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/osal-ar, has fingerprint
hash://md5/13a7912d20fa969dca345fe0028b14f1, is 460MiB in size and
contains 42,487 interaction with 5 unique types of associations (e.g.,
interactsWith) between 3,000 primary taxon (e.g., Hannemania) and 2,988
associated taxon (e.g., Bos taurus). 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catalogs, and an archived version of the dataset from which the reviews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.
Introduction
Data Review and Archive
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:
Klompen H, Johnson N (2018). Ohio State Acarology Laboratory (OSAL),
Ohio State University. Museum of Biological Diversity, The Ohio State
University. Accessed via
https://mbd-db.osu.edu/hol/taxon_name/05fbf4bb-f8e1-404e-a27c-759d345aa4d0
on 2023-11-06
hash://sha256/fb23140e60f4889de35ae174b2570cf294012bff4f2c8c419c292af51c98c25f
https://github.com/globalbioticinteractions/osal-ar/archive/eaa0ff7fa87f0217b2d1313eec7f2c9ddb0ad232.zip
2025-04-12T10:06:47.585Z hash://md5/13a7912d20fa969dca345fe0028b14f1
For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/osal-ar
and inspect associated metadata files including, but not limited to,
README.md, eml.xml, and/or globi.json.
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.
The review process can be described in the form of the script below
1.
# get versioned copy of the dataset (size approx. 460MiB) under review
elton pull globalbioticinteractions/osal-ar
# generate review notes
elton review globalbioticinteractions/osal-ar\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/osal-ar\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/osal-ar\
| nomer append col\
> name-alignment.tsv
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)
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)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
metadata of this review expressed in Zenodo record metadata
Archived Dataset
Note that data.zip file in this
archive contains the complete, unmodified archived dataset under
review.
Biotic Interactions
Biotic Interaction Data
Model
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/osal-ar, has
fingerprint hash://md5/13a7912d20fa969dca345fe0028b14f1, is 460MiB in
size and contains 42,487 interaction with 5 unique types of associations
(e.g., interactsWith) between 3,000 primary taxon (e.g., Hannemania) and
2,988 associated taxon (e.g., Bos taurus).
An exhaustive list of indexed interaction claims can be found in
gzipped csv and tsv archives. To facilitate
discovery, a preview of claims available in the gzipped html page at indexed-interactions.html.gz are
shown below.
The exhaustive list was used to create the following data summaries
below.
Most Frequently Mentioned Interaction Types (up to 20 most
frequent)
interactionTypeName
count
interactsWith
21617
parasiteOf
19229
eats
1598
preysOn
42
coRoostsWith
1
Most Frequently Mentioned Primary Taxa (up to 20 most
frequent)
sourceTaxonName
count
Hannemania
1568
Euschoengastia peromysci
856
Euschoengastia brevipes
787
Uropodina
695
Trombiculidae
674
Harpirhynchidae
631
Uropodidae
618
Euschoengastia setosa
612
Harpirhynchus
598
Amblyomma testudinarium
567
Hyalomma anatolicum anatolicum
547
Boophilus microplus
505
Tarsonemus krantzi
390
Hyalomma
340
Dermacentor variabilis
337
Parasitidae
323
Rhipicephalus sanguineus
313
Insectolaelaps quadrisetus
311
Hyalomma dromedarii
292
Most Frequently Mentioned Associate Taxa (up to 20 most
frequent)
targetTaxonName
count
Bos taurus
1233
Peromyscus
1009
Peromyscus leucopus
968
Pinus
853
Lithobates pipiens
852
Quercus
817
Pinus taeda
734
Myodes
726
Myodes gapperi
707
Sus scrofa
697
Bubalus bubalis
610
Dendroctonus frontalis
428
Equus caballus
423
Mus musculus
418
Capra hircus
323
Ovis aries
308
Bambusa
304
Canis lupus
283
Ips typographus
280
Most Frequent Interactions between Primary and Associate Taxa
(up to 20 most frequent)
sourceTaxonName
interactionTypeName
targetTaxonName
count
Hannemania
parasiteOf
Lithobates pipiens
705
Euschoengastia brevipes
parasiteOf
Myodes
551
Euschoengastia setosa
parasiteOf
Peromyscus leucopus
365
Trombiculidae
parasiteOf
Myodes gapperi
350
Amblyomma testudinarium
parasiteOf
Sus scrofa
344
Boophilus microplus
parasiteOf
Bos taurus
286
Myobia murismusculi
parasiteOf
Mus musculus
251
Insectolaelaps quadrisetus
interactsWith
Ips typographus
245
Euschoengastia setosa
interactsWith
Peromyscus
241
Euschoengastia peromysci
parasiteOf
Myodes gapperi
239
Euschoengastia peromysci
interactsWith
Peromyscus
198
Tarsonemus krantzi
interactsWith
Dendroctonus frontalis
195
Tarsonemus krantzi
interactsWith
Pinus taeda
195
Galendromus occidentalis
interactsWith
Vitis vinifera
183
Hyalomma anatolicum anatolicum
parasiteOf
Bubalus bubalis
174
Euschoengastia peromysci
parasiteOf
Peromyscus leucopus
167
Hyalomma anatolicum anatolicum
parasiteOf
Bos taurus
166
Neotrombicula japonica
parasiteOf
Apodemus agrarius
161
Bdellorhynchus
interactsWith
Anas clypeata
158
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.
