A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/sdnhm-sdmc

By Nomer and Elton, two naive review bots.

2023-09-28

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 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/sdnhm-sdmc) contains 8,686 interactions with 4 (e.g., interactsWith) unique types of associations between 746 primary taxa (e.g., Gelechiidae) and 380 associated taxa (e.g., Oak). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple perspectives.

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:

San Diego Natural History Museum https://github.com/globalbioticinteractions/sdnhm-sdmc/archive/7238d8b804f543250eb487b43144e1125fb3688a.zip 2023-09-23T10:49:23.227Z 045c0ec86487b73de58a74a61ed5b14a94c7618275a11e4c54745b076c4f9137

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 0.12.7
nomer 0.5.5
mlr 6.0.0
pandoc 3.1.6.1

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

# get versioned copy of the dataset under review 
elton pull globalbioticinteractions/sdnhm-sdmc

# generate review notes
elton review globalbioticinteractions/sdnhm-sdmc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/sdnhm-sdmc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/sdnhm-sdmc\
 | 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 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/sdnhm-sdmc) contains 8,686 interactions with 4 (e.g., interactsWith) unique types of associations between 746 primary taxa (e.g., Gelechiidae) and 380 associated taxa (e.g., Oak).

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
Poanes melane interactsWith Aira caespitosa https://scan-bugs.org:443/portal/collections/individual/index.php?occid=37440031
Tortricidae interactsWith Pine https://scan-bugs.org:443/portal/collections/individual/index.php?occid=37440229
Tortricidae hasHost diseased pine tree https://scan-bugs.org:443/portal/collections/individual/index.php?occid=37440229
Argyrotaenia citrana interactsWith Christmas cactus https://scan-bugs.org:443/portal/collections/individual/index.php?occid=37441158
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 8159
adjacentTo 440
hasHost 88
eats 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Gelechiidae 292
Orthosia erythrolita 192
Glaucina epiphysaria 169
Malacosoma californicum andreasum 162
Plataea personaria 145
Gnorimoschema 136
Apodemia mormo 132
Hymenoptera 122
Stamnodes annellata 118
Zenophleps lignicolorata 109
Ethmia discostrigella 104
Miodera stigmata 102
Amydria 96
Eucosma pulveratana 92
Notarctia proxima 80
Stamnodes coenonymphata 79
Grammia ornata 78
Speranza marcescaria 77
Pherne subpunctata 67
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Oak 2100
Sycamore 1885
Sage 1327
Willow 853
Manzanita 516
Coleogyne ramosissima 153
Hemizonia conjugens 103
Bebbia 86
Eriogonum fasciculatum 69
Bebbia flowers 63
Pogogyne nudiuscula 45
Pine 44
Penstemon 42
Yucca 40
Baccharis sarothroides 36
Alfalfa 33
Foeniculum vulgare 26
Lasthenia californica 24
Eriogonum 21
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Gelechiidae interactsWith Sycamore 95
Gelechiidae interactsWith Sage 83
Gelechiidae interactsWith Oak 75
Malacosoma californicum andreasum interactsWith Coleogyne ramosissima 75
Malacosoma californicum andreasum hasHost Coleogyne ramosissima 75
Apodemia mormo interactsWith Bebbia 66
Orthosia erythrolita interactsWith Sycamore 58
Stamnodes annellata interactsWith Oak 57
Stamnodes annellata interactsWith Sycamore 56
Apodemia mormo adjacentTo Bebbia flowers 55
Glaucina epiphysaria interactsWith Sage 51
Ethmia discostrigella interactsWith Sycamore 50
Ethmia discostrigella interactsWith Oak 50
Glaucina epiphysaria interactsWith Sycamore 49
Plataea personaria interactsWith Sage 49
Gnorimoschema interactsWith Willow 46
Orthosia erythrolita interactsWith Oak 44
Gnorimoschema interactsWith Sage 43
Miodera stigmata interactsWith Sage 43

