A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/byu-byuc

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/byu-byuc/issues

2024-07-22

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/byu-byuc, is 18.0MiB in size and contains 37,906 interaction with 7 unique types of associations (e.g., hasHost) between 1,424 primary taxon (e.g., Aetheca wagneri) and 2,371 associated taxon (e.g., Peromyscus maniculatus). 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:

Brigham Young University Arthropod Museum https://github.com/globalbioticinteractions/byu-byuc/archive/4a609ac6a9a03425e2720b6cdebca6438488f029.zip 2024-07-19T22:50:06.143Z f8cf85ca8364ed1e59ec637a717733643ce827bec64958f2c487251ab7f1d966

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/byu-byuc 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 0.13.4
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. 18.0MiB) under review 
elton pull globalbioticinteractions/byu-byuc

# generate review notes
elton review globalbioticinteractions/byu-byuc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/byu-byuc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/byu-byuc\
 | 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/byu-byuc, is 18.0MiB in size and contains 37,906 interaction with 7 unique types of associations (e.g., hasHost) between 1,424 primary taxon (e.g., Aetheca wagneri) and 2,371 associated taxon (e.g., Peromyscus maniculatus).

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
Axinopalpus biplagiatus hasHost Ex nest of Neotoma https://scan-bugs.org:443/portal/collections/individual/index.php?occid=14982529
Axinopalpus biplagiatus hasHost Ex nest of Neotoma https://scan-bugs.org:443/portal/collections/individual/index.php?occid=14982531
Axinopalpus biplagiatus hasHost Ex nest of Neotoma https://scan-bugs.org:443/portal/collections/individual/index.php?occid=14982534
Amara farcta interactsWith Salsola pestifer https://scan-bugs.org:443/portal/collections/individual/index.php?occid=14983553
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
hasHost 24965
interactsWith 12649
adjacentTo 251
hostOf 36
hasParasite 9
eats 1
visits 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Aetheca wagneri 4727
Meringis parkeri 2951
Thrassis bacchi 1364
Spilopsyllus inaequalis 1010
Orchopeas sexdentatus 933
Hoplopsyllus anomalus 911
Monopsyllus wagneri wagneri 851
Eumolpianus eumolpi 840
Thrassis pandorae 730
Opisodasys keeni 641
Atyphloceras multidentatus multidentatus 636
Oropsylla idahoensis 632
Foxella ignota 629
Hoplopleura hesperomydis 604
Thrassis aridis 586
Thrassis francisi 468
Atyphloceras multidentatus 453
Oropsylla montanus 443
Anomiopsyllus amphibolus 429
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Peromyscus maniculatus 7445
Dipodomys ordii 2147
Ammospermophilus leucurus 1255
Microtus 1172
Neotoma lepida 1019
Spermophilus armatus 865
Eutamias minimus 644
Spermophilus townsendii 620
Lepus californicus 560
Onychomys leucogaster 532
Citellus leucurus 479
Peromyscus Maniculatus 430
Neotoma cinerea 427
Citellus variegatus 374
Lepus Californicus 333
Citellus armatus 320
Dipodomys microps 309
Sylvilagus 301
Abrothrix longipilis 270
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Aetheca wagneri hasHost Peromyscus maniculatus 3455
Meringis parkeri hasHost Dipodomys ordii 1745
Monopsyllus wagneri wagneri interactsWith Peromyscus maniculatus 742
Atyphloceras multidentatus multidentatus hasHost Microtus 636
Hoplopleura hesperomydis hasHost Peromyscus maniculatus 570
Thrassis bacchi interactsWith Ammospermophilus leucurus 536
Aetheca wagneri interactsWith Peromyscus maniculatus 455
Thrassis pandorae hasHost Spermophilus armatus 410
Thrassis bacchi hasHost Ammospermophilus leucurus 382
Opisodasys keeni interactsWith Peromyscus maniculatus 329
Atyphloceras multidentatus hasHost Microtus 325
Aetheca wagneri hasHost Peromyscus Maniculatus 318
Anomiopsyllus amphibolus interactsWith Neotoma lepida 292
Thrassis francisi interactsWith Spermophilus townsendii 282
Meringis parkeri interactsWith Dipodomys ordii 266
Oropsylla montanus hasHost Citellus variegatus 262
Oropsylla idahoensis hasHost Spermophilus armatus 235
Hoplopsyllus anomalus hasHost Ammospermophilus leucurus 235
Opisocrostis t. tuberculatus hasHost Spermophilus townsendii 219

