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:
Muñoz, G., Trøjelsgaard, K., & W.D. Kissling. 2018. A synthesis
of animal-mediated seed dispersal of palms reveals distinct
biogeographic differences in species interactions. Journal of
Biogeography (in progress)
github.com
2025-04-04T23:04:08.703Z hash://md5/e78ebb6deef2e7f0f711b2fac9edfbad
For additional metadata related to this dataset, please visit
github.com
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.
Tools used in this review process
tool name
version
preston
0.10.1
elton
0.15.9
nomer
0.5.13
globinizer
0.4.0
mlr
6.0.0
jq
1.6
yq
4.25.3
pandoc
3.1.6.1
The review process can be described in the form of the script below
1.
# get versioned copy of the dataset (size approx. 357KiB) under review
elton pull fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics
# generate review notes
elton review fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics\
> review.tsv
# export indexed interaction records
elton interactions fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics\
| nomer append col\
> name-alignment.tsv
or visually, in a process diagram.
Review Process Overview
You can find a copy of the full review script at check-data.sh. See also GitHub
and Codeberg.
Results
In the following sections, the results of the review are summarized
2. Then, links to the detailed review
reports are provided.
Files
The following files are produced in this review:
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 Preston (Elliott et al. 2025) 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-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-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-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-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-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-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-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-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-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-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-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-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
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
fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics, has
fingerprint hash://md5/e78ebb6deef2e7f0f711b2fac9edfbad, is 357KiB in
size and contains 1,175 interaction with 1 unique type of association
(e.g., eats) between 342 primary taxa (e.g., Pecari tajacu) and 126
associated taxa (e.g., Euterpe edulis).
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.
Sample of Indexed Interaction Claims
sourceTaxonName
interactionTypeName
targetTaxonName
referenceCitation
Lepilemur dorsalis
eats
Dypsis madagascariensis
Zona, S. & Henderson, A. (1989) A review of animal mediated seed
dispersal of palms. Selbyana, 11, 6-21. Online Update 2006
((
virtualherbarium.org).
Hapalemur occidentalis
eats
Dypsis madagascariensis
Zona, S. & Henderson, A. (1989) A review of animal mediated seed
dispersal of palms. Selbyana, 11, 6-21. Online Update 2006
((
virtualherbarium.org).
Eulemur macaco
eats
Dypsis madagascariensis
Zona, S. & Henderson, A. (1989) A review of animal mediated seed
dispersal of palms. Selbyana, 11, 6-21. Online Update 2006
((
virtualherbarium.org).
Eulemur macaco
eats
Dypsis madagascariensis
Birkinshaw, C. . 2001. Fruit charateristics of species dispersed by
black lemur (Eulemur macaco) in the Lokobe forest Madagascar.
Biotropica. 478-486
Most Frequently Mentioned Interaction Types (up to 20 most
frequent)
interactionTypeName
count
eats
1175
Most Frequently Mentioned Primary Taxa (up to 20 most
frequent)
sourceTaxonName
count
Pecari tajacu
54
Tayassu pecari
50
Tapirus terrestris
42
Dasyprocta punctata
34
Dasyprocta leporina
24
Cuniculus paca
23
Sciurus granatensis
22
Sapajus apella
19
Colossoma macropomum
18
Proechimys semispinosus
15
Heteromys desmarestianus
15
Ceratogymna atrata
14
Sciurus aestuans
12
Ateles belzebuth
12
Anodorhynchus hyacinthinus
11
Ateles geoffroyi
11
Ara ararauna
10
Piaractus brachypomus
10
Tapirus bairdii
9
Most Frequently Mentioned Associate Taxa (up to 20 most
frequent)
targetTaxonName
count
Euterpe edulis
125
Oenocarpus bataua
86
Syagrus romanzoffiana
85
Astrocaryum jauari
63
Mauritia flexuosa
55
Attalea maripa
53
Attalea butyracea
46
Astrocaryum standleyanum
44
Attalea phalerata
31
Astrocaryum murumuru
27
Phoenix reclinata
27
Elaeis guineensis
26
Acrocomia aculeata
23
Iriartea deltoidea
23
Astrocaryum mexicanum
22
Copernicia alba
21
Astrocaryum gratum
16
Socratea exorrhiza
16
Oenocarpus mapora
16
Most Frequent Interactions between Primary and Associate Taxa
(up to 20 most frequent)
sourceTaxonName
interactionTypeName
targetTaxonName
count
Dasyprocta punctata
eats
Astrocaryum standleyanum
12
Heteromys desmarestianus
eats
Astrocaryum mexicanum
11
Sciurus granatensis
eats
Attalea butyracea
9
Tapirus terrestris
eats
Attalea maripa
9
Proechimys semispinosus
eats
Astrocaryum standleyanum
8
Pecari tajacu
eats
Attalea maripa
8
Pecari tajacu
eats
Mauritia flexuosa
7
Tayassu pecari
eats
Mauritia flexuosa
7
Tapirus terrestris
eats
Syagrus romanzoffiana
7
Turdus albicollis
eats
Euterpe edulis
7
Proechimys semispinosus
eats
Attalea butyracea
6
Dasyprocta punctata
eats
Attalea butyracea
6
Sciurus granatensis
eats
Astrocaryum standleyanum
6
Dasyprocta leporina
eats
Attalea maripa
6
Tayassu pecari
eats
Oenocarpus bataua
6
Sciurus ingrami
eats
Syagrus romanzoffiana
6
Tayassu pecari
eats
Syagrus romanzoffiana
6
Turdus flavipes
eats
Euterpe edulis
6
Pteroglossus bailloni
eats
Euterpe edulis
6
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
svg
Interactions on the taxonomic family rank
as interpreted by the Catalogue of Life. download
svg
You can download the indexed dataset under review at indexed-interactions.csv.gz. A
tab-separated file can be found at indexed-interactions.tsv.gz
Learn more about the structure of this download at GloBI website, by
opening a GitHub
issue, or by sending an email.
