A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/asu-asuhic

By Nomer and Elton, two naive review bots.



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 describe a review process of such an openly accessible digital interaction datasets of known origin, and discuss their outcome. The dataset under review (aka globalbioticinteractions/asu-asuhic) contains 21,452 interactions with 4 (e.g., interactsWith) unique types of associations between 541 primary taxa (e.g., Acmaeodera pubiventris lanata) and 733 associated taxa (e.g., Allionia incarnata L. (trailing windmills) [USDA]). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple perspectives.


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:

Arizona State University Hasbrouck Insect Collection https://github.com/globalbioticinteractions/asu-asuhic/archive/4ed77cb9ca8e526269d4678692e2844c950022f8.zip 2023-09-22T22:26:29.315Z 4209c270399e8d6446cc0457edb818cc5dd9a1c29862201b839710b6fbfc0ab1


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 0.12.7
nomer 0.5.5
mlr 6.0.0

The review process can be described in the form of a script:

# get versioned copy of the dataset under review 
elton pull globalbioticinteractions/asu-asuhic

# generate review notes
elton review globalbioticinteractions/asu-asuhic\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/asu-asuhic\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/asu-asuhic\
 | 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.


In the following sections, the results of the review are summarized 1. 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 (aka globalbioticinteractions/asu-asuhic) contains 21,452 interactions with 4 (e.g., interactsWith) unique types of associations between 541 primary taxa (e.g., Acmaeodera pubiventris lanata) and 733 associated taxa (e.g., Allionia incarnata L. (trailing windmills) [USDA]).

An exhaustive list of indexed interaction claims can be found at indexed-interactions (csv/tsv/html). The list was used to create the following data summaries.

Sample of Indexed Interaction Claims
sourceTaxonName interactionTypeName targetTaxonName referenceCitation
Hirmoneura flavipes adjacentTo palm shaped leaves https://ecdysis.org/collections/individual/index.php?occid=419701
Neorhynchocephalus sackenii hasHost Ex. Morseiella flaviventris (Bruner) https://ecdysis.org/collections/individual/index.php?occid=419705
Neorhynchocephalus sackenii hasHost Ex. Morseiella flaviventris (Bruner) https://ecdysis.org/collections/individual/index.php?occid=419706
Neorhynchocephalus sackenii hasHost Ex. Morseiella flaviventris (Bruner) https://ecdysis.org/collections/individual/index.php?occid=419707
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 11386
adjacentTo 9791
hasHost 263
eats 12
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Acmaeodera pubiventris lanata 745
Acmaeodera gibbula 689
Acmaeodera lanata 673
Apidae 646
Acmaeodera diffusa 615
Acmaeodera bowditchi 609
Acmaeodera pulchella 589
Acmaeodera acanthicola 583
Acmaeodera decipiens 560
Acmaeodera cazieri 544
Acmaeodera flavopicta 521
Gyascutus planicosta cribriceps 509
Acmaeodera yuccavora 466
Ripiphorus vierecki 434
Hippomelas sphenicus 422
Acmaeodera parkeri 408
Hippomelas planicosta 404
Acmaeodera amplicollis 400
Perdita 398
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Allionia incarnata L. (trailing windmills) [USDA] 1282
Prosopis juliflora (Sw.) DC. (mesquite) [USDA] 878
Sphaeralcea laxa Wooton & Standl. (caliche globemallow) [USDA] 757
Asclepias erosa Torr. (desert milkweed) [USDA] 669
Larrea tridentata (DC.) Coville (creosote bush) [USDA] 622
Poliomintha incana (Torr.) A. Gray (frosted mint) [USDA] 591
Cercidum microphyllum (Torr.) Rose & I.M. Johnst. (yellow paloverde) [USDA] 536
Poliomintha incana (Torr). Gray (frosted mint) [USDA] 464
Tamarix pentandra Pall. (salt cedar) [USDA] 445
Ephedra trifurca Torr. ex S. Watson (longleaf jointfir) [USDA] 429
Baileya multiradiata Harv. & A. Gray ex A. Gray (desert marigold) [USDA] 380
dead Hilaria rigida (Thurb.) Benth 379
Dalea spinosa A. Gray (smoketree) [USDA] 378
grass stems 367
Acacia constricta Benth. (whitethorn acacia) [USDA] 360
yellow Compositae sp. 318
Asclepias subverticillata (A. Gray) Vail (horsetail milkweed) [USDA] 305
Sphaeralcea A. St.-Hil. sp. (globemallow) [USDA] 296
Juniperus monosperma (Engelm.) Sarg. (oneseed juniper) [USDA] 282
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Acmaeodera diffusa adjacentTo Sphaeralcea laxa Wooton & Standl. (caliche globemallow) [USDA] 559
Acmaeodera acanthicola interactsWith Cercidum microphyllum (Torr.) Rose & I.M. Johnst. (yellow paloverde) [USDA] 517
Acmaeodera yuccavora adjacentTo Allionia incarnata L. (trailing windmills) [USDA] 462
Hippomelas planicosta interactsWith Larrea tridentata (DC.) Coville (creosote bush) [USDA] 382
Acmaeodera parkeri adjacentTo Allionia incarnata L. (trailing windmills) [USDA] 381
Acmaeodera pubiventris lanata adjacentTo dead Hilaria rigida (Thurb.) Benth 379
Acmaeodera barri interactsWith Dalea spinosa A. Gray (smoketree) [USDA] 376
Heteropogon johnsoni adjacentTo grass stems 359
Hippomelas sphenicus adjacentTo Prosopis juliflora (Sw.) DC. (mesquite) [USDA] 353
Gyascutus planicosta cribriceps interactsWith Tamarix pentandra Pall. (salt cedar) [USDA] 345
Acmaeodera cazieri adjacentTo Allionia incarnata L. (trailing windmills) [USDA] 335
Acmaeodera pubiventris lanata interactsWith Poliomintha incana (Torr). Gray (frosted mint) [USDA] 332
Macrosiagon fernaldum interactsWith Asclepias erosa Torr. (desert milkweed) [USDA] 329
Acmaeodera decipiens adjacentTo yellow Compositae sp. 252
Apidae interactsWith Poliomintha incana (Torr.) A. Gray (frosted mint) [USDA] 239
Acmaeodera ligulata interactsWith Erigeron divergens Torr. & A. Gray (spreading fleabane) [USDA] 233
Protoxaea gloriosa interactsWith Condalia spathulata A. Gray (knifeleaf condalia) [USDA] 222
Ptiloglossa arizonensis interactsWith Solanum elaeagnifolium Cav. (silverleaf nightshade) [USDA] 222
Coenonycha acuta hasHost ex Purshia glandulosa Curran (desert bitterbrush) [USDA] 218

