A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/tamuic-ent

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/tamuic-ent/issues

2024-11-18

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 process of such an openly accessible digital interactions dataset of known origin, and discuss its outcome. The dataset under review, named globalbioticinteractions/tamuic-ent, is 574MiB in size and contains 11,958 interaction with 4 unique types of associations (e.g., interactsWith) between 1,215 primary taxon (e.g., Anthonomus) and 1,857 associated taxon (e.g., post oak savanna w/pasture). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple catalogs.

Introduction

Data Review

Data review can be a time consuming process, especially when done manually. This review report aims to help facilitate data review of species interaction claims made in datasets registered with Global Biotic Interactions (Poelen, Simons, and Mungall 2014). The review includes summary statistics of, and observations about, the dataset under review:

Texas A&M University Insect Collection https://github.com/globalbioticinteractions/tamuic-ent/archive/f261a8c192021408da67c39626a4aac56e3bac41.zip 2024-11-16T12:21:33.091Z b660443a72014c4e58655a6aebf141ae219b859868f38d88974bbbaab8575a03

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/tamuic-ent 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, Elton, Nomer combined with third-party tools like grep, mlr, tail and head.

Tools used in this review process
tool name version
elton 0.13.9
nomer 0.5.13
mlr 6.0.0
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.  574MiB) under review 
elton pull globalbioticinteractions/tamuic-ent

# generate review notes
elton review globalbioticinteractions/tamuic-ent\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/tamuic-ent\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/tamuic-ent\
 | nomer append col\
 > name-alignment.tsv

or visually, in a process diagram.

review origin dataset origin elton Elton (a naive review bot) elton->origin pull (1) interactions indexed interactions elton->interactions generates (2) alignment name alignments nomer Nomer (a naive review bot) nomer->interactions extract names (3) nomer->alignment generates (5) catalog name catalog nomer->catalog uses (4)

You can find a recent copy of the full review script at check-data.sh.

Results

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

Biotic Interactions

model primaryTaxon Primary Taxon associatedTaxon Associated Taxon primaryOrganism Primary Organism primaryOrganism->primaryTaxon classifiedAs associatedOrganism Associated Organism primaryOrganism->associatedOrganism interactsWith associatedOrganism->associatedTaxon classifiedAs

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/tamuic-ent, is 574MiB in size and contains 11,958 interaction with 4 unique types of associations (e.g., interactsWith) between 1,215 primary taxon (e.g., Anthonomus) and 1,857 associated taxon (e.g., post oak savanna w/pasture).

An exhaustive list of indexed interaction claims can be found in csv and tsv archives. To facilitate discovery, the first 500 claims available on the html page at indexed-interactions.html are shown below.