Interactions on taxonomic kingdom rank as
interpreted by the Catalogue of Life download
svgInteractions on the taxonomic family rank
as interpreted by the Catalogue of Life. download
svg
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.
Sample of Name Alignments
providedName
relationName
resolvedCatalogName
resolvedName
Dysdercus splendidus
NONE
col
Dysdercus splendidus
Melanerpes formicivorus
HAS_ACCEPTED_NAME
col
Melanerpes formicivorus
Laelaps stupkai
NONE
col
Laelaps stupkai
Psorergates musculinus
HAS_ACCEPTED_NAME
col
Psorergates musculinus
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
1776
col
class
9
col
family
246
col
genus
735
col
infraorder
2
col
kingdom
1
col
order
29
col
phylum
1
col
species
3109
col
subclass
1
col
subfamily
1
col
subgenus
52
col
suborder
2
col
subspecies
54
col
subtribe
1
col
superfamily
2
col
superorder
1
col
tribe
1
col
variety
10
discoverlife
NA
5936
discoverlife
species
9
gbif
NA
959
gbif
class
10
gbif
family
249
gbif
genus
1034
gbif
kingdom
1
gbif
order
29
gbif
phylum
1
gbif
species
3633
gbif
subspecies
63
gbif
variety
16
itis
NA
2188
itis
class
9
itis
division
1
itis
family
247
itis
genus
664
itis
infraorder
1
itis
kingdom
1
itis
order
32
itis
species
2757
itis
subclass
2
itis
subfamily
1
itis
suborder
2
itis
subphylum
1
itis
subspecies
36
itis
superfamily
3
itis
superorder
1
itis
variety
3
mdd
NA
5945
ncbi
NA
2306
ncbi
clade
4
ncbi
class
8
ncbi
family
240
ncbi
genus
833
ncbi
infraorder
1
ncbi
kingdom
1
ncbi
order
30
ncbi
species
2498
ncbi
subclass
2
ncbi
subfamily
2
ncbi
subgenus
17
ncbi
suborder
2
ncbi
subphylum
1
ncbi
subspecies
15
ncbi
superfamily
2
ncbi
superorder
1
ncbi
varietas
2
pbdb
NA
4600
pbdb
class
9
pbdb
family
156
pbdb
genus
405
pbdb
infraorder
3
pbdb
kingdom
1
pbdb
order
34
pbdb
phylum
1
pbdb
species
726
pbdb
subclass
2
pbdb
subfamily
3
pbdb
suborder
2
pbdb
subspecies
3
pbdb
superclass
1
pbdb
superfamily
1
pbdb
superorder
1
pbdb
tribe
1
pbdb
unranked clade
8
tpt
NA
3283
tpt
family
44
tpt
genus
151
tpt
order
6
tpt
species
2458
tpt
specificepithet
2
tpt
subspecificepithet
5
wfo
NA
5166
wfo
class
1
wfo
family
29
wfo
genus
278
wfo
order
5
wfo
species
457
wfo
subspecies
9
wfo
variety
7
worms
NA
4793
worms
class
7
worms
family
160
worms
genus
369
worms
infraorder
1
worms
kingdom
1
worms
order
30
worms
phylum (division)
1
worms
species
575
worms
subclass
3
worms
subgenus
1
worms
suborder
2
worms
subspecies
3
worms
superfamily
2
worms
superorder
1
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
NONE
1798
col
HAS_ACCEPTED_NAME
3997
col
SYNONYM_OF
919
discoverlife
NONE
5975
discoverlife
HAS_ACCEPTED_NAME
9
discoverlife
SYNONYM_OF
2
gbif
NONE
970
gbif
HAS_ACCEPTED_NAME
5079
gbif
SYNONYM_OF
1310
itis
NONE
2215
itis
HAS_ACCEPTED_NAME
3495
itis
SYNONYM_OF
357
mdd
NONE
5406
mdd
HAS_ACCEPTED_NAME
565
mdd
SYNONYM_OF
13
ncbi
NONE
2319
ncbi
SAME_AS
3461
ncbi
SYNONYM_OF
244
pbdb
NONE
4635
pbdb
HAS_ACCEPTED_NAME
1323
pbdb
SYNONYM_OF
92
tpt
NONE
3313
tpt
HAS_ACCEPTED_NAME
2715
tpt
SYNONYM_OF
778
wfo
NONE
5205
wfo
HAS_ACCEPTED_NAME
708
wfo
SYNONYM_OF
146
wfo
HAS_UNCHECKED_NAME
75
worms
NONE
4826
worms
HAS_ACCEPTED_NAME
1122
worms
SYNONYM_OF
94
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)
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.
First few lines in the review notes.
reviewDate
reviewCommentType
reviewComment
2025-04-12T16:17:16Z
note
target taxon name missing
2025-04-12T16:17:16Z
note
invalid date string [Mar-1926]
2025-04-12T16:17:16Z
note
invalid date string [Mar-1926]
2025-04-12T16:17:16Z
note
target taxon name missing
In addition, you can find the most frequently occurring notes in the
table below.
Most frequently occurring review notes, if any.
reviewComment
count
target taxon name missing
19777
invalid date string [id-68]
152
invalid date string [DEC-1987]
98
invalid date string [OCT-1926]
74
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.
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.
Poelen, Jorrit H. (ed.). 2024. “Nomer Corpus of Taxonomic
Resources Hash://Sha256/
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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.
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
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