A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/mcz

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/mcz) contains 7,347 interactions with 8 (e.g., interactsWith) unique types of associations between 1,747 primary taxa (e.g., Perdita sp. Smith, 1853) and 2,092 associated taxa (e.g., ground). 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:

Museum of Comparative Zoology, Harvard University - Version 162.390 http://digir.mcz.harvard.edu/ipt/archive.do?r=mczbase 2023-09-23T04:43:10.297Z 04a214d42105ae302af82c6f72fcbe45ab09a147423c3b4f1e6d382750d87abd


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/mcz

# generate review notes
elton review globalbioticinteractions/mcz\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/mcz\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/mcz\
 | 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/mcz) contains 7,347 interactions with 8 (e.g., interactsWith) unique types of associations between 1,747 primary taxa (e.g., Perdita sp. Smith, 1853) and 2,092 associated taxa (e.g., ground).

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
Hemidactylus frenatus adjacentTo wall of building http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192777
Draco timorensis Kuhl, 1820 adjacentTo large tree by road http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192808
Cyrtodactylus Gray, 1827 adjacentTo rocks http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192930
Gehyra mutilata adjacentTo walls of building http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192850
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 3913
adjacentTo 2550
hasHost 752
parasiteOf 98
eats 18
hasParasite 9
eatenBy 8
visits 4
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Perdita sp. Smith, 1853 536
Gasterosteus aculeatus Linnaeus, 1758 533
Symbion americanus Obst, Funch & Kristensen, 2006 208
Camponotus sp. Mayr, 1861 197
Pheidole sp. Westwood, 1839 184
Andrena hirticincta Provancher, 1888 102
Hepialidae Stephens, 1829 94
Bdelloura candida (Girard, 1850) 65
Andrena sp. Fabricius 1775 62
Pontoniinae 60
Formicidae Latreille, 1809 57
Pheidole Westwood, 1839 54
Hylaeus modestus Say, 1837 54
Globicephala melaena (Traill, 1809) 49
Andrena erigeniae Robertson, 1891 47
Pseudopanurgus pauper (Cresson, 1878) 47
Lapethus newtoni Slipinski 45
Andrena rehni Viereck, 1907 41
Trigona ceophloei Schwarz 38
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
ground 437
Stylopized 172
Ceanothus 167
Heterotheca 141
ex rotten log 131
Solidago 109
Ophiocordyceps 94
ex dead twig 89
under 88
low vegetation 86
Mentzelia 83
Haplopappus 80
tree 60
gilled mushrooms 56
vegetation 49
Chamaesaracha 46
Globicephala melaena (Traill, 1809) 40
trees and vegetation 39
Ex stomach of Ceoploeus lineatus 38
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Perdita sp. Smith, 1853 interactsWith Heterotheca 136
Hepialidae Stephens, 1829 interactsWith Ophiocordyceps 94
Andrena hirticincta Provancher, 1888 interactsWith Stylopized 90
Perdita sp. Smith, 1853 interactsWith Mentzelia 83
Perdita sp. Smith, 1853 interactsWith Haplopappus 77
Perdita sp. Smith, 1853 interactsWith Chamaesaracha 46
Camponotus sp. Mayr, 1861 adjacentTo ground 45
Globicephala melaena (Traill, 1809) interactsWith Globicephala melaena (Traill, 1809) 40
Lapethus newtoni Slipinski adjacentTo gilled mushrooms 40
Pseudopanurgus pauper (Cresson, 1878) interactsWith Ceanothus 40
Trigona ceophloei Schwarz hasHost Ex stomach of Ceoploeus lineatus 38
Perdita sp. Smith, 1853 interactsWith Solidago 38
Crematogaster laeviuscula Mayr, 1870 adjacentTo cotton wood tree 37
Andrena rehni Viereck, 1907 interactsWith Ceanothus 35
Camponotus sp. Mayr, 1861 adjacentTo low vegetation 34
Symbion americanus Obst, Funch & Kristensen, 2006 interactsWith MCZ:IZ:154727 33
Perdita sp. Smith, 1853 interactsWith Bailyea 33
Pheidole sp. Westwood, 1839 adjacentTo ground and trees 31
Pheidole sp. Westwood, 1839 adjacentTo ground 29

