A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/utah-piper

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/utah-piper/issues

2024-04-22

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/utah-piper, is 2.23MiB in size and contains 14,491 interaction with 2 unique types of associations (e.g., interactsWith) between 2,792 primary taxon (e.g., Anomiopsyllus amphibolus) and 2,611 associated taxon (e.g., Neotoma lepida). 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:

Price Institute of Parasite Research, School of Biological Sciences, University of Utah https://github.com/globalbioticinteractions/utah-piper/archive/43da8db550b5776c1e3d17803831c696fe9b8285.zip 2024-04-20T06:10:19.092Z 7a6b77bdd41825ca03becb1c75b50f276443a97775a7c7741e4daf3fed9b873d

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/utah-piper 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 0.13.2
nomer 0.5.8
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. 2.23MiB) under review 
elton pull globalbioticinteractions/utah-piper

# generate review notes
elton review globalbioticinteractions/utah-piper\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/utah-piper\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/utah-piper\
 | 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/utah-piper, is 2.23MiB in size and contains 14,491 interaction with 2 unique types of associations (e.g., interactsWith) between 2,792 primary taxon (e.g., Anomiopsyllus amphibolus) and 2,611 associated taxon (e.g., Neotoma lepida).

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
Laemobothrion vulturis hasHost ex. Aquila chrysaetos https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41509935
Brueelia interactsWith Dicrurus hottentottus https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41509936
Colpocephalum unciferum interactsWith pelecanus erythrorhynchos https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41654518
Colpocephalum impressum hasHost ex. Bald Eagle [Haliaeetus leucocephalus] https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41654906
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 14312
hasHost 179
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Anomiopsyllus amphibolus 1641
Monopsyllus wagneri 1394
Malaraeus sinomus 783
Hoplopsyllus anomalus 612
Meringis dipodomys 598
Megabothris abantis 345
Myrsidea 257
Monopsyllus 253
Philopterus 198
Megarthroglossus smiti 195
Monopsyllus wagneri wagneri 181
Anatoecus 153
Menopon gallinae 127
Anaticola crassicornis 127
Degeeriella 122
Malaraeus euphorbi 120
Monopsyllus exilis 106
Meringis californicus 94
Cummingsiella longristratus 77
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Neotoma lepida 1382
Peromyscus maniculatus sonoriensis 1061
Peromyscus maniculatus 904
Dipodomys microps 438
Peromyscus crinitus pergracilis 331
Neotoma lepida lepida 286
Spermophilus variegatus utah 232
Microtus longicaudus latus 162
Fulica americana 142
Peromyscus crinitus 137
Peromyscus truei nevadensis 116
Ammospermophilus leucurus leucurus 113
Peromyscus maniculatus gambelii 109
Onychomys leucogaster utahensis 106
Citellus l. leucurus 100
Dipodomys ordii 97
Citellus leucurus 93
Numenius americanus 89
Himantopus mexicanus 85
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Anomiopsyllus amphibolus interactsWith Neotoma lepida 1273
Monopsyllus wagneri interactsWith Peromyscus maniculatus sonoriensis 759
Meringis dipodomys interactsWith Dipodomys microps 426
Monopsyllus wagneri interactsWith Peromyscus maniculatus 365
Malaraeus sinomus interactsWith Peromyscus crinitus pergracilis 291
Anomiopsyllus amphibolus interactsWith Neotoma lepida lepida 238
Hoplopsyllus anomalus interactsWith Spermophilus variegatus utah 230
Monopsyllus interactsWith Peromyscus maniculatus 211
Monopsyllus wagneri wagneri interactsWith Peromyscus maniculatus 149
Megabothris abantis interactsWith Microtus longicaudus latus 124
Malaraeus sinomus interactsWith Peromyscus crinitus 115
Hoplopsyllus anomalus interactsWith Ammospermophilus leucurus leucurus 113
Hoplopsyllus anomalus interactsWith Citellus l. leucurus 100
Monopsyllus exilis interactsWith Onychomys leucogaster utahensis 100
Monopsyllus wagneri interactsWith Peromyscus maniculatus gambelii 92
Malaraeus euphorbi interactsWith Peromyscus maniculatus sonoriensis 91
Hoplopsyllus anomalus interactsWith Citellus leucurus 89
Meringis dipodomys interactsWith Dipodomys ordii 82
Megarthroglossus smiti interactsWith Neotoma lepida nest 78