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
Acoelorrhaphe wrightii
NONE
col
Acoelorrhaphe wrightii
Acridotheres tristis
HAS_ACCEPTED_NAME
col
Acridotheres tristis
Acrocomia aculeata
HAS_ACCEPTED_NAME
col
Acrocomia aculeata
Aiphanes horrida
HAS_ACCEPTED_NAME
col
Aiphanes horrida
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
14
col
genus
9
col
species
441
col
subspecies
4
col
variety
1
discoverlife
NA
468
gbif
NA
8
gbif
genus
9
gbif
species
446
gbif
subspecies
5
gbif
variety
1
itis
NA
102
itis
genus
9
itis
species
353
itis
subspecies
4
mdd
NA
468
ncbi
NA
23
ncbi
genus
9
ncbi
species
435
ncbi
subspecies
1
pbdb
NA
311
pbdb
genus
2
pbdb
species
155
tpt
NA
195
tpt
genus
1
tpt
species
272
wfo
NA
344
wfo
species
124
worms
NA
398
worms
genus
8
worms
species
62
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
resolvedCatalogName
relationName
count
col
NONE
14
col
HAS_ACCEPTED_NAME
429
col
SYNONYM_OF
34
discoverlife
NONE
468
gbif
SYNONYM_OF
56
gbif
HAS_ACCEPTED_NAME
455
gbif
NONE
8
itis
SYNONYM_OF
24
itis
HAS_ACCEPTED_NAME
346
itis
NONE
102
mdd
NONE
341
mdd
HAS_ACCEPTED_NAME
127
ncbi
SYNONYM_OF
23
ncbi
SAME_AS
422
ncbi
NONE
23
pbdb
NONE
311
pbdb
HAS_ACCEPTED_NAME
152
pbdb
SYNONYM_OF
5
tpt
NONE
195
tpt
HAS_ACCEPTED_NAME
271
tpt
SYNONYM_OF
2
wfo
NONE
344
wfo
HAS_ACCEPTED_NAME
120
wfo
SYNONYM_OF
3
wfo
HAS_UNCHECKED_NAME
2
worms
NONE
398
worms
HAS_ACCEPTED_NAME
67
worms
SYNONYM_OF
3
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
2025-04-10T03:10:14Z
summary
github.com
2025-04-10T03:10:14Z
summary
1175 interaction(s)
2025-04-10T03:10:14Z
summary
0 note(s)
2025-04-10T03:10:14Z
summary
1175 info(s)
In addition, you can find the most frequently occurring notes in the
table below.
: Most frequently occurring review notes, if any.
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.
Picture of a GloBI Review Badge 3
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.
Picture of a GloBI Index Badge 4
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
github.com 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.
References
Elliott, Michael, Jorrit Poelen, Icaro Alzuru, Emilio Berti, and
partha04patel. 2025. "Bio-Guoda/Preston: 0.10.5." Zenodo.
doi.org.
ICZN. 1999. "International Code of Zoological
Nomenclature." The International Trust for Zoological
Nomenclature, London, UK.
iczn.org.
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.
doi.org.
Poelen, Jorrit H. (ed.). 2024. "Nomer Corpus of Taxonomic
Resources Hash://Sha256/
B60c0d25a16ae77b24305782017b1a270b79b5d1746f832650 F2027ba536e276
Hash://Md5/17f1363a277ee0e4ecaf1b91c665e47e." Zenodo.
doi.org.
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.
doi.org.
Poelen, Jorrit, Katja Seltmann, and Daniel Mietchen. 2024.
"Globalbioticinteractions/Globinizer: 0.4.0." Zenodo.
doi.org.
Salim, José Augusto, and Jorrit Poelen. 2025.
"Globalbioticinteractions/Nomer: 0.5.15." Zenodo.
doi.org.
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.
doi.org.
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).
doi.org.
Note that you have to first get the data (e.g., via
elton pull fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics)
before being able to generate reviews (e.g., elton review
fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics), extract
interaction claims (e.g., elton interactions
fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics), or list
taxonomic names (e.g., elton names
fgabriel1891/Palm-Frugivore_Interactions_Neo-Afrotropics)↩︎
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 (2025-04-10) the version of the GloBI
dataset index was available at
globalbioticinteractions.org
According to
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."↩︎