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

Sample of Indexed Interaction Claims
sourceTaxonName interactionTypeName targetTaxonName referenceCitation
Gnaphosa sericata interactsWith sandy open prairie (L. Koch),
Drassyllus creolus interactsWith live oak woodland Chamberlin & Gertsch,
Anthonomus suturalis interactsWith Phylloxera gall on pecan LeConte,
Anthonomus suturalis interactsWith Phylloxera gall on pecan LeConte,
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 12104
hasHost 209
adjacentTo 169
eats 38
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Anthonomus 560
Anthonomus hunteri 260
Tricorynus 240
Dieunomia heteropoda 230
Amblyomma cajennense 222
Anthonomus tectus 216
Anthonomus squamans 207
Anthonomopsis mixta 180
Anthonomus testaceosquamosus 179
Phantyna segregata 172
Falconina gracilis 169
Anthonomus rileyi 143
Talanites exlineae 138
Dermacentor variabilis 137
Amblyomma inornatum 135
Anthonomus rufipennis 127
Elaver excepta 118
Anthonomus sphaeralciae 116
Drassyllus 110
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
post oak savanna w/pasture 612
pecan 359
dense coastal brush 317
Byrsonima crassifolia (L.) H. B. K. 305
palm forest 280
cotton 224
Cottontail 169
Javelina 165
Cotton 162
re-vegetated site 155
Hampea trilobata 153
ebony-guayacan association 149
managed 136
Raccoon 131
loblolly pine 130
Horse 125
peanuts 121
spices 120
Tandoori blend 120
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Anthonomus interactsWith Byrsonima crassifolia (L.) H. B. K. 305
Anthonomus hunteri interactsWith Hampea trilobata 150
Tricorynus interactsWith spices 120
Tricorynus interactsWith Tandoori blend 120
Anthonomus sphaeralciae interactsWith Sphaeralcea emoryi 107
Anthonomus hunteri interactsWith Hamp. trilobata 105
Anthonomus tectus interactsWith Heterotheca 96
Haemaphysalis leporispalustris interactsWith Cottontail 94
Anthonomopsis mixta interactsWith Prunus sp. 88
Anthonomopsis mixta interactsWith Wild prune 86
Amblyomma cajennense interactsWith Javelina 85
Falconina gracilis interactsWith post oak savanna w/pasture 79
Anthonomus rileyi interactsWith Juniperus ashei 77
Dieunomia heteropoda interactsWith Verbesina encelioides 72
Tabanus stenocephalus interactsWith Horse 68
Mazax pax interactsWith palm forest 67
Anthonomus squamans interactsWith Malvastrum aurantiacum 67
Anthonomus squamans interactsWith Sphaeralcea lindheimeri 65
Dieunomia heteropoda interactsWith sunflower 65

