Versioned Archive and Review of Biotic Interactions and Taxon Names Found within globalbioticinteractions/mycoportal hash://md5/f62336a2556e2614859163221315e686

Abstract

Life on Earth is sustained by complex interactions between organisms and their environment. These biotic interactions can be captured in datasets and published digitally. We present a review and archiving process for such an openly accessible digital interactions dataset of known origin and discuss its outcome. The dataset under review, named globalbioticinteractions/mycoportal, has fingerprint hash://md5/f62336a2556e2614859163221315e686, is 632MiB in size and contains 2,000,614 interactions with 7 unique types of associations (e.g., hasHost) between 118,301 primary taxa (e.g., Erysiphe cichoracearum) and 182,199 associated taxa (e.g., Substrate Undetermined). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.

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

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

Methods

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

Results

Tools used in this review process
tool name	version
preston	0.11.1
elton	0.16.11
nomer	0.6.5
globinizer	0.4.0
mlr	6.0.0
jq	1.6
yq	4.25.3
pandoc	3.1.6.1
duckdb	1.3.1
mapserver	7.6.4

In the following sections, the results of the review are summarized ². Then, links to the detailed review reports are provided.

Files

An extensive list of files produced as part of the review process can be found in Appendix A. Review Files.

Archived Dataset

Note that data.zip file in this archive contains the complete, unmodified archived dataset under review.

Biotic Interactions

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

The dataset under review, named globalbioticinteractions/mycoportal, has fingerprint hash://md5/f62336a2556e2614859163221315e686, is 632MiB in size and contains 2,000,614 interactions with 7 unique types of associations (e.g., hasHost) between 118,301 primary taxa (e.g., Erysiphe cichoracearum) and 182,199 associated taxa (e.g., Substrate Undetermined).

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

Interaction Networks

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

Geospatial Distribution

Sample of Indexed Interaction Claims
sourceTaxonName	interactionTypeName	targetTaxonName	referenceCitation
Micropuccinia millefolii	hasHost	Achillea millefolium	https://mycoportal.org/portal/collections/individual/index.php?occid=14705292
Micropuccinia ornata	hasHost	Rumex britannica	https://mycoportal.org/portal/collections/individual/index.php?occid=14705293
Micropuccinia ranunculi	hasHost	Cyrtorhyncha neglecta	https://mycoportal.org/portal/collections/individual/index.php?occid=14704819
Micropuccinia recedens	hasHost	Senecio pseudaureus	https://mycoportal.org/portal/collections/individual/index.php?occid=14707528

Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName	count
hasHost	1521644
adjacentTo	378752
interactsWith	100182
visitsFlowersOf	19
killedBy	11
eats	5
hostOf	1

Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName	count
Erysiphe cichoracearum	8567
Puccinia graminis	8557
Coleosporium solidaginis	6608
Puccinia coronata	5454
Puccinia helianthi	5203
Puccinia menthae	5199
Cronartium ribicola	5027
Puccinia recondita	4892
Puccinia hieracii	4756
Erysiphe polygoni	4613
Puccinia polygoni-amphibii	3915
Otidea onotica	3731
Microsphaera alni	3595
Melampsora bigelowii	3477
Puccinia violae	3431
Puccinia dioicae	3354
Puccinia andropogonis	3046
Puccinia rubigo-vera	2992
Claviceps purpurea	2942

Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName	count
Substrate Undetermined	181477
indet.	91748
indet	16728
ground	13729
Quercus sp.	13477
leaves	13201
Salix sp.	8166
Populus tremuloides	6559
Pseudotsuga menziesii	6486
Abies balsamea	6066
Populus sp.	5810
soil	5787
Pinus strobus	5565
Zea mays	5394
Betula sp.	5000
Acer sp.	4973
Quercus	4835
Rosa sp.	4769
wood	4661

Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName	interactionTypeName	targetTaxonName	count
Puccinia podophylli	hasHost	Podophyllum peltatum	1485
Poria	hasHost	Substrate Undetermined	1361
Puccinia sorghi	hasHost	Zea mays	1145
Puccinia helianthi	hasHost	Helianthus annuus	1067
Polyporus	hasHost	Substrate Undetermined	1000
Puccinia coronata	hasHost	Avena sativa	983
Puccinia hieracii	hasHost	Taraxacum officinale	973
Ustilago avenae	hasHost	Avena sativa	931
Cortinarius	hasHost	Substrate Undetermined	875
Uromyces polygoni	hasHost	Polygonum aviculare	849
Puccinia malvacearum	hasHost	Althaea rosea	845
Cronartium ribicola	hasHost	Ribes nigrum	828
Puccinia asparagi	hasHost	Asparagus officinalis	818
Puccinia convolvuli	hasHost	Convolvulus sepium	764
Otidea onotica	interactsWith	Pseudotsuga menziesii	756
Gymnosporangium juniperi-virginianae	hasHost	Juniperus virginiana	755
Puccinia circaeae	hasHost	Circaea lutetiana	736
Polyporus gilvus	hasHost	Substrate Undetermined	696
Uromyces caladii	hasHost	Arisaema triphyllum	694