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
interactions Ancistronidae Ancistronidae Alcidae Alcidae Ancistronidae->Alcidae Anatidae Anatidae Ancistronidae->Anatidae Caprimulgidae Caprimulgidae Ancistronidae->Caprimulgidae Charadriidae Charadriidae Ancistronidae->Charadriidae Diomedeidae Diomedeidae Ancistronidae->Diomedeidae Estrildidae Estrildidae Ancistronidae->Estrildidae Glareolidae Glareolidae Ancistronidae->Glareolidae Gruidae Gruidae Ancistronidae->Gruidae Haematopodidae Haematopodidae Ancistronidae->Haematopodidae Laridae Laridae Ancistronidae->Laridae Meropidae Meropidae Ancistronidae->Meropidae Phalacrocoracidae Phalacrocoracidae Ancistronidae->Phalacrocoracidae Procellariidae Procellariidae Ancistronidae->Procellariidae Recurvirostridae Recurvirostridae Ancistronidae->Recurvirostridae Scolopacidae Scolopacidae Ancistronidae->Scolopacidae Sulidae Sulidae Ancistronidae->Sulidae Boopiidae Boopiidae Canidae Canidae Boopiidae->Canidae Dasyuridae Dasyuridae Boopiidae->Dasyuridae Macropodidae Macropodidae Boopiidae->Macropodidae Peramelidae Peramelidae Boopiidae->Peramelidae Vombatidae Vombatidae Boopiidae->Vombatidae Ceratophyllidae Ceratophyllidae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Dipodidae Dipodidae Ceratophyllidae->Dipodidae Heteromyidae Heteromyidae Ceratophyllidae->Heteromyidae Leporidae Leporidae Ceratophyllidae->Leporidae Mephitidae Mephitidae Ceratophyllidae->Mephitidae Muridae Muridae Ceratophyllidae->Muridae Procyonidae Procyonidae Ceratophyllidae->Procyonidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Soricidae Soricidae Ceratophyllidae->Soricidae Colpocephalidae Colpocephalidae Colpocephalidae->Anatidae Accipitridae Accipitridae Colpocephalidae->Accipitridae Ardeidae Ardeidae Colpocephalidae->Ardeidae Cariamidae Cariamidae Colpocephalidae->Cariamidae Cathartidae Cathartidae Colpocephalidae->Cathartidae Ciconiidae Ciconiidae Colpocephalidae->Ciconiidae Columbidae Columbidae Colpocephalidae->Columbidae Corvidae Corvidae Colpocephalidae->Corvidae Cuculidae Cuculidae Colpocephalidae->Cuculidae Falconidae Falconidae Colpocephalidae->Falconidae Fregatidae Fregatidae Colpocephalidae->Fregatidae Megapodiidae Megapodiidae Colpocephalidae->Megapodiidae Mimidae Mimidae Colpocephalidae->Mimidae Pandionidae Pandionidae Colpocephalidae->Pandionidae Pelecanidae Pelecanidae Colpocephalidae->Pelecanidae Phasianidae Phasianidae Colpocephalidae->Phasianidae Picidae Picidae Colpocephalidae->Picidae Psittacidae Psittacidae Colpocephalidae->Psittacidae Sagittariidae Sagittariidae Colpocephalidae->Sagittariidae Strigidae Strigidae Colpocephalidae->Strigidae Threskiornithidae Threskiornithidae Colpocephalidae->Threskiornithidae Tytonidae Tytonidae Colpocephalidae->Tytonidae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Canidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Dipodidae Ctenophthalmidae->Heteromyidae Ctenophthalmidae->Mephitidae Ctenophthalmidae->Sciuridae Gliricolidae Gliricolidae Caviidae Caviidae Gliricolidae->Caviidae Echimyidae Echimyidae Gliricolidae->Echimyidae Gyropidae Gyropidae Gyropidae->Caviidae Gyropidae->Echimyidae Aotidae Aotidae Gyropidae->Aotidae Chinchillidae Chinchillidae Gyropidae->Chinchillidae Ctenomyidae Ctenomyidae Gyropidae->Ctenomyidae Cuniculidae Cuniculidae Gyropidae->Cuniculidae Dasyproctidae Dasyproctidae Gyropidae->Dasyproctidae Myocastoridae Myocastoridae Gyropidae->Myocastoridae Tayassuidae Tayassuidae Gyropidae->Tayassuidae Haematomyzidae Haematomyzidae Elephantidae Elephantidae Haematomyzidae->Elephantidae Suidae Suidae Haematomyzidae->Suidae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Soricidae Ischnopsyllidae Ischnopsyllidae Vespertilionidae Vespertilionidae Ischnopsyllidae->Vespertilionidae Laemobothriidae Laemobothriidae Laemobothriidae->Scolopacidae Laemobothriidae->Accipitridae Laemobothriidae->Cathartidae Rallidae Rallidae Laemobothriidae->Rallidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Muridae