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 Animalia Animalia Animalia->Animalia Animalia->Animalia Plantae Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Fungi Fungi Animalia->Fungi Plantae->Plantae
interactions Andrenidae Andrenidae Asteraceae Asteraceae Andrenidae->Asteraceae Cactaceae Cactaceae Andrenidae->Cactaceae Ehretiaceae Ehretiaceae Andrenidae->Ehretiaceae Lamiaceae Lamiaceae Andrenidae->Lamiaceae Malvaceae Malvaceae Andrenidae->Malvaceae Papaveraceae Papaveraceae Andrenidae->Papaveraceae Rubiaceae Rubiaceae Andrenidae->Rubiaceae Solanaceae Solanaceae Andrenidae->Solanaceae Anthocoridae Anthocoridae Anthocoridae->Asteraceae Anthocoridae->Cactaceae Anacardiaceae Anacardiaceae Anthocoridae->Anacardiaceae Apiaceae Apiaceae Anthocoridae->Apiaceae Fabaceae Fabaceae Anthocoridae->Fabaceae Fagaceae Fagaceae Anthocoridae->Fagaceae Poaceae Poaceae Anthocoridae->Poaceae Aphididae Aphididae Aphididae->Asteraceae Apocynaceae Apocynaceae Aphididae->Apocynaceae Apidae Apidae Apidae->Asteraceae Apidae->Cactaceae Apidae->Lamiaceae Alismataceae Alismataceae Apidae->Alismataceae Asphodelaceae Asphodelaceae Apidae->Asphodelaceae Euphorbiaceae Euphorbiaceae Apidae->Euphorbiaceae Hydrophyllaceae Hydrophyllaceae Apidae->Hydrophyllaceae Verbenaceae Verbenaceae Apidae->Verbenaceae Aradidae Aradidae Aradidae->Asteraceae Araneidae Araneidae Araneidae->Asteraceae Araneidae->Malvaceae Araneidae->Fabaceae Araneidae->Poaceae Baetidae Baetidae Baetidae->Poaceae Braconidae Braconidae Pieridae Pieridae Braconidae->Pieridae Pyralidae Pyralidae Braconidae->Pyralidae Tortricidae Tortricidae Braconidae->Tortricidae Brassicaceae Brassicaceae Pieridae->Brassicaceae Pinaceae Pinaceae Pyralidae->Pinaceae Dactylopiidae Dactylopiidae Pyralidae->Dactylopiidae Tortricidae->Asteraceae Cerambycidae Cerambycidae Cerambycidae->Asteraceae Ceratophyllidae Ceratophyllidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Cheiracanthiidae Cheiracanthiidae Cheiracanthiidae->Asteraceae Chrysomelidae Chrysomelidae Chrysomelidae->Asteraceae Cimicidae Cimicidae Vespertilionidae Vespertilionidae Cimicidae->Vespertilionidae Clubionidae Clubionidae Clubionidae->Lamiaceae Colletidae Colletidae Colletidae->Solanaceae Corinnidae Corinnidae Ulmaceae Ulmaceae Corinnidae->Ulmaceae Cosmopterigidae Cosmopterigidae Cosmopterigidae->Fabaceae Crambidae Crambidae Crambidae->Solanaceae Crambidae->Poaceae Ctenophthalmidae Ctenophthalmidae Didelphidae Didelphidae Ctenophthalmidae->Didelphidae Culicidae Culicidae Cricetidae Cricetidae Culicidae->Cricetidae Curculionidae Curculionidae Curculionidae->Asteraceae Curculionidae->Lamiaceae Curculionidae->Malvaceae Curculionidae->Solanaceae Curculionidae->Apiaceae Curculionidae->Fabaceae Curculionidae->Fabaceae Curculionidae->Fagaceae Curculionidae->Poaceae Curculionidae->Euphorbiaceae Rosaceae Rosaceae Curculionidae->Rosaceae Curculionidae->Rosaceae Aquifoliaceae Aquifoliaceae Curculionidae->Aquifoliaceae Berberidaceae Berberidaceae Curculionidae->Berberidaceae Betulaceae Betulaceae Curculionidae->Betulaceae Curculionidae->Brassicaceae Cannabaceae Cannabaceae Curculionidae->Cannabaceae Cordiaceae Cordiaceae Curculionidae->Cordiaceae Cornaceae Cornaceae Curculionidae->Cornaceae Cupressaceae Cupressaceae Curculionidae->Cupressaceae Ericaceae Ericaceae Curculionidae->Ericaceae Hypericaceae Hypericaceae Curculionidae->Hypericaceae Malpighiaceae Malpighiaceae Curculionidae->Malpighiaceae Myrtaceae Myrtaceae Curculionidae->Myrtaceae Curculionidae->Pinaceae Rutaceae Rutaceae Curculionidae->Rutaceae Salicaceae Salicaceae Curculionidae->Salicaceae Dictynidae Dictynidae Dictynidae->Asteraceae Dictynidae->Malvaceae Dictynidae->Fagaceae Dictynidae->Ulmaceae Dictynidae->Cupressaceae Doidae Doidae Doidae->Euphorbiaceae Elateridae Elateridae Rhamnaceae Rhamnaceae Elateridae->Rhamnaceae Epipyropidae Epipyropidae Flatidae Flatidae Epipyropidae->Flatidae Erebidae Erebidae Erebidae->Asteraceae Erebidae->Asteraceae Erebidae->Fabaceae Erebidae->Fagaceae Erebidae->Poaceae Erebidae->Apocynaceae Erebidae->Ulmaceae Erebidae->Rosaceae Erebidae->Cannabaceae Erebidae->Cupressaceae Erebidae->Ericaceae Caliciaceae Caliciaceae Erebidae->Caliciaceae Convolvulaceae Convolvulaceae Erebidae->Convolvulaceae Cyperaceae Cyperaceae Erebidae->Cyperaceae Ebenaceae Ebenaceae Erebidae->Ebenaceae Moraceae Moraceae Erebidae->Moraceae Sapindaceae Sapindaceae Erebidae->Sapindaceae Sapotaceae Sapotaceae Erebidae->Sapotaceae Ethmiidae Ethmiidae Ethmiidae->Hydrophyllaceae Eupelmidae Eupelmidae Eupelmidae->Pyralidae Gelechiidae Gelechiidae Gelechiidae->Asteraceae Globipedidae Globipedidae Globipedidae->Pinaceae Gnaphosidae Gnaphosidae Gnaphosidae->Ulmaceae Gnaphosidae->Rutaceae Halictidae Halictidae Halictidae->Asteraceae Halictidae->Cactaceae Halictidae->Lamiaceae Halictidae->Rubiaceae Halictidae->Fabaceae Halictidae->Euphorbiaceae Halictidae->Verbenaceae Halictidae->Salicaceae Halictidae->Rhamnaceae Combretaceae Combretaceae Halictidae->Combretaceae Commelinaceae Commelinaceae Halictidae->Commelinaceae Namaceae Namaceae Halictidae->Namaceae Polygonaceae Polygonaceae Halictidae->Polygonaceae Hesperiidae Hesperiidae Hesperiidae->Malvaceae Hesperiidae->Fabaceae Hesperiidae->Malpighiaceae Hesperiidae->Combretaceae Amaranthaceae Amaranthaceae Hesperiidae->Amaranthaceae Cannaceae Cannaceae Hesperiidae->Cannaceae Hippoboscidae Hippoboscidae Phyllostomidae Phyllostomidae Hippoboscidae->Phyllostomidae Ischnopsyllidae Ischnopsyllidae Ischnopsyllidae->Cricetidae Ixodidae Ixodidae Armadillidae Armadillidae Ixodidae->Armadillidae Bovidae Bovidae Ixodidae->Bovidae Canidae Canidae Ixodidae->Canidae Iguanidae Iguanidae Ixodidae->Iguanidae Lacturidae Lacturidae Lacturidae->Sapotaceae Lasiocampidae Lasiocampidae Lasiocampidae->Fagaceae Lasiocampidae->Rosaceae Limacodidae Limacodidae Limacodidae->Sapindaceae Lycaenidae Lycaenidae Lycaenidae->Malvaceae Lycaenidae->Fabaceae Lycaenidae->Euphorbiaceae Lycaenidae->Verbenaceae Lycaenidae->Sapindaceae Lycaenidae->Amaranthaceae Asparagaceae Asparagaceae Lycaenidae->Asparagaceae Viscaceae Viscaceae Lycaenidae->Viscaceae Megachilidae Megachilidae Megachilidae->Asteraceae Megachilidae->Lamiaceae Megachilidae->Malvaceae Megachilidae->Fabaceae Megachilidae->Alismataceae Megachilidae->Euphorbiaceae Megachilidae->Hydrophyllaceae Megachilidae->Verbenaceae Megachilidae->Rhamnaceae Megachilidae->Namaceae Cleomaceae Cleomaceae Megachilidae->Cleomaceae Lythraceae Lythraceae Megachilidae->Lythraceae Plantaginaceae Plantaginaceae Megachilidae->Plantaginaceae Vitaceae Vitaceae Megachilidae->Vitaceae Mordellidae Mordellidae Mordellidae->Asteraceae Mordellidae->Cactaceae Mordellidae->Malvaceae Mymaridae Mymaridae Mymaridae->Curculionidae Miridae Miridae Mymaridae->Miridae Nabidae Nabidae Nabidae->Fagaceae Nabidae->Poaceae Nabidae->Ulmaceae Nabidae->Pinaceae Ranunculaceae Ranunculaceae Nabidae->Ranunculaceae Noctuidae Noctuidae Noctuidae->Asteraceae Noctuidae->Malvaceae Noctuidae->Fagaceae Noctuidae->Poaceae Noctuidae->Cannabaceae Noctuidae->Salicaceae Noctuidae->Rhamnaceae Noctuidae->Ebenaceae Noctuidae->Vitaceae Notodontidae Notodontidae Notodontidae->Anacardiaceae Notodontidae->Fagaceae Notodontidae->Salicaceae Notodontidae->Sapindaceae Notodontidae->Ranunculaceae Juglandaceae Juglandaceae Notodontidae->Juglandaceae Nymphalidae Nymphalidae Nymphalidae->Asteraceae Nymphalidae->Malvaceae Nymphalidae->Solanaceae Nymphalidae->Poaceae Nymphalidae->Apocynaceae Nymphalidae->Euphorbiaceae Nymphalidae->Verbenaceae Nymphalidae->Ulmaceae Nymphalidae->Cannabaceae Nymphalidae->Salicaceae Nymphalidae->Sapindaceae Nymphalidae->Plantaginaceae Acanthaceae Acanthaceae Nymphalidae->Acanthaceae Arecaceae Arecaceae Nymphalidae->Arecaceae Passifloraceae Passifloraceae Nymphalidae->Passifloraceae Turneraceae Turneraceae Nymphalidae->Turneraceae Urticaceae Urticaceae Nymphalidae->Urticaceae Violaceae Violaceae Nymphalidae->Violaceae Oxycarenidae Oxycarenidae Oxycarenidae->Fabaceae Protolophidae Protolophidae Protolophidae->Asteraceae Protolophidae->Pinaceae Pseudococcidae Pseudococcidae Pseudococcidae->Asteraceae Psychodidae Psychodidae Gentianaceae Gentianaceae Psychodidae->Gentianaceae Pteromalidae Pteromalidae Agromyzidae Agromyzidae Pteromalidae->Agromyzidae Cecidomyiidae Cecidomyiidae Pteromalidae->Cecidomyiidae Pulicidae Pulicidae Pulicidae->Sciuridae Pulicidae->Didelphidae Reduviidae Reduviidae Reduviidae->Fagaceae Reduviidae->Ulmaceae Reduviidae->Cupressaceae Rhizophyllidaceae Rhizophyllidaceae Rhizophyllidaceae->Asteraceae Riodinidae Riodinidae Riodinidae->Asteraceae Riodinidae->Fabaceae Riodinidae->Cannabaceae Riodinidae->Myrtaceae Riodinidae->Ranunculaceae Nyctaginaceae Nyctaginaceae Riodinidae->Nyctaginaceae Saturniidae Saturniidae Saturniidae->Fagaceae Saturniidae->Fagaceae Platanaceae Platanaceae Saturniidae->Platanaceae Scarabaeidae Scarabaeidae Scarabaeidae->Cactaceae Sphingidae Sphingidae Sphingidae->Rubiaceae Tabanidae Tabanidae Tabanidae->Apiaceae Phyllanthaceae Phyllanthaceae Tabanidae->Phyllanthaceae Tenthredinidae Tenthredinidae Tenthredinidae->Fagaceae Tenuipalpidae Tenuipalpidae Tenuipalpidae->Passifloraceae Tephritidae Tephritidae Tephritidae->Sapotaceae Tephritidae->Tephritidae Schoepfiaceae Schoepfiaceae Tephritidae->Schoepfiaceae Thyrididae Thyrididae Thyrididae->Malvaceae Torymidae Torymidae Torymidae->Asteraceae Torymidae->Cecidomyiidae Trichogrammatidae Trichogrammatidae Trichogrammatidae->Pieridae Trichogrammatidae->Tortricidae Varroidae Varroidae Varroidae->Apidae

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

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
Year old girl NONE col Year old girl
Ft high tree NONE col Ft high tree
Abies fraseri HAS_ACCEPTED_NAME col Abies fraseri
Abies HAS_ACCEPTED_NAME col Abies
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 1261
col family 8
col genus 284
col kingdom 2
col order 1
col species 1243
col subfamily 1
col subgenus 10
col subspecies 45
col superfamily 1
col variety 17
discoverlife NA 2744
discoverlife species 95
gbif NA 1119
gbif family 8
gbif form 1
gbif genus 306
gbif kingdom 2
gbif order 1
gbif species 1331
gbif subspecies 67
gbif variety 28
itis NA 1461
itis family 8
itis genus 247
itis kingdom 2
itis order 2
itis phylum 1
itis species 1049
itis subfamily 1
itis subspecies 54
itis variety 15
mdd NA 2838
ncbi NA 1557
ncbi family 7
ncbi genus 277
ncbi kingdom 1
ncbi order 1
ncbi species 957
ncbi subfamily 1
ncbi subgenus 8
ncbi subspecies 37
ncbi varietas 2
pbdb NA 2671
pbdb family 8
pbdb genus 123
pbdb infraorder 1
pbdb kingdom 2
pbdb order 2
pbdb species 30
pbdb subfamily 1
pbdb suborder 2
pbdb unranked clade 2
tpt NA 2787
tpt genus 2
tpt species 49
wfo NA 2313
wfo family 6
wfo genus 107
wfo phylum 1
wfo species 399
wfo subspecies 9
wfo variety 13
worms NA 2484
worms family 7
worms genus 126
worms kingdom 2
worms order 1
worms species 212
worms suborder 1
worms subspecies 3
worms variety 2
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 1404
col HAS_ACCEPTED_NAME 1535
col SYNONYM_OF 478
discoverlife NONE 2975
discoverlife HAS_ACCEPTED_NAME 95
discoverlife SYNONYM_OF 13
discoverlife HOMONYM_OF 1
gbif NONE 1256
gbif HAS_ACCEPTED_NAME 1804
gbif SYNONYM_OF 628
itis NONE 1604
itis HAS_ACCEPTED_NAME 1341
itis SYNONYM_OF 156
mdd NONE 3056
mdd HAS_ACCEPTED_NAME 6
ncbi NONE 1718
ncbi SAME_AS 1287
ncbi SYNONYM_OF 81
ncbi COMMON_NAME_OF 7
pbdb NONE 2861
pbdb HAS_ACCEPTED_NAME 201
pbdb SYNONYM_OF 19
tpt NONE 3011
tpt HAS_ACCEPTED_NAME 62
tpt SYNONYM_OF 7
wfo NONE 2465
wfo HAS_ACCEPTED_NAME 494
wfo HAS_UNCHECKED_NAME 35
wfo SYNONYM_OF 191
worms NONE 2661
worms HAS_ACCEPTED_NAME 392
worms SYNONYM_OF 53
List of Available Name Alignment Reports
catalog name alignment results
col associated names alignments (first 500, full csv/tsv)
ncbi associated names alignments (first 500, full csv/tsv)
discoverlife associated names alignments (first 500, full csv/tsv)
gbif associated names alignments (first 500, full csv/tsv)
itis associated names alignments (first 500, full csv/tsv)
wfo associated names alignments (first 500, full csv/tsv)
mdd associated names alignments (first 500, full csv/tsv)
tpt associated names alignments (first 500, full csv/tsv)
pbdb associated names alignments (first 500, full csv/tsv)
worms associated names alignments (first 500, full csv/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
2024-11-18T07:24:07Z note target taxon name missing
2024-11-18T07:24:07Z note target taxon name missing
2024-11-18T07:24:07Z note target taxon name missing
2024-11-18T07:24:07Z note target taxon name missing

In addtion, 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 1093026
found unsupported interaction type with name: [larval food plant] 1

For addition information on review notes, please have a look at the first 500 Review Notes or the download full 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.

review 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.

Picture of a GloBI Index Badge

If you’d like to keep track of reviews or index status of the dataset under review, please visit [GloBI’s dataset index ^[At time of writing (2024-11-18) the version of the GloBI dataset index was available at https://globalbioticinteractions.org/datasets for badge examples.

Discussion

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-ness5 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.

Author contributions

Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes.

References

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