3 (1).\nhttps://doi.org/10.1038/sdata.2016.18.\n
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