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. Note that both network graphs were first aligned taxonomically via 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 Plantae Plantae Animalia->Plantae Animalia->Plantae Plantae->Plantae
interactions Apidae Apidae Brassicaceae Brassicaceae Apidae->Brassicaceae Asilidae Asilidae Asilidae->Asilidae Cricetidae Cricetidae Asilidae->Cricetidae Masaridae Masaridae Asilidae->Masaridae Buprestidae Buprestidae Asteraceae Asteraceae Buprestidae->Asteraceae Curculionidae Curculionidae Anacardiaceae Anacardiaceae Curculionidae->Anacardiaceae Cactaceae Cactaceae Curculionidae->Cactaceae Pinaceae Pinaceae Curculionidae->Pinaceae Rutaceae Rutaceae Curculionidae->Rutaceae Halictidae Halictidae Rosaceae Rosaceae Halictidae->Rosaceae Lycaenidae Lycaenidae Fagaceae Fagaceae Lycaenidae->Fagaceae Poaceae Poaceae Poaceae->Asteraceae Sphecidae Sphecidae Sphecidae->Asteraceae

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 globi mdd tpt). These alignments may serve as a way to review name usage or aid in selecting of a suitable taxonomic name resource to use.

Sample of Name Alignments
providedName relationName resolvedCatalogName resolvedName
Abies concolor white fir NONE col Abies concolor white fir
Abies concolor white fir NONE ncbi Abies concolor white fir
Abies concolor white fir NONE discoverlife Abies concolor white fir
Abies concolor white fir NONE gbif Abies concolor white fir
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
tpt NA 1108
tpt genus 2
ncbi NA 728
ncbi species 246
ncbi genus 112
ncbi family 16
ncbi subgenus 10
ncbi subspecies 3
ncbi superfamily 2
ncbi tribe 1
ncbi varietas 1
mdd NA 1110
itis NA 556
itis species 404
itis genus 106
itis family 17
itis subspecies 15
itis variety 8
itis superfamily 2
itis subfamily 1
itis tribe 1
itis kingdom 1
globi NA 622
globi species 486
globi genus 194
globi family 20
globi subgenus 19
globi subspecies 19
globi variety 10
globi subfamily 4
globi superfamily 2
globi kingdom 2
globi phylum 1
globi class 1
globi tribe 1
globi order 1
gbif NA 490
gbif species 464
gbif genus 121
gbif subspecies 19
gbif family 18
gbif variety 2
gbif kingdom 1
discoverlife NA 1057
discoverlife species 53
col NA 541
col species 423
col genus 112
col family 17
col subspecies 10
col infraspecific name 2
col superfamily 2
col subgenus 2
col section 1
col subfamily 1
col tribe 1
col variety 1
col kingdom 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 NONE 541
discoverlife NONE 1065
discoverlife HAS_ACCEPTED_NAME 50
discoverlife SYNONYM_OF 13
gbif NONE 490
gbif SYNONYM_OF 132
globi NONE 473
globi SAME_AS 5655
itis NONE 556
itis SYNONYM_OF 66
mdd NONE 1118
ncbi NONE 728
ncbi SAME_AS 394
ncbi SYNONYM_OF 19
tpt NONE 1116
List of Available Name Alignment Reports
catalog name alignment results
col associated names alignments (csv/tsv/html)
ncbi associated names alignments (csv/tsv/html)
discoverlife associated names alignments (csv/tsv/html)
gbif associated names alignments (csv/tsv/html)
itis associated names alignments (csv/tsv/html)
globi associated names alignments (csv/tsv/html)
mdd associated names alignments (csv/tsv/html)
tpt associated names alignments (csv/tsv/html)

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
2023-09-28T00:05:51Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2023-09-28T00:05:51Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2023-09-28T00:05:51Z note found unsupported interaction type with name: [7]
2023-09-28T00:05:52Z 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
found unsupported interaction type with name: [attacks] 54
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 26
found unsupported interaction type with name: [Cupressaceae] 3
found unsupported interaction type with name: [Pinaceae] 3

For more exhaustive list of review notes, please have a look at the Review Notes (csv/tsv/html).

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.

Sample 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 4 for badge examples.


This review is intended to provide a perspective on the dataset to aid understanding of species interaction claims discovered. However, this review should not be considered as fitness of use or other kind of quality assessment. Instead, the review may be used as in indication of the open-ness5 and FAIRness (Wilkinson et al. 2016; Trekels et al. 2023) of the dataset: in order to perform this review, the data was likely openly available, Findable, Accessible, Interoperable and Reusable. Currently, this Open-FAIR assessment is qualitative, and with measurement units specified, a more quantitative approach can be implemented.


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.


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.