If geospatial information was extracted from the dataset under review, the map below will show their distribution. These maps were generated using MapServer (McKenna et al. 2025) tools configured via map configuration indexed-interactions.map :

Another way to discover the dataset under review is by searching for it on the GloBI website.

Taxonomic Alignment

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

Additional Reviews

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

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

Sample of Name Alignments
providedName	relationName	resolvedCatalogName	resolvedName
Fraxinus	HAS_ACCEPTED_NAME	col	Fraxinus
Arachnopeziza candidofulva	HAS_ACCEPTED_NAME	col	Arachnopeziza candidofulva
Arachnopeziza cornuta	HAS_ACCEPTED_NAME	col	Arachnopeziza cornuta
Arachnopeziza delicatula	SYNONYM_OF	col	Gorgoniceps delicatula

Distribution of Taxonomic Ranks of Aligned Names by Catalog. Names that were not aligned with a catalog are counted as NAs. So, the total number of unaligned names for a catalog will be listed in their NA row.
resolvedCatalogName	resolvedRank	count
col	NA	113070
col	class	13
col	domain	1
col	family	332
col	form	15
col	genus	6857
col	infraorder	3
col	kingdom	3
col	order	42
col	phylum	9
col	species	102810
col	subfamily	21
col	subgenus	83
col	suborder	6
col	subphylum	1
col	subspecies	3363
col	subterclass	1
col	subtribe	1
col	superfamily	3
col	superorder	3
col	tribe	30
col	variety	1340
discoverlife	NA	226205
discoverlife	species	8
gbif	NA	106289
gbif	class	13
gbif	family	346
gbif	form	102
gbif	genus	7033
gbif	kingdom	5
gbif	order	38
gbif	phylum	11
gbif	species	108544
gbif	subspecies	4262
gbif	variety	2451
itis	NA	203268
itis	class	10
itis	division	11
itis	family	312
itis	form	1
itis	genus	2940
itis	infraorder	2
itis	kingdom	7
itis	order	47
itis	phylum	3
itis	species	17689
itis	subclass	3
itis	subdivision	2
itis	subfamily	15
itis	subgenus	7
itis	subkingdom	1
itis	suborder	9
itis	subphylum	1
itis	subsection	1
itis	subspecies	827
itis	subtribe	1
itis	superfamily	5
itis	superorder	2
itis	tribe	16
itis	variety	1140
mdd	NA	226212
ncbi	NA	178174
ncbi	clade	11
ncbi	class	11
ncbi	cohort	1
ncbi	family	298
ncbi	forma	13
ncbi	forma specialis	6
ncbi	genus	5160
ncbi	infraorder	3
ncbi	kingdom	2
ncbi	order	46
ncbi	parvorder	1
ncbi	phylum	8
ncbi	section	5
ncbi	series	1
ncbi	species	41882
ncbi	subclass	2
ncbi	subfamily	19
ncbi	subgenus	33
ncbi	suborder	5
ncbi	subphylum	4
ncbi	subspecies	268
ncbi	subtribe	1
ncbi	superfamily	4
ncbi	superkingdom	2
ncbi	superorder	2
ncbi	tribe	23
ncbi	varietas	258
pbdb	NA	223931
pbdb	class	11
pbdb	family	237
pbdb	genus	1435
pbdb	infraclass	1
pbdb	infraorder	6
pbdb	kingdom	4
pbdb	order	37
pbdb	phylum	9
pbdb	species	492
pbdb	subclass	2
pbdb	subfamily	20
pbdb	subgenus	2
pbdb	suborder	14
pbdb	subphylum	1
pbdb	superfamily	4
pbdb	superorder	1
pbdb	superphylum	1
pbdb	tribe	18
pbdb	unranked clade	14
tpt	NA	226119
tpt	family	2
tpt	genus	37
tpt	order	1
tpt	species	52
tpt	specificepithet	1
tpt	subspecificepithet	1
wfo	NA	189406
wfo	family	167
wfo	form	14
wfo	genus	2971
wfo	order	1
wfo	phylum	2
wfo	section	7
wfo	series	1
wfo	species	31701
wfo	subgenus	1
wfo	subsection	1
wfo	subspecies	1549
wfo	tribe	4
wfo	variety	1122
worms	NA	216342
worms	class	11
worms	family	234
worms	genus	2191
worms	infraorder	2
worms	kingdom	4
worms	order	41
worms	phylum	3
worms	phylum (division)	8
worms	section	1
worms	species	7022
worms	subclass	4
worms	subfamily	9
worms	subgenus	3
worms	suborder	9
worms	subphylum	1
worms	subphylum (subdivision)	2
worms	subspecies	313
worms	subterclass	1
worms	superorder	2
worms	tribe	4
worms	variety	272