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 Animalia->Animalia Plantae Plantae Animalia->Plantae Animalia->Plantae
interactions Andrenidae Andrenidae Salicaceae Salicaceae Andrenidae->Salicaceae Apidae Apidae Asteraceae Asteraceae Apidae->Asteraceae Polygonaceae Polygonaceae Apidae->Polygonaceae Chrysogorgiidae Chrysogorgiidae Cladorhizidae Cladorhizidae Chrysogorgiidae->Cladorhizidae Cladorhizidae->Chrysogorgiidae Cosmetidae Cosmetidae Ampycidae Ampycidae Cosmetidae->Ampycidae Delphinidae Delphinidae Delphinidae->Delphinidae Eulophidae Eulophidae Fabaceae Fabaceae Eulophidae->Fabaceae Gonyleptidae Gonyleptidae Araucariaceae Araucariaceae Gonyleptidae->Araucariaceae Neopilionidae Neopilionidae Neopilionidae->Neopilionidae Thomisidae Thomisidae Apiaceae Apiaceae Thomisidae->Apiaceae Tretodictyidae Tretodictyidae Tretodictyidae->Tretodictyidae

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
NONE ncbi
NONE discoverlife
NONE globi
Abundant cutting fungus ant NONE col Abundant cutting fungus ant
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 3163
tpt species 39
tpt genus 2
ncbi NA 1757
ncbi species 1055
ncbi genus 312
ncbi family 54
ncbi subspecies 11
ncbi subgenus 6
ncbi order 5
ncbi class 4
ncbi subfamily 4
ncbi varietas 2
ncbi phylum 1
mdd NA 3204
itis NA 1661
itis species 1123
itis genus 297
itis family 55
itis subspecies 44
itis variety 11
itis order 5
itis class 4
itis subfamily 4
itis phylum 1
itis kingdom 1
globi NA 1993
globi species 1440
globi genus 499
globi subspecies 73
globi family 67
globi order 22
globi variety 19
globi subgenus 14
globi class 10
globi subfamily 9
globi phylum 5
globi kingdom 3
globi infraorder 2
globi subclass 2
globi infrakingdom 1
globi suborder 1
globi subphylum 1
globi subtribe 1
globi tribe 1
globi superorder 1
gbif species 1499
gbif NA 1233
gbif genus 351
gbif family 60
gbif subspecies 58
gbif variety 12
gbif order 5
gbif class 4
gbif kingdom 2
gbif phylum 1
discoverlife NA 2941
discoverlife species 264
col NA 1475
col species 1289
col genus 320
col family 56
col subspecies 47
col variety 7
col order 5
col subfamily 5
col class 4
col section 1
col phylum 1
col kingdom 1
col infraspecific name 1
col subgenus 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 1479
col SYNONYM_OF 304
discoverlife NONE 2964
discoverlife HAS_ACCEPTED_NAME 244
discoverlife SYNONYM_OF 73
discoverlife HOMONYM_OF 14
gbif NONE 1233
gbif SYNONYM_OF 436
globi NONE 1314
globi SAME_AS 17380
itis NONE 1665
itis SYNONYM_OF 109
mdd NONE 3216
ncbi NONE 1761
ncbi SAME_AS 1425
ncbi SYNONYM_OF 57
tpt NONE 3181
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
2023-09-28T03:55:04Z note found unresolved reference [MCZ:Cryo:14052]
2023-09-28T03:55:04Z note found unresolved reference [MCZ:Cryo:14068]
2023-09-28T03:55:04Z note found unresolved reference [MCZ:Cryo:14075]
2023-09-28T03:55:04Z note found unresolved reference [MCZ:Cryo:14076]

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

Most frequently occurring review notes, if any.
reviewComment count
found unresolved reference [MCZ:Cryo:14052] 1
found unresolved reference [MCZ:Cryo:14068] 1
found unresolved reference [MCZ:Cryo:14075] 1
found unresolved reference [MCZ:Cryo:14076] 1

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.