Menoponidae Menoponidae Menoponidae->Anatidae Menoponidae->Estrildidae Menoponidae->Meropidae Menoponidae->Phalacrocoracidae Menoponidae->Procellariidae Menoponidae->Accipitridae Menoponidae->Ardeidae Menoponidae->Cathartidae Menoponidae->Columbidae Menoponidae->Corvidae Menoponidae->Cuculidae Menoponidae->Falconidae Menoponidae->Fregatidae Menoponidae->Megapodiidae Menoponidae->Mimidae Menoponidae->Pelecanidae Menoponidae->Phasianidae Menoponidae->Picidae Menoponidae->Psittacidae Menoponidae->Threskiornithidae Alaudidae Alaudidae Menoponidae->Alaudidae Alcedinidae Alcedinidae Menoponidae->Alcedinidae Anhimidae Anhimidae Menoponidae->Anhimidae Apodidae Apodidae Menoponidae->Apodidae Artamidae Artamidae Menoponidae->Artamidae Bucerotidae Bucerotidae Menoponidae->Bucerotidae Bucorvidae Bucorvidae Menoponidae->Bucorvidae Capitonidae Capitonidae Menoponidae->Capitonidae Cardinalidae Cardinalidae Menoponidae->Cardinalidae Cettiidae Cettiidae Menoponidae->Cettiidae Cotingidae Cotingidae Menoponidae->Cotingidae Cracidae Cracidae Menoponidae->Cracidae Curculionidae Curculionidae Menoponidae->Curculionidae Dicruridae Dicruridae Menoponidae->Dicruridae Eurylaimidae Eurylaimidae Menoponidae->Eurylaimidae Fringillidae Fringillidae Menoponidae->Fringillidae Furnariidae Furnariidae Menoponidae->Furnariidae Hirundinidae Hirundinidae Menoponidae->Hirundinidae Icteridae Icteridae Menoponidae->Icteridae Irenidae Irenidae Menoponidae->Irenidae Laniidae Laniidae Menoponidae->Laniidae Leiothrichidae Leiothrichidae Menoponidae->Leiothrichidae Locustellidae Locustellidae Menoponidae->Locustellidae Menuridae Menuridae Menoponidae->Menuridae Monarchidae Monarchidae Menoponidae->Monarchidae Motacillidae Motacillidae Menoponidae->Motacillidae Muscicapidae Muscicapidae Menoponidae->Muscicapidae Nectariniidae Nectariniidae Menoponidae->Nectariniidae Numididae Numididae Menoponidae->Numididae Opisthocomidae Opisthocomidae Menoponidae->Opisthocomidae Paridae Paridae Menoponidae->Paridae Parulidae Parulidae Menoponidae->Parulidae Passerellidae Passerellidae Menoponidae->Passerellidae Passeridae Passeridae Menoponidae->Passeridae Petroicidae Petroicidae Menoponidae->Petroicidae Pittidae Pittidae Menoponidae->Pittidae Ploceidae Ploceidae Menoponidae->Ploceidae Prunellidae Prunellidae Menoponidae->Prunellidae Pycnonotidae Pycnonotidae Menoponidae->Pycnonotidae Ramphastidae Ramphastidae Menoponidae->Ramphastidae Rhipiduridae Rhipiduridae Menoponidae->Rhipiduridae Sturnidae Sturnidae Menoponidae->Sturnidae Tephrodornithidae Tephrodornithidae Menoponidae->Tephrodornithidae Thamnophilidae Thamnophilidae Menoponidae->Thamnophilidae Thraupidae Thraupidae Menoponidae->Thraupidae Troglodytidae Troglodytidae Menoponidae->Troglodytidae Turdidae Turdidae Menoponidae->Turdidae Tyrannidae Tyrannidae Menoponidae->Tyrannidae Vireonidae Vireonidae Menoponidae->Vireonidae Philopteridae Philopteridae Philopteridae->Alcidae Philopteridae->Anatidae Philopteridae->Caprimulgidae Philopteridae->Charadriidae Philopteridae->Diomedeidae Philopteridae->Estrildidae Philopteridae->Glareolidae Philopteridae->Laridae Philopteridae->Meropidae Philopteridae->Phalacrocoracidae Philopteridae->Procellariidae Philopteridae->Recurvirostridae Philopteridae->Scolopacidae Philopteridae->Sulidae Philopteridae->Accipitridae Philopteridae->Ardeidae Philopteridae->Cathartidae Philopteridae->Ciconiidae Philopteridae->Columbidae Philopteridae->Corvidae Philopteridae->Cuculidae Philopteridae->Falconidae Philopteridae->Fregatidae Philopteridae->Megapodiidae Philopteridae->Mimidae Philopteridae->Pelecanidae Philopteridae->Phasianidae Philopteridae->Picidae Philopteridae->Psittacidae Philopteridae->Strigidae Philopteridae->Threskiornithidae Philopteridae->Tytonidae Philopteridae->Rallidae Philopteridae->Alaudidae Philopteridae->Alcedinidae Philopteridae->Bucerotidae Philopteridae->Bucorvidae Philopteridae->Cardinalidae Philopteridae->Cotingidae Philopteridae->Cracidae Philopteridae->Dicruridae Philopteridae->Fringillidae Philopteridae->Furnariidae Philopteridae->Hirundinidae Philopteridae->Icteridae Philopteridae->Laniidae Philopteridae->Leiothrichidae Philopteridae->Motacillidae Philopteridae->Muscicapidae Philopteridae->Nectariniidae Philopteridae->Numididae Philopteridae->Opisthocomidae Philopteridae->Paridae Philopteridae->Parulidae Philopteridae->Passerellidae Philopteridae->Passeridae Philopteridae->Pittidae Philopteridae->Pycnonotidae Philopteridae->Ramphastidae Philopteridae->Rhipiduridae Philopteridae->Sturnidae Philopteridae->Tephrodornithidae Philopteridae->Thamnophilidae Philopteridae->Turdidae Philopteridae->Tyrannidae Philopteridae->Vireonidae Anhingidae Anhingidae Philopteridae->Anhingidae Aramidae Aramidae Philopteridae->Aramidae Bombycillidae Bombycillidae Philopteridae->Bombycillidae Burhinidae Burhinidae Philopteridae->Burhinidae Campephagidae Campephagidae Philopteridae->Campephagidae Chloropseidae Chloropseidae Philopteridae->Chloropseidae Coraciidae Coraciidae Philopteridae->Coraciidae Formicariidae Formicariidae Philopteridae->Formicariidae Gaviidae Gaviidae Philopteridae->Gaviidae Heliornithidae Heliornithidae Philopteridae->Heliornithidae Hydrobatidae Hydrobatidae Philopteridae->Hydrobatidae Jacanidae Jacanidae Philopteridae->Jacanidae Lybiidae Lybiidae Philopteridae->Lybiidae Megalaimidae Megalaimidae Philopteridae->Megalaimidae Momotidae Momotidae Philopteridae->Momotidae Noctuidae Noctuidae Philopteridae->Noctuidae Odontophoridae Odontophoridae Philopteridae->Odontophoridae Pelecanoididae Pelecanoididae Philopteridae->Pelecanoididae Phaethontidae Phaethontidae Philopteridae->Phaethontidae Podargidae Podargidae Philopteridae->Podargidae Podicipedidae Podicipedidae Philopteridae->Podicipedidae Psophiidae Psophiidae Philopteridae->Psophiidae Ptilogonatidae Ptilogonatidae Philopteridae->Ptilogonatidae Sittidae Sittidae Philopteridae->Sittidae Spheniscidae Spheniscidae Philopteridae->Spheniscidae Struthionidae Struthionidae Philopteridae->Struthionidae Sylviidae Sylviidae Philopteridae->Sylviidae Timaliidae Timaliidae Philopteridae->Timaliidae Tinamidae Tinamidae Philopteridae->Tinamidae Upupidae Upupidae Philopteridae->Upupidae Pseudomenoponidae Pseudomenoponidae Pseudomenoponidae->Anatidae Pseudomenoponidae->Rallidae Pseudomenoponidae->Heliornithidae Pseudomenoponidae->Jacanidae Pulicidae Pulicidae Pulicidae->Heteromyidae Pulicidae->Sciuridae Erinaceidae Erinaceidae Pulicidae->Erinaceidae Rhopalopsyllidae Rhopalopsyllidae Rhopalopsyllidae->Apodidae Ricinidae Ricinidae Ricinidae->Alaudidae Ricinidae->Cardinalidae Ricinidae->Dicruridae Ricinidae->Fringillidae Ricinidae->Motacillidae Ricinidae->Muscicapidae Ricinidae->Parulidae Ricinidae->Passerellidae Ricinidae->Thamnophilidae Ricinidae->Tyrannidae Ricinidae->Vireonidae Somaphantidae Somaphantidae Somaphantidae->Columbidae Somaphantidae->Phasianidae Somaphantidae->Cracidae Somaphantidae->Numididae Somaphantidae->Odontophoridae Trichodectidae Trichodectidae Trichodectidae->Canidae Trichodectidae->Mephitidae Trichodectidae->Muridae Trichodectidae->Procyonidae Bovidae Bovidae Trichodectidae->Bovidae Cervidae Cervidae Trichodectidae->Cervidae Equidae Equidae Trichodectidae->Equidae Erethizontidae Erethizontidae Trichodectidae->Erethizontidae Felidae Felidae Trichodectidae->Felidae Geomyidae Geomyidae Trichodectidae->Geomyidae Herpestidae Herpestidae Trichodectidae->Herpestidae Lorisidae Lorisidae Trichodectidae->Lorisidae Mustelidae Mustelidae Trichodectidae->Mustelidae Nandiniidae Nandiniidae Trichodectidae->Nandiniidae Procaviidae Procaviidae Trichodectidae->Procaviidae Viverridae Viverridae Trichodectidae->Viverridae Trimenoponidae Trimenoponidae Trimenoponidae->Cricetidae Trimenoponidae->Caviidae Trimenoponidae->Echimyidae Trimenoponidae->Chinchillidae Caenolestidae Caenolestidae Trimenoponidae->Caenolestidae Didelphidae Didelphidae Trimenoponidae->Didelphidae Trinotonidae Trinotonidae Trinotonidae->Anatidae