Name relationship types per catalog. Name relationship type “NONE” means that a name was not recognized by the associated catalog. “SAME_AS” indicates either a “HAS_ACCEPTED_NAME” or “SYNONYM_OF” name relationship type. We recognize that “SYNONYM_OF” encompasses many types of nomenclatural synonymies (ICZN 1999) (e.g., junior synonym, senior synonyms).
resolvedCatalogName	relationName	count
col	HAS_ACCEPTED_NAME	241034
col	SYNONYM_OF	263967
col	NONE	217107
discoverlife	NONE	621195
discoverlife	HAS_ACCEPTED_NAME	13
discoverlife	SYNONYM_OF	9
gbif	HAS_ACCEPTED_NAME	302397
gbif	SYNONYM_OF	321101
gbif	NONE	203355
itis	HAS_ACCEPTED_NAME	102450
itis	NONE	477864
itis	SYNONYM_OF	47722
mdd	NONE	620212
mdd	HAS_ACCEPTED_NAME	25
ncbi	SAME_AS	178928
ncbi	NONE	398238
ncbi	SYNONYM_OF	45980
ncbi	COMMON_NAME_OF	174
pbdb	HAS_ACCEPTED_NAME	24830
pbdb	NONE	595282
pbdb	SYNONYM_OF	1542
tpt	NONE	619947
tpt	HAS_ACCEPTED_NAME	300
tpt	SYNONYM_OF	16
wfo	HAS_ACCEPTED_NAME	112079
wfo	NONE	449641
wfo	SYNONYM_OF	86448
wfo	HAS_UNCHECKED_NAME	23458
worms	NONE	558925
worms	HAS_ACCEPTED_NAME	59282
worms	SYNONYM_OF	20629

List of Available Name Alignment Reports
catalog name	alignment results
col	associated names alignments report in gzipped html, csv, and tsv)
ncbi	associated names alignments report in gzipped html, csv, and tsv)
discoverlife	associated names alignments report in gzipped html, csv, and tsv)
gbif	associated names alignments report in gzipped html, csv, and tsv)
itis	associated names alignments report in gzipped html, csv, and tsv)
wfo	associated names alignments report in gzipped html, csv, and tsv)
mdd	associated names alignments report in gzipped html, csv, and tsv)
tpt	associated names alignments report in gzipped html, csv, and tsv)
pbdb	associated names alignments report in gzipped html, csv, and tsv)
worms	associated names alignments report in gzipped html, csv, and tsv)

First few lines in the review notes.
reviewDate	reviewCommentType	reviewComment
2026-06-03T13:09:49Z	summary	https://github.com/globalbioticinteractions/mycoportal/archive/646fe260d16e7ae85451d1813a1df332e8525a8d.zip
2026-06-03T13:09:49Z	summary	2000614 interaction(s)
2026-06-03T13:09:49Z	summary	0 note(s)
2026-06-03T13:09:49Z	summary	106 info(s)

For additional information on review notes, please have a look at the first 500 Review Notes in html format or the download full gzipped csv or tsv archives.

GloBI Review Badge

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

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

GloBI Index Badge

If the dataset under review has been registered with GloBI, and has been succesfully indexed by GloBI, the GloBI Index Status Badge will turn green. This means that the dataset under review was indexed by GloBI and is available through GloBI services and derived data products.

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

Discussion

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

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

This report also showcases the reuse of machine-actionable (meta)data, something highly recommended by the FAIR Data Principles (Wilkinson et al. 2016). Making (meta)data machine-actionable enables more precise procesing by computers, enabling even naive review bots like Nomer and Elton to interpret the data effectively. This capability is crucial for not just automating the generation of reports, but also for facilitating seamless data exchanges, promoting interoperability.

Acknowledgements

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

Author contributions

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

Appendix A. Review Files

References

filename	description
biblio.bib	list of bibliographic reference of this review
check-dataset.sh	data review workflow/process as expressed in a bash script
data.zip	a versioned archive of the data under review
HEAD	the digital signature of the data under review
index.docx	review in MS Word format
index.html	review in HTML format
index.md	review in Pandoc markdown format
index.pdf	review in PDF format
indexed-citations.csv.gz	list of distinct reference citations for reviewed species interaction claims in gzipped comma-separated values file format
indexed-citations.html.gz	list of distinct reference citations for reviewed species interactions claims in gzipped html file format
indexed-citations.tsv.gz	list of distinct reference citations for reviewed species interaction claims in gzipped tab-separated values format
indexed-interactions-col-family-col-family.svg	network diagram showing the taxon family to taxon family interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024)
indexed-interactions-col-kingdom-col-kingdom.svg	network diagram showing the taxon kingdom to taxon kingom interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024)
indexed-interactions.csv.gz	species interaction claims indexed from the dataset under review in gzipped comma-separated values format
indexed-interactions.html.gz	species interaction claims indexed from the dataset under review in gzipped html format
indexed-interactions.tsv.gz	species interaction claims indexed from the dataset under review in gzipped tab-separated values format
indexed-interactions.parquet	species interaction claims indexed from the dataset under review in Apache Parquet format
indexed-interactions.png	species interaction claims indexed from the dataset under review plotted on a map
indexed-interactions.map	mapserver configuration to plot species interaction claims indexed from the dataset under review on a map
indexed-interactions.gpkg	species interaction claims indexed from the dataset under review in GeoPackage format
indexed-interactions-h3.gpkg	geospatially clustered h3 species interaction claims indexed from the dataset under review in GeoPackage format
indexed-interactions-sample.csv	list of species interaction claims indexed from the dataset under review in gzipped comma-separated values format
indexed-interactions-sample.html	first 500 species interaction claims indexed from the dataset under review in html format
indexed-interactions-sample.tsv	first 500 species interaction claims indexed from the dataset under review in tab-separated values format
indexed-names.csv.gz	taxonomic names indexed from the dataset under review in gzipped comma-separated values format
indexed-names.html.gz	taxonomic names found in the dataset under review in gzipped html format
indexed-names.tsv.gz	taxonomic names found in the dataset under review in gzipped tab-separated values format
indexed-names.parquet	taxonomic names found in the dataset under review in Apache Parquet format
indexed-names-resolved-col.csv.gz	taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-col.html.gz	taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-col.tsv.gz	taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-col.parquet	taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-discoverlife.csv.gz	taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-discoverlife.html.gz	taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-discoverlife.tsv.gz	taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-discoverlife.parquet	taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-gbif.csv.gz	taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-gbif.html.gz	taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-gbif.tsv.gz	taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-gbif.parquet	taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-itis.csv.gz	taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-itis.html.gz	taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-itis.tsv.gz	taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-itis.parquet	taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-mdd.csv.gz	taxonomic names found in the dataset under review aligned with the Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-mdd.html.gz	taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-mdd.tsv.gz	taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-mdd.parquet	taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-ncbi.csv.gz	taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-ncbi.html.gz	taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-ncbi.tsv.gz	taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-ncbi.parquet	taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-pbdb.csv.gz	taxonomic names found in the dataset under review aligned with the Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-pbdb.html.gz	taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-pbdb.tsv.gz	taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-pbdb.parquet	taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-tpt.csv.gz	taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-tpt.html.gz	taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-tpt.tsv.gz	taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-tpt.parquet	taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-wfo.csv.gz	taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-wfo.html.gz	taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-wfo.tsv.gz	taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-wfo.parquet	taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-worms.csv.gz	taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-worms.html.gz	taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-worms.tsv.gz	taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-worms.parquet	taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-sample.csv	first 500 taxonomic names found in the dataset under review in comma-separated values format
indexed-names-sample.html	first 500 taxonomic names found in the dataset under review in html format
indexed-names-sample.tsv	first 500 taxonomic names found in the dataset under review in tab-separated values format
interaction.svg	diagram summarizing the data model used to index species interaction claims
nanopub-sample.trig	first 500 species interaction claims as expressed in the nanopub format (Kuhn and Dumontier 2014)
nanopub.trig.gz	species interaction claims as expressed in the nanopub format (Kuhn and Dumontier 2014)
process.svg	diagram summarizing the data review processing workflow
prov.nq	origin of the dataset under review as expressed in rdf/nquads
review.csv.gz	review notes associated with the dataset under review in gzipped comma-separated values format
review.html.gz	review notes associated with the dataset under review in gzipped html format
review.tsv.gz	review notes associated with the dataset under review in gzipped tab-separated values format
review-sample.csv	first 500 review notes associated with the dataset under review in comma-separated values format
review-sample.html	first 500 review notes associated with the dataset under review in html format
review-sample.tsv	first 500 review notes associated with the dataset under review in tab-separated values format
review.svg	a review badge generated as part of the dataset review process
zenodo.json	metadata of this review expressed in Zenodo record metadata

Elliott, Michael, Jorrit Poelen, Icaro Alzuru, Emilio Berti, and partha04patel. 2025. “Bio-Guoda/Preston: 0.10.5.” Zenodo. https://doi.org/10.5281/zenodo.14662206.

ICZN. 1999. “International Code of Zoological Nomenclature.” The International Trust for Zoological Nomenclature, London, UK. https://www.iczn.org/the-code/the-code-online/.

Kuhn, Tobias, and Michel Dumontier. 2014. “Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data.” In The Semantic Web: Trends and Challenges, edited by Valentina Presutti, Claudia d’Amato, Fabien Gandon, Mathieu d’Aquin, Steffen Staab, and Anna Tordai, 395–410. Cham: Springer International Publishing.

Kuhn, Tobias, Jorrit Poelen, and Katrin Leinweber. 2025. “Globalbioticinteractions/Elton: 0.15.1.” Zenodo. https://doi.org/10.5281/zenodo.14927734.

McKenna, Jeff, Steve Lime, Thomas Bonfort, Jérome Boué, Howard Butler, Seth Girvin, Tom Kralidis, et al. 2025. “MapServer.” Zenodo. https://doi.org/10.5281/zenodo.17807263.

Poelen, Jorrit H. (ed.). 2024. “Nomer Corpus of Taxonomic Resources Hash://Sha256/ B60c0d25a16ae77b24305782017b1a270b79b5d1746f832650 F2027ba536e276 Hash://Md5/17f1363a277ee0e4ecaf1b91c665e47e.” Zenodo. https://doi.org/10.5281/zenodo.12695629.

Poelen, Jorrit H., James D. Simons, and Chris J. Mungall. 2014. “Global Biotic Interactions: An Open Infrastructure to Share and Analyze Species-Interaction Datasets.” Ecological Informatics 24 (November): 148–59. https://doi.org/10.1016/j.ecoinf.2014.08.005.

Poelen, Jorrit, Katja Seltmann, and Daniel Mietchen. 2024. “Globalbioticinteractions/Globinizer: 0.4.0.” Zenodo. https://doi.org/10.5281/zenodo.10647565.

Salim, José Augusto, and Jorrit Poelen. 2025. “Globalbioticinteractions/Nomer: 0.5.15.” Zenodo. https://doi.org/10.5281/zenodo.14893840.

Trekels, Maarten, Debora Pignatari Drucker, José Augusto Salim, Jeff Ollerton, Jorrit Poelen, Filipi Miranda Soares, Max Rünzel, Muo Kasina, Quentin Groom, and Mariano Devoto. 2023. “WorldFAIR Project (D10.1) Agriculture-related pollinator data standards use cases report.” Zenodo. https://doi.org/10.5281/zenodo.8176978.

Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” Scientific Data 3 (1). https://doi.org/10.1038/sdata.2016.18.

Note that you have to first get the data (e.g., via elton pull globalbioticinteractions/mycoportal) before being able to generate reviews (e.g., elton review globalbioticinteractions/mycoportal), extract interaction claims (e.g., elton interactions globalbioticinteractions/mycoportal), or list taxonomic names (e.g., elton names globalbioticinteractions/mycoportal)↩︎
Disclaimer: The results in this review should be considered friendly, yet naive, notes from an unsophisticated robot. Please keep that in mind when considering the review results.↩︎
Up-to-date status of the GloBI Review Badge can be retrieved from the GloBI Review Depot ↩︎
Up-to-date status of the GloBI Index Badge can be retrieved from GloBI’s API ↩︎
At time of writing (2026-06-03) the version of the GloBI dataset index was available at https://globalbioticinteractions.org/datasets ↩︎
According to http://opendefinition.org/: “Open data is data that can be freely used, re-used and redistributed by anyone - subject only, at most, to the requirement to attribute and sharealike.”↩︎