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 Animalia->Animalia Animalia->Animalia Plantae Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Plantae->Animalia
interactions Acrididae Acrididae Zygophyllaceae Zygophyllaceae Acrididae->Zygophyllaceae Acrididae->Zygophyllaceae Amaranthaceae Amaranthaceae Acrididae->Amaranthaceae Ancistronidae Ancistronidae Scolopacidae Scolopacidae Ancistronidae->Scolopacidae Andrenidae Andrenidae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Apidae Apidae Apocynaceae Apocynaceae Apidae->Apocynaceae Asteraceae Asteraceae Apidae->Asteraceae Argasidae Argasidae Alaudidae Alaudidae Argasidae->Alaudidae Bovidae Bovidae Argasidae->Bovidae Canidae Canidae Argasidae->Canidae Cervidae Cervidae Argasidae->Cervidae Cricetidae Cricetidae Argasidae->Cricetidae Diomedeidae Diomedeidae Argasidae->Diomedeidae Fringillidae Fringillidae Argasidae->Fringillidae Heteromyidae Heteromyidae Argasidae->Heteromyidae Laridae Laridae Argasidae->Laridae Leporidae Leporidae Argasidae->Leporidae Passerellidae Passerellidae Argasidae->Passerellidae Sciuridae Sciuridae Argasidae->Sciuridae Sulidae Sulidae Argasidae->Sulidae Tayassuidae Tayassuidae Argasidae->Tayassuidae Vespertilionidae Vespertilionidae Argasidae->Vespertilionidae Cricetidae->Cricetidae Cricetidae->Cricetidae Sciuridae->Sciuridae Vespertilionidae->Vespertilionidae Asilidae Asilidae Asilidae->Asteraceae Buprestidae Buprestidae Buprestidae->Amaranthaceae Carabidae Carabidae Carabidae->Amaranthaceae Ceratophyllidae Ceratophyllidae Ceratophyllidae->Canidae Ceratophyllidae->Canidae Ceratophyllidae->Cricetidae Ceratophyllidae->Cricetidae Ceratophyllidae->Heteromyidae Ceratophyllidae->Heteromyidae Ceratophyllidae->Leporidae Ceratophyllidae->Leporidae Ceratophyllidae->Sciuridae Ceratophyllidae->Sciuridae Ceratophyllidae->Sciuridae Ceratophyllidae->Ceratophyllidae Didelphidae Didelphidae Ceratophyllidae->Didelphidae Dipodidae Dipodidae Ceratophyllidae->Dipodidae Felidae Felidae Ceratophyllidae->Felidae Geomyidae Geomyidae Ceratophyllidae->Geomyidae Ceratophyllidae->Geomyidae Hirundinidae Hirundinidae Ceratophyllidae->Hirundinidae Ceratophyllidae->Hirundinidae Mephitidae Mephitidae Ceratophyllidae->Mephitidae Ceratophyllidae->Mephitidae Muridae Muridae Ceratophyllidae->Muridae Ceratophyllidae->Muridae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Ceratophyllidae->Mustelidae Ochotonidae Ochotonidae Ceratophyllidae->Ochotonidae Ceratophyllidae->Ochotonidae Procyonidae Procyonidae Ceratophyllidae->Procyonidae Soricidae Soricidae Ceratophyllidae->Soricidae Ceratophyllidae->Soricidae Tupaiidae Tupaiidae Ceratophyllidae->Tupaiidae Ceratophyllidae->Tupaiidae Gliridae Gliridae Ceratophyllidae->Gliridae Mimidae Mimidae Ceratophyllidae->Mimidae Psychodidae Psychodidae Ceratophyllidae->Psychodidae Sittidae Sittidae Ceratophyllidae->Sittidae Spalacidae Spalacidae Ceratophyllidae->Spalacidae Turdidae Turdidae Ceratophyllidae->Turdidae Muridae->Muridae Chimaeropsyllidae Chimaeropsyllidae Chimaeropsyllidae->Muridae Chimaeropsyllidae->Muridae Chimaeropsyllidae->Soricidae Chimaeropsyllidae->Soricidae Macroscelididae Macroscelididae Chimaeropsyllidae->Macroscelididae Chimaeropsyllidae->Macroscelididae Cisticolidae Cisticolidae