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, and pbdb). 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
Auricotes affinis HAS_ACCEPTED_NAME col Auricotes affinis
Auricotes carpophagae HAS_ACCEPTED_NAME col Auricotes carpophagae
Auricotes limbatus HAS_ACCEPTED_NAME col Auricotes limbatus
Auricotes obscurus HAS_ACCEPTED_NAME col Auricotes obscurus
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 2560
col family 3
col genus 175
col species 2212
col subgenus 14
col subspecies 262
discoverlife NA 5201
gbif NA 2474
gbif family 3
gbif form 2
gbif genus 183
gbif species 2273
gbif subspecies 280
gbif variety 1
itis NA 3864
itis family 3
itis genus 100
itis species 1001
itis subspecies 232
mdd NA 5200
ncbi NA 3533
ncbi family 3
ncbi genus 167
ncbi species 1394
ncbi subgenus 1
ncbi subspecies 104
pbdb NA 4562
pbdb family 2
pbdb genus 82
pbdb species 550
pbdb subspecies 4
tpt NA 3024
tpt family 6
tpt genus 160
tpt species 2011
wfo NA 5197
wfo genus 3
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 2611
col SYNONYM_OF 470
col NONE 2591
discoverlife NONE 5457
gbif HAS_ACCEPTED_NAME 2726
gbif SYNONYM_OF 809
gbif NONE 2503
itis NONE 3974
itis HAS_ACCEPTED_NAME 1246
itis SYNONYM_OF 241
mdd NONE 5224
mdd HAS_ACCEPTED_NAME 225
ncbi SAME_AS 1655
ncbi NONE 3620
ncbi SYNONYM_OF 185
pbdb NONE 4701
pbdb HAS_ACCEPTED_NAME 671
pbdb SYNONYM_OF 81
tpt SYNONYM_OF 508
tpt HAS_ACCEPTED_NAME 2305
tpt NONE 3070
wfo NONE 5445
wfo HAS_ACCEPTED_NAME 3
wfo HAS_UNCHECKED_NAME 1
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)

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
2024-04-22T08:11:46Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-22T08:11:46Z note found unsupported interaction type with name: [Genus]
2024-04-22T08:11:47Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-22T08:11:47Z 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 811
found unsupported interaction type with name: [Genus] 1
found unsupported interaction type with name: [Ave] 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 5 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-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.

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.