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 Animalia->Plantae Plantae->Plantae Plantae->Plantae
interactions Ampulicidae Ampulicidae Asteraceae Asteraceae Ampulicidae->Asteraceae Andrenidae Andrenidae Andrenidae->Asteraceae Boraginaceae Boraginaceae Andrenidae->Boraginaceae Anobiidae Anobiidae Anobiidae->Asteraceae Anobiidae->Asteraceae Apidae Apidae Apidae->Asteraceae Apidae->Asteraceae Lamiaceae Lamiaceae Apidae->Lamiaceae Apidae->Lamiaceae Plantaginaceae Plantaginaceae Apidae->Plantaginaceae Polygonaceae Polygonaceae Apidae->Polygonaceae Apidae->Polygonaceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Rosaceae Rosaceae Apidae->Rosaceae Attevidae Attevidae Simaroubaceae Simaroubaceae Attevidae->Simaroubaceae Bombyliidae Bombyliidae Bombyliidae->Asteraceae Bombyliidae->Lamiaceae Bombyliidae->Lamiaceae Buprestidae Buprestidae Cannabaceae Cannabaceae Buprestidae->Cannabaceae Fagaceae Fagaceae Buprestidae->Fagaceae Pinaceae Pinaceae Buprestidae->Pinaceae Ulmaceae Ulmaceae Buprestidae->Ulmaceae Cicadellidae Cicadellidae Cicadellidae->Asteraceae Orobanchaceae Orobanchaceae Cicadellidae->Orobanchaceae Cicadidae Cicadidae Cicadidae->Asteraceae Cixiidae Cixiidae Cixiidae->Asteraceae Coccinellidae Coccinellidae Coccinellidae->Asteraceae Coccinellidae->Asteraceae Coccinellidae->Lamiaceae Coccinellidae->Lamiaceae Conopidae Conopidae Conopidae->Asteraceae Crabronidae Crabronidae Crabronidae->Asteraceae Dermestidae Dermestidae Dermestidae->Asteraceae Doidae Doidae Euphorbiaceae Euphorbiaceae Doidae->Euphorbiaceae Erebidae Erebidae Erebidae->Asteraceae Erebidae->Asteraceae Erebidae->Boraginaceae Erebidae->Polygonaceae Fabaceae Fabaceae Erebidae->Fabaceae Rhamnaceae Rhamnaceae Erebidae->Rhamnaceae Ethmiidae Ethmiidae Hydrophyllaceae Hydrophyllaceae Ethmiidae->Hydrophyllaceae Namaceae Namaceae Ethmiidae->Namaceae Gelechiidae Gelechiidae Gelechiidae->Polygonaceae Gelechiidae->Rosaceae Gelechiidae->Fabaceae Gelechiidae->Fabaceae Geometridae Geometridae Geometridae->Rosaceae Geometridae->Fagaceae Geometridae->Rhamnaceae Anacardiaceae Anacardiaceae Geometridae->Anacardiaceae Salicaceae Salicaceae Geometridae->Salicaceae Halictidae Halictidae Halictidae->Asteraceae Heliodinidae Heliodinidae Nyctaginaceae Nyctaginaceae Heliodinidae->Nyctaginaceae Heliozelidae Heliozelidae Ericaceae Ericaceae Heliozelidae->Ericaceae Hesperiidae Hesperiidae Hesperiidae->Asteraceae Hesperiidae->Lamiaceae Hesperiidae->Lamiaceae Hesperiidae->Plantaginaceae Hesperiidae->Polygonaceae Hesperiidae->Polygonaceae Hesperiidae->Fabaceae Asparagaceae Asparagaceae Hesperiidae->Asparagaceae Hesperiidae->Asparagaceae Lasiocampidae Lasiocampidae Lasiocampidae->Polygonaceae Lasiocampidae->Rosaceae Cupressaceae Cupressaceae Lasiocampidae->Cupressaceae Lycaenidae Lycaenidae Lycaenidae->Asteraceae Lycaenidae->Boraginaceae Lycaenidae->Polygonaceae Lycaenidae->Fabaceae Verbenaceae Verbenaceae Lycaenidae->Verbenaceae Lycaenidae->Verbenaceae Solanaceae Solanaceae Lycaenidae->Solanaceae Viscaceae Viscaceae Lycaenidae->Viscaceae Lygaeidae Lygaeidae Lygaeidae->Asteraceae Megachilidae Megachilidae Megachilidae->Asteraceae Megachilidae->Fabaceae Meloidae Meloidae Meloidae->Asteraceae Miridae Miridae Miridae->Asteraceae Miridae->Asteraceae Miridae->Lamiaceae Miridae->Orobanchaceae Apiaceae Apiaceae Miridae->Apiaceae Muscidae Muscidae Muscidae->Asteraceae Muscidae->Asteraceae Mutillidae Mutillidae Mutillidae->Asteraceae Myrmeleontidae Myrmeleontidae Myrmeleontidae->Asteraceae Noctuidae Noctuidae Noctuidae->Asteraceae Noctuidae->Boraginaceae Noctuidae->Plantaginaceae Noctuidae->Rosaceae Macrothricidae Macrothricidae Noctuidae->Macrothricidae Rutaceae Rutaceae Noctuidae->Rutaceae Notodontidae Notodontidae Notodontidae->Anacardiaceae Nymphalidae Nymphalidae Nymphalidae->Asteraceae Nymphalidae->Boraginaceae Nymphalidae->Plantaginaceae Nymphalidae->Polygonaceae Nymphalidae->Polygonaceae Nymphalidae->Rosaceae Nymphalidae->Fagaceae Nymphalidae->Fabaceae Nymphalidae->Anacardiaceae Nymphalidae->Salicaceae Nymphalidae->Asparagaceae Nymphalidae->Lycaenidae Nymphalidae->Verbenaceae Nymphalidae->Verbenaceae Malvaceae Malvaceae Nymphalidae->Malvaceae Urticaceae Urticaceae Nymphalidae->Urticaceae Varunidae Varunidae Nymphalidae->Varunidae Papilionidae Papilionidae Papilionidae->Rosaceae Papilionidae->Salicaceae Papilionidae->Apiaceae Papilionidae->Rutaceae Aristolochