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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

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

2024-12-16

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/cas-ent, is 13.3MiB in size and contains 17,532 interaction with 5 unique types of associations (e.g., interactsWith) between 2,126 primary taxon (e.g., Callidium antennatum hesperum Casey, 1912) and 2,089 associated taxon (e.g., Pseudotsuga menziesii). 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:

CAS Entomology (ENT) - Version 6.308 http://ipt.calacademy.org:8080/archive.do?r=ent 2024-12-14T00:46:16.609Z 2bbe613531729edaa0f57e775e9e0acbaf853ff743bd26af09167ef80fdcd201 CAS Entomology Type (TYPE) - Version 1.267 http://ipt.calacademy.org:8080/archive.do?r=type 2024-12-14T00:46:16.609Z 2bbe613531729edaa0f57e775e9e0acbaf853ff743bd26af09167ef80fdcd201

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/cas-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. 13.3MiB) under review 
elton pull globalbioticinteractions/cas-ent

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/cas-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/cas-ent, is 13.3MiB in size and contains 17,532 interaction with 5 unique types of associations (e.g., interactsWith) between 2,126 primary taxon (e.g., Callidium antennatum hesperum Casey, 1912) and 2,089 associated taxon (e.g., Pseudotsuga menziesii).

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
Lepthyphantes Menge, 1866 interactsWith walls of Bear Gulch Cave urn:catalog:CAS:ENT:9068645
Physocyclus globosus (Taczanowski, 1874) adjacentTo cave wall in web urn:catalog:CAS:ENT:9069617
Strophiona laeta (LeConte, 1857) adjacentTo Quercus dumosa urn:catalog:CAS:ENT:8383067
Strophiona laeta (LeConte, 1857) adjacentTo Quercus dumosa urn:catalog:CAS:ENT:8383083
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 10964
adjacentTo 6226
hasHost 354
killedBy 3
eats 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Callidium antennatum hesperum Casey, 1912 493
Euaresta aequalis 332
Anthaxia Eschscholtz, 1829 298
Neoclytus conjunctus (LeConte, 1857) 268
Omus californicus ssp. californicus 230
Phymatodes nitidus LeConte, 1874 204
Campiglossa genalis 183
Acmaeodera holsteni White, 1939 180
Phymatodes Mulsant, 1839 176
Anthaxia pseudotsugae Chamberlin 130
Copidosoma 125
Xylotrechus nauticus (Mannerheim, 1843) 122
Tephritis californica Doane, 1899 119
Trupanea californica 118
Chimoptesis chrysopyla Powell, 1964 108
Neoclytus balteatus LeConte, 1873 107
Phymatodes decussatus ssp. decussatus 104
Euarestoides acutangulus (Thomson, 1869) 104
Anastrangalia laetifica (LeConte, 1859) 103
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Pseudotsuga menziesii 954
Eucalyptus 368
Xanthium canadense 329
Adenostoma fasciculatum 307
Nothofagus 307
Pinus ponderosa 270
Sequoia sempervirens 260
Chrysothamnus sp. 260
Ceanothus 220
Quercus kelloggii 196
juniper 194
snow at night 186
Baccharis pilularis 185
Quercus 183
Casaurina 174
Quercus dumosa 170
Artemisia tridentata 162
Quercus agrifolia 159
Pinus sabiniana 150
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Euaresta aequalis interactsWith Xanthium canadense 326
Callidium antennatum hesperum Casey, 1912 interactsWith Pseudotsuga menziesii 260
Acmaeodera holsteni White, 1939 adjacentTo Adenostoma fasciculatum 142
Omus californicus ssp. californicus interactsWith O. sequoiarum laevis 121
Neoclytus conjunctus (LeConte, 1857) adjacentTo madrone 120
Phymatodes Mulsant, 1839 interactsWith Pseudotsuga menziesii 113
Tephritis californica Doane, 1899 interactsWith Baccharis pilularis 105
Anthaxia pseudotsugae Chamberlin interactsWith Pseudotsuga menziesii 102
Callidium antennatum hesperum Casey, 1912 interactsWith Pinus monophylla 100
Trupanea californica interactsWith Gnaphalium chilense 99
Anthaxia retifer LeConte, 1860 adjacentTo Notholithocarpus densiflorum 93
Andricus bakkeri adjacentTo Quercus dumosa 86
Holopleura marginata LeConte, 1873 interactsWith Pseudotsuga menziesii 80
Phymatodes maculicollis LeConte, 1878 adjacentTo Pseudotsuga menziesii 79
Campiglossa genalis interactsWith Senecio jacobaea 77
Nebria turmaduodecima Kavanaugh, 1981 adjacentTo snow at night 75
Aciurina maculata interactsWith Chrysothamnus sp. 73
Neoclytus balteatus LeConte, 1873 interactsWith Ceanothus thyrsiflorus 70
Nebria spatulata ssp. sierrae adjacentTo snow at night 69

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
interactions Acrididae Acrididae Myrtaceae Myrtaceae Acrididae->Myrtaceae Acropsopilionidae Acropsopilionidae Araucariaceae Araucariaceae Acropsopilionidae->Araucariaceae Aleyrodidae Aleyrodidae Fagaceae Fagaceae Aleyrodidae->Fagaceae Aphididae Aphididae Aphididae->Fagaceae Amaryllidaceae Amaryllidaceae Aphididae->Amaryllidaceae Apiaceae Apiaceae Aphididae->Apiaceae Asteraceae Asteraceae Aphididae->Asteraceae Betulaceae Betulaceae Aphididae->Betulaceae Fabaceae Fabaceae Aphididae->Fabaceae Poaceae Poaceae Aphididae->Poaceae Rosaceae Rosaceae Aphididae->Rosaceae Sapindaceae Sapindaceae Aphididae->Sapindaceae Apidae Apidae Apidae->Apiaceae Apidae->Apiaceae Apidae->Asteraceae Apidae->Asteraceae Apidae->Fabaceae Apidae->Rosaceae Onagraceae Onagraceae Apidae->Onagraceae Apidae->Onagraceae Polygonaceae Polygonaceae Apidae->Polygonaceae Apidae->Polygonaceae Apocynaceae Apocynaceae Apidae->Apocynaceae Boraginaceae Boraginaceae Apidae->Boraginaceae Convolvulaceae Convolvulaceae Apidae->Convolvulaceae Ericaceae Ericaceae Apidae->Ericaceae Rhamnaceae Rhamnaceae Apidae->Rhamnaceae Ascidae Ascidae Muridae Muridae Ascidae->Muridae Asilidae Asilidae Asilidae->Rosaceae Asilidae->Onagraceae Asilidae->Polygonaceae Asparagaceae Asparagaceae Asilidae->Asparagaceae Grossulariaceae Grossulariaceae Asilidae->Grossulariaceae Plantaginaceae Plantaginaceae Asilidae->Plantaginaceae Verbenaceae Verbenaceae Asilidae->Verbenaceae Bombyliidae Bombyliidae Bombyliidae->Fagaceae Bombyliidae->Asteraceae Buprestidae Buprestidae Buprestidae->Fagaceae Buprestidae->Asteraceae Buprestidae->Asteraceae Buprestidae->Rosaceae Buprestidae->Polygonaceae Buprestidae->Rhamnaceae Buprestidae->Rhamnaceae Ephedraceae Ephedraceae Buprestidae->Ephedraceae Buprestidae->Ephedraceae Malvaceae Malvaceae Buprestidae->Malvaceae Buprestidae->Malvaceae Namaceae Namaceae Buprestidae->Namaceae Pinaceae Pinaceae Buprestidae->Pinaceae Campodeidae Campodeidae Campodeidae->Fagaceae Campodeidae->Rhamnaceae Cupressaceae Cupressaceae Campodeidae->Cupressaceae Cerambycidae Cerambycidae Cerambycidae->Pinaceae Cerococcidae Cerococcidae Cerococcidae->Fagaceae Chrysididae Chrysididae Chrysididae->Polygonaceae Chrysididae->Polygonaceae Chrysididae->Rhamnaceae Chrysididae->Pinaceae Chrysididae->Pinaceae Chrysididae->Cupressaceae Brassicaceae Brassicaceae Chrysididae->Brassicaceae Chrysopidae Chrysopidae Chrysopidae->Fabaceae Coccidae Coccidae Coccidae->Asteraceae Coccidae->Poaceae Coccidae->Rosaceae Coccidae->Pinaceae Amaranthaceae Amaranthaceae Coccidae->Amaranthaceae Celastraceae Celastraceae Coccidae->Celastraceae Moraceae Moraceae Coccidae->Moraceae Coenagrionidae Coenagrionidae Coenagrionidae->Polygonaceae Crabronidae Crabronidae Crabronidae->Fagaceae Crabronidae->Asteraceae Crabronidae->Asteraceae Crabronidae->Rosaceae Culicidae Culicidae Culicidae->Myrtaceae Culicidae->Fagaceae Culicidae->Asteraceae Culicidae->Betulaceae Culicidae->Boraginaceae Culicidae->Malvaceae Culicidae->Pinaceae Culicidae->Cupressaceae Culicidae->Culicidae Cephalotaxaceae Cephalotaxaceae Culicidae->Cephalotaxaceae Gentianaceae Gentianaceae Culicidae->Gentianaceae Pandanaceae Pandanaceae Culicidae->Pandanaceae Salicaceae Salicaceae Culicidae->Salicaceae Cynipidae Cynipidae Cynipidae->Fagaceae Dactylopiidae Dactylopiidae Cactaceae Cactaceae Dactylopiidae->Cactaceae Diaspididae Diaspididae Diaspididae->Fagaceae Diaspididae->Poaceae Diaspididae->Rosaceae Diaspididae->Sapindaceae Diaspididae->Ericaceae Diaspididae->Rhamnaceae Diaspididae->Pinaceae Diaspididae->Cupressaceae Diaspididae->Salicaceae Araliaceae Araliaceae Diaspididae->Araliaceae Diaspididae->Araliaceae Lauraceae Lauraceae Diaspididae->Lauraceae Arecaceae Arecaceae Diaspididae->Arecaceae Cycadaceae Cycadaceae Diaspididae->Cycadaceae Juglandaceae Juglandaceae Diaspididae->Juglandaceae Orchidaceae Orchidaceae Diaspididae->Orchidaceae Pittosporaceae Pittosporaceae Diaspididae->Pittosporaceae Tamaricaceae Tamaricaceae Diaspididae->Tamaricaceae Taxaceae Taxaceae Diaspididae->Taxaceae Theaceae Theaceae Diaspididae->Theaceae Vitaceae Vitaceae Diaspididae->Vitaceae Encyrtidae Encyrtidae Encyrtidae->Myrtaceae Encyrtidae->Fagaceae Encyrtidae->Fagaceae Encyrtidae->Aphididae Encyrtidae->Apiaceae Encyrtidae->Asteraceae Encyrtidae->Asteraceae Encyrtidae->Fabaceae Encyrtidae->Rosaceae Encyrtidae->Rhamnaceae Encyrtidae->Pinaceae Encyrtidae->Pinaceae Encyrtidae->Coccidae Encyrtidae->Coccidae Encyrtidae->Salicaceae Encyrtidae->Lauraceae Encyrtidae->Lauraceae Pseudococcidae Pseudococcidae Encyrtidae->Pseudococcidae Chamaemyiidae Chamaemyiidae Encyrtidae->Chamaemyiidae Coreidae Coreidae Encyrtidae->Coreidae Eriococcidae Eriococcidae Encyrtidae->Eriococcidae Noctuidae Noctuidae Encyrtidae->Noctuidae Notodontidae Notodontidae Encyrtidae->Notodontidae Pseudococcidae->Fagaceae Pseudococcidae->Rosaceae Pseudococcidae->Cupressaceae Hypericaceae Hypericaceae Pseudococcidae->Hypericaceae Phrymaceae Phrymaceae Pseudococcidae->Phrymaceae Eriococcidae->Fagaceae Eriococcidae->Rosaceae Ulmaceae Ulmaceae Eriococcidae->Ulmaceae Eurytomidae Eurytomidae Anacardiaceae Anacardiaceae Eurytomidae->Anacardiaceae Fulgoridae Fulgoridae Fulgoridae->Cactaceae Fulgoridae->Anacardiaceae Hemerobiidae Hemerobiidae Hemerobiidae->Pinaceae Hippoboscidae Hippoboscidae Malaconotidae Malaconotidae Hippoboscidae->Malaconotidae Histiostomatidae Histiostomatidae Carabidae Carabidae Histiostomatidae->Carabidae Ichneumonidae Ichneumonidae Ichneumonidae->Fagaceae Inocelliidae Inocelliidae Inocelliidae->Fagaceae Inocelliidae->Pinaceae Ixodidae Ixodidae Canidae Canidae Ixodidae->Canidae Kermesidae Kermesidae Kermesidae->Fagaceae Lecanodiaspididae Lecanodiaspididae Lecanodiaspididae->Rosaceae Lecanodiaspididae->Anacardiaceae Margarodidae Margarodidae Platanaceae Platanaceae Margarodidae->Platanaceae Mydidae Mydidae Mydidae->Polygonaceae Mydidae->Boraginaceae Mydidae->Rhamnaceae Myrmeleontidae Myrmeleontidae Myrmeleontidae->Pinaceae Cricetidae Cricetidae Myrmeleontidae->Cricetidae Mythicomyiidae Mythicomyiidae Mythicomyiidae->Asteraceae Mythicomyiidae->Asteraceae Mythicomyiidae->Salicaceae Oonopidae Oonopidae Combretaceae Combretaceae Oonopidae->Combretaceae Philopteridae Philopteridae Laridae Laridae Philopteridae->Laridae Megapodiidae Megapodiidae Philopteridae->Megapodiidae Sturnidae Sturnidae Philopteridae->Sturnidae Tinamidae Tinamidae Philopteridae->Tinamidae Pompilidae Pompilidae Pompilidae->Anacardiaceae Pulicidae Pulicidae Pulicidae->Canidae Suidae Suidae Pulicidae->Suidae Raphidiidae Raphidiidae Raphidiidae->Fagaceae Raphidiidae->Fagaceae Raphidiidae->Asteraceae Raphidiidae->Asteraceae Raphidiidae->Betulaceae Raphidiidae->Rosaceae Raphidiidae->Polygonaceae Raphidiidae->Ericaceae Raphidiidae->Rhamnaceae Raphidiidae->Namaceae Raphidiidae->Pinaceae Raphidiidae->Pinaceae Simuliidae Simuliidae Simuliidae->Salicaceae Tephritidae Tephritidae Tephritidae->Myrtaceae Tephritidae->Fagaceae Tephritidae->Apiaceae Tephritidae->Asteraceae Tephritidae->Poaceae Tephritidae->Rosaceae Tephritidae->Polygonaceae Tephritidae->Apocynaceae Tephritidae->Grossulariaceae Tephritidae->Malvaceae Tephritidae->Pinaceae Tephritidae->Brassicaceae Tephritidae->Amaranthaceae Tephritidae->Salicaceae Tephritidae->Juglandaceae Tephritidae->Pittosporaceae Aizoaceae Aizoaceae Tephritidae->Aizoaceae Eremiaphilidae Eremiaphilidae Tephritidae->Eremiaphilidae Parkinsoniidae Parkinsoniidae Tephritidae->Parkinsoniidae Rubiaceae Rubiaceae Tephritidae->Rubiaceae Timematidae Timematidae Timematidae->Fagaceae Timematidae->Rosaceae Timematidae->Rhamnaceae Torymidae Torymidae Torymidae->Anacardiaceae Triaenonychidae Triaenonychidae Podocarpaceae Podocarpaceae Triaenonychidae->Podocarpaceae

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
Angelica SYNONYM_OF col Bunaea
Angelica HAS_ACCEPTED_NAME col Angelica
Slopes NONE col Slopes
January NONE col January
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 1302
col class 4
col family 99
col genus 462
col infraspecific name 2
col kingdom 1
col order 12
col parvorder 1
col phylum 1
col section 1
col species 1855
col subfamily 2
col subgenus 20
col subspecies 55
col tribe 2
col variety 21
discoverlife NA 3703
discoverlife species 99
gbif NA 1179
gbif class 4
gbif family 105
gbif genus 494
gbif kingdom 1
gbif order 12
gbif phylum 1
gbif species 1946
gbif subspecies 70
gbif variety 25
itis NA 1679
itis class 4
itis family 103
itis genus 394
itis kingdom 1
itis order 15
itis phylum 1
itis species 1536
itis subclass 1
itis subfamily 2
itis subgenus 1
itis suborder 1
itis subspecies 43
itis tribe 1
itis variety 21
mdd NA 3801
ncbi NA 2192
ncbi clade 2
ncbi class 4
ncbi family 101
ncbi genus 436
ncbi order 15
ncbi phylum 1
ncbi species 1025
ncbi subclass 1
ncbi subfamily 4
ncbi subgenus 11
ncbi suborder 1
ncbi subspecies 14
ncbi tribe 1
ncbi varietas 6
pbdb NA 3354
pbdb class 6
pbdb family 87
pbdb genus 220
pbdb infraorder 1
pbdb kingdom 1
pbdb order 15
pbdb phylum 1
pbdb species 111
pbdb subclass 1
pbdb subfamily 2
pbdb superfamily 1
pbdb tribe 3
pbdb unranked clade 3
tpt NA 3639
tpt family 2
tpt genus 23
tpt species 137
wfo NA 3149
wfo family 7
wfo genus 215
wfo phylum 1
wfo species 414
wfo subspecies 13
wfo variety 14
worms NA 3302
worms class 3
worms family 57
worms genus 194
worms kingdom 1
worms order 14
worms species 222
worms subclass 2
worms suborder 1
worms subspecies 2
worms variety 7
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 SYNONYM_OF 770
col HAS_ACCEPTED_NAME 2492
col NONE 1568
discoverlife NONE 4211
discoverlife HAS_ACCEPTED_NAME 99
discoverlife SYNONYM_OF 8
discoverlife HOMONYM_OF 1
gbif HAS_ACCEPTED_NAME 2797
gbif SYNONYM_OF 1231
gbif NONE 1442
itis HAS_ACCEPTED_NAME 2136
itis NONE 1956
itis SYNONYM_OF 257
mdd NONE 4285
mdd HAS_ACCEPTED_NAME 18
ncbi SAME_AS 1697
ncbi NONE 2495
ncbi SYNONYM_OF 142
ncbi COMMON_NAME_OF 11
pbdb NONE 3741
pbdb HAS_ACCEPTED_NAME 545
pbdb SYNONYM_OF 38
tpt NONE 4137
tpt HAS_ACCEPTED_NAME 164
tpt SYNONYM_OF 53
wfo HAS_ACCEPTED_NAME 666
wfo NONE 3464
wfo HAS_UNCHECKED_NAME 79
wfo SYNONYM_OF 250
worms HAS_ACCEPTED_NAME 577
worms NONE 3694
worms SYNONYM_OF 97
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
2024-12-16T01:32:18Z summary https://github.com/globalbioticinteractions/cas-ent/archive/47d385b73a63aa379cd5e6d3615005ba78b0ffc1.zip
2024-12-16T01:32:18Z summary 17548 interaction(s)
2024-12-16T01:32:18Z summary 0 note(s)
2024-12-16T01:32:18Z summary 4 info(s)

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

: Most frequently occurring review notes, if any.

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 (2024-12-16) 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.