Chimaeropsyllidae->Cisticolidae Nesomyidae Nesomyidae Chimaeropsyllidae->Nesomyidae Cicadidae Cicadidae Cicadidae->Asteraceae Coccinellidae Coccinellidae Anacardiaceae Anacardiaceae Coccinellidae->Anacardiaceae Colletidae Colletidae Colletidae->Brassicaceae Fabaceae Fabaceae Colletidae->Fabaceae Tamaricaceae Tamaricaceae Colletidae->Tamaricaceae Malvaceae Malvaceae Colletidae->Malvaceae Colpocephalidae Colpocephalidae Falconidae Falconidae Colpocephalidae->Falconidae Coptopsyllidae Coptopsyllidae Coptopsyllidae->Muridae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Heteromyidae Ctenophthalmidae->Heteromyidae Ctenophthalmidae->Heteromyidae Ctenophthalmidae->Leporidae Ctenophthalmidae->Leporidae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Didelphidae Ctenophthalmidae->Didelphidae Ctenophthalmidae->Dipodidae Ctenophthalmidae->Geomyidae Ctenophthalmidae->Geomyidae Ctenophthalmidae->Muridae Ctenophthalmidae->Muridae Ctenophthalmidae->Mustelidae Ctenophthalmidae->Mustelidae Ctenophthalmidae->Ochotonidae Ctenophthalmidae->Soricidae Ctenophthalmidae->Soricidae Abrocomidae Abrocomidae Ctenophthalmidae->Abrocomidae Aplodontiidae Aplodontiidae Ctenophthalmidae->Aplodontiidae Ctenophthalmidae->Aplodontiidae Octodontidae Octodontidae Ctenophthalmidae->Octodontidae Talpidae Talpidae Ctenophthalmidae->Talpidae Ctenophthalmidae->Talpidae Mysidae Mysidae Ctenophthalmidae->Mysidae Spirostreptidae Spirostreptidae Ctenophthalmidae->Spirostreptidae Strigidae Strigidae Ctenophthalmidae->Strigidae Octodontidae->Octodontidae Enderleinellidae Enderleinellidae Enderleinellidae->Cricetidae Enderleinellidae->Sciuridae Erebidae Erebidae Melanthiaceae Melanthiaceae Erebidae->Melanthiaceae Eumastacidae Eumastacidae Boraginaceae Boraginaceae Eumastacidae->Boraginaceae Formicidae Formicidae Formicidae->Amaranthaceae Gliricolidae Gliricolidae Echimyidae Echimyidae Gliricolidae->Echimyidae Gyropidae Gyropidae Gyropidae->Echimyidae Halictidae Halictidae Halictidae->Amaranthaceae Halictidae->Asteraceae Halictidae->Anacardiaceae Halictidae->Malvaceae Berberidaceae Berberidaceae Halictidae->Berberidaceae Cactaceae Cactaceae Halictidae->Cactaceae Poaceae Poaceae Halictidae->Poaceae Scrophulariaceae Scrophulariaceae Halictidae->Scrophulariaceae Hesperiidae Hesperiidae Hesperiidae->Muridae Hoplopleuridae Hoplopleuridae Hoplopleuridae->Cricetidae Hoplopleuridae->Cricetidae Hoplopleuridae->Fringillidae Hoplopleuridae->Heteromyidae Hoplopleuridae->Leporidae Hoplopleuridae->Sciuridae Hoplopleuridae->Sciuridae Hoplopleuridae->Muridae Juncaceae Juncaceae Hoplopleuridae->Juncaceae Phrynosomatidae Phrynosomatidae Hoplopleuridae->Phrynosomatidae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Heteromyidae Hystrichopsyllidae->Sciuridae Hystrichopsyllidae->Didelphidae Hystrichopsyllidae->Muridae Hystrichopsyllidae->Muridae Hystrichopsyllidae->Soricidae Hystrichopsyllidae->Aplodontiidae Hystrichopsyllidae->Talpidae Ischnopsyllidae Ischnopsyllidae Ischnopsyllidae->Cricetidae Ischnopsyllidae->Vespertilionidae Ischnopsyllidae->Vespertilionidae Ischnopsyllidae->Muridae Arixeniidae Arixeniidae Ischnopsyllidae->Arixeniidae Hipposideridae Hipposideridae Ischnopsyllidae->Hipposideridae Miniopteridae Miniopteridae Ischnopsyllidae->Miniopteridae Molossidae Molossidae Ischnopsyllidae->Molossidae Phyllostomidae Phyllostomidae Ischnopsyllidae->Phyllostomidae Pteropodidae Pteropodidae Ischnopsyllidae->Pteropodidae Ischnopsyllidae->Pteropodidae Rhinolophidae Rhinolophidae Ischnopsyllidae->Rhinolophidae Ixodidae Ixodidae Ixodidae->Bovidae Ixodidae->Canidae Ixodidae->Cervidae Equidae Equidae Ixodidae->Equidae Hominidae Hominidae Ixodidae->Hominidae Laemobothriidae Laemobothriidae Accipitridae Accipitridae Laemobothriidae->Accipitridae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Canidae Leptopsyllidae->Cricetidae Leptopsyllidae->Cricetidae Leptopsyllidae->Leporidae Leptopsyllidae->Leporidae Leptopsyllidae->Sciuridae Leptopsyllidae->Dipodidae Leptopsyllidae->Dipodidae Leptopsyllidae->Felidae Leptopsyllidae->Muridae Leptopsyllidae->Muridae Leptopsyllidae->Mustelidae Leptopsyllidae->Ochotonidae Leptopsyllidae->Ochotonidae Leptopsyllidae->Soricidae Leptopsyllidae->Soricidae Leptopsyllidae->Macroscelididae Leptopsyllidae->Nesomyidae Leptopsyllidae->Aplodontiidae Ctenodactylidae Ctenodactylidae Leptopsyllidae->Ctenodactylidae Erinaceidae Erinaceidae Leptopsyllidae->Erinaceidae Picidae Picidae Leptopsyllidae->Picidae Calomyscidae Calomyscidae Leptopsyllidae->Calomyscidae Tettigoniidae Tettigoniidae Leptopsyllidae->Tettigoniidae Rosaceae Rosaceae Tettigoniidae->Rosaceae Linognathidae Linognathidae Linognathidae->Canidae Malacopsyllidae Malacopsyllidae Dasypodidae Dasypodidae Malacopsyllidae->Dasypodidae Malacopsyllidae->Dasypodidae Megachilidae Megachilidae Megachilidae->Fabaceae Megachilidae->Boraginaceae Megachilidae->Cactaceae Megachilidae->Scrophulariaceae Lamiaceae Lamiaceae Megachilidae->Lamiaceae Melittidae Melittidae Melittidae->Asteraceae Menoponidae Menoponidae Menoponidae->Alaudidae Menoponidae->Fringillidae Icteridae Icteridae Menoponidae->Icteridae Mycetophilidae Mycetophilidae Mycetophilidae->Sciuridae Nitidulidae Nitidulidae Nitidulidae->Anacardiaceae Pediculidae Pediculidae Pediculidae->Hominidae Philopteridae Philopteridae Philopteridae->Scolopacidae Philopteridae->Alaudidae Philopteridae->Fringillidae Philopteridae->Passerellidae Philopteridae->Mimidae Philopteridae->Falconidae Philopteridae->Accipitridae Columbidae Columbidae Philopteridae->Columbidae Phasianidae Phasianidae Philopteridae->Phasianidae Recurvirostridae Recurvirostridae Philopteridae->Recurvirostridae Troglodytidae Troglodytidae Philopteridae->Troglodytidae Phlaeothripidae Phlaeothripidae Phlaeothripidae->Poaceae Polyplacidae Polyplacidae Polyplacidae->Alaudidae Polyplacidae->Cricetidae Polyplacidae->Heteromyidae Polyplacidae->Leporidae Polyplacidae->Muridae Polyplacidae->Muridae Polyplacidae->Icteridae Polyplacidae->Phasianidae Polyplacidae->Troglodytidae Pseudomenoponidae Pseudomenoponidae Rallidae Rallidae Pseudomenoponidae->Rallidae Pulicidae Pulicidae Pulicidae->Canidae Pulicidae->Canidae Pulicidae->Cervidae Pulicidae->Cricetidae Pulicidae->Cricetidae Pulicidae->Heteromyidae Pulicidae->Leporidae Pulicidae->Leporidae Pulicidae->Sciuridae Pulicidae->Sciuridae Pulicidae->Vespertilionidae Pulicidae->Vespertilionidae Pulicidae->Didelphidae Pulicidae->Didelphidae Pulicidae->Dipodidae Pulicidae->Dipodidae Pulicidae->Felidae Pulicidae->Felidae Pulicidae->Geomyidae Pulicidae->Mephitidae Pulicidae->Mephitidae Pulicidae->Muridae Pulicidae->Muridae Pulicidae->Mustelidae Pulicidae->Mustelidae Pulicidae->Procyonidae Pulicidae->Macroscelididae Pulicidae->Macroscelididae Pulicidae->Nesomyidae Pulicidae->Nesomyidae Pulicidae->Strigidae Pulicidae->Echimyidae Pulicidae->Hominidae Pulicidae->Erinaceidae Pulicidae->Dasypodidae Eupleridae Eupleridae Pulicidae->Eupleridae Herpestidae Herpestidae Pulicidae->Herpestidae Pulicidae->Herpestidae Hyaenidae Hyaenidae Pulicidae->Hyaenidae Pulicidae->Hyaenidae Megadermatidae Megadermatidae Pulicidae->Megadermatidae Tenrecidae Tenrecidae Pulicidae->Tenrecidae Hystricidae Hystricidae Pulicidae->Hystricidae Malaconotidae Malaconotidae Pulicidae->Malaconotidae Procaviidae Procaviidae Pulicidae->Procaviidae Procellariidae Procellariidae Pulicidae->Procellariidae Viverridae Viverridae Pulicidae->Viverridae Pygiopsyllidae Pygiopsyllidae Peramelidae Peramelidae Pygiopsyllidae->Peramelidae Rhopalopsyllidae Rhopalopsyllidae Rhopalopsyllidae->Canidae Rhopalopsyllidae->Cervidae Rhopalopsyllidae->Cricetidae Rhopalopsyllidae->Cricetidae Rhopalopsyllidae->Diomedeidae Rhopalopsyllidae->Didelphidae Rhopalopsyllidae->Didelphidae Rhopalopsyllidae->Muridae Rhopalopsyllidae->Mustelidae Rhopalopsyllidae->Abrocomidae Rhopalopsyllidae->Octodontidae Rhopalopsyllidae->Phyllostomidae Rhopalopsyllidae->Dasypodidae Rhopalopsyllidae->Procellariidae Rhopalopsyllidae->Procellariidae Rhopalopsyllidae->Rhopalopsyllidae Caviidae Caviidae Rhopalopsyllidae->Caviidae Rhopalopsyllidae->Caviidae Chinchillidae Chinchillidae Rhopalopsyllidae->Chinchillidae Ctenomyidae Ctenomyidae Rhopalopsyllidae->Ctenomyidae Cuniculidae Cuniculidae Rhopalopsyllidae->Cuniculidae Dasyproctidae Dasyproctidae Rhopalopsyllidae->Dasyproctidae Spheniscidae Spheniscidae Rhopalopsyllidae->Spheniscidae Rhopalopsyllidae->Spheniscidae Psittacidae Psittacidae Rhopalopsyllidae->Psittacidae Ricinidae Ricinidae Ricinidae->Alaudidae Ricinidae->Passerellidae Ricinidae->Turdidae Rutaceae Rutaceae Rutaceae->Echimyidae Stephanocircidae Stephanocircidae Stephanocircidae->Cricetidae Stephanocircidae->Cricetidae Stephanocircidae->Didelphidae Stephanocircidae->Muridae Stephanocircidae->Peramelidae Stephanocircidae->Ctenomyidae Stephanocircidae->Ctenomyidae Dasyuridae Dasyuridae Stephanocircidae->Dasyuridae Microbiotheriidae Microbiotheriidae Stephanocircidae->Microbiotheriidae Stephanocircidae->Microbiotheriidae Stivaliidae Stivaliidae Stivaliidae->Sciuridae Stivaliidae->Muridae Stivaliidae->Muridae Stivaliidae->Tupaiidae Stivaliidae->Peramelidae Stivaliidae->Peramelidae Stivaliidae->Dasyuridae Petauridae Petauridae Stivaliidae->Petauridae Tachinidae Tachinidae Tachinidae->Geomyidae Tenebrionidae Tenebrionidae Tenebrionidae->Poaceae Thripidae Thripidae Thripidae->Asteraceae Solanaceae Solanaceae Thripidae->Solanaceae Tipulidae Tipulidae Tipulidae->Soricidae Trichodectidae Trichodectidae Trichodectidae->Leporidae Trichodectidae->Geomyidae Trichodectidae->Mustelidae Tungidae Tungidae Tungidae->Cricetidae Suidae Suidae Tungidae->Suidae Vermipsyllidae Vermipsyllidae Vermipsyllidae->Mustelidae Xiphiopsyllidae Xiphiopsyllidae Xiphiopsyllidae->Rhinolophidae Zopheridae Zopheridae Pinaceae Pinaceae Zopheridae->Pinaceae

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
Baculomeris schmidti HAS_ACCEPTED_NAME col Baculomeris schmidti
Barreropsylla excelsa HAS_ACCEPTED_NAME col Barreropsylla excelsa
Caenopsylla mira HAS_ACCEPTED_NAME col Caenopsylla mira
Callopsylla caspia HAS_ACCEPTED_NAME col Callopsylla caspia
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 1744
col family 17
col genus 218
col kingdom 1
col nanorder 1
col order 2
col parvorder 1
col phylum 2
col species 1194
col subfamily 3
col subgenus 29
col subspecies 102
col subtribe 1
col variety 3
discoverlife NA 3262
discoverlife species 19
gbif NA 1660
gbif family 17
gbif genus 241
gbif kingdom 2
gbif order 2
gbif phylum 2
gbif species 1244
gbif subspecies 121
gbif variety 3
itis NA 2332
itis family 17
itis genus 164
itis kingdom 1
itis order 3
itis phylum 2
itis species 703
itis subfamily 3
itis subgenus 1
itis suborder 2
itis subspecies 54
itis variety 1
mdd NA 3280
ncbi NA 2140
ncbi family 17
ncbi genus 207
ncbi order 3
ncbi phylum 2
ncbi species 862
ncbi subfamily 3
ncbi subgenus 8
ncbi suborder 1
ncbi subspecies 46
pbdb NA 2817
pbdb family 13
pbdb genus 133
pbdb kingdom 1
pbdb order 3
pbdb phylum 2
pbdb species 309
pbdb subfamily 2
pbdb suborder 1
pbdb unranked clade 1
tpt NA 2152
tpt family 7
tpt genus 109
tpt order 1
tpt species 1011
wfo NA 3195
wfo family 1
wfo genus 30
wfo species 52
wfo subspecies 2
wfo variety 2
worms NA 3069
worms family 12
worms genus 85
worms kingdom 1
worms order 3
worms phylum 2
worms species 106
worms suborder 2
worms subspecies 1
worms variety 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 HAS_ACCEPTED_NAME 1822
col SYNONYM_OF 285
col NONE 1915
discoverlife NONE 3808
discoverlife SYNONYM_OF 6
discoverlife HAS_ACCEPTED_NAME 18
gbif HAS_ACCEPTED_NAME 1897
gbif SYNONYM_OF 434
gbif NONE 1830
itis NONE 2565
itis HAS_ACCEPTED_NAME 1096
itis SYNONYM_OF 177
mdd NONE 3318
mdd HAS_ACCEPTED_NAME 472
mdd SYNONYM_OF 29
ncbi SAME_AS 1334
ncbi NONE 2365
ncbi SYNONYM_OF 141
ncbi COMMON_NAME_OF 4
pbdb NONE 3072
pbdb HAS_ACCEPTED_NAME 671
pbdb SYNONYM_OF 84
tpt HAS_ACCEPTED_NAME 1577
tpt SYNONYM_OF 230
tpt NONE 2383
wfo NONE 3727
wfo SYNONYM_OF 25
wfo HAS_ACCEPTED_NAME 76
wfo HAS_UNCHECKED_NAME 5
worms NONE 3475
worms HAS_ACCEPTED_NAME 307
worms SYNONYM_OF 57
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
2024-07-22T18:19:57Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-07-22T18:19:57Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-07-22T18:19:57Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-07-22T18:19:57Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder

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

Most frequently occurring review notes, if any.
reviewComment count
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 273
found unsupported interaction type with name: [Peromyscus maniculatus sonoriensis (found] 68
found unsupported interaction type with name: [hasH] 25
found unsupported interaction type with name: [lfp] 12

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 (2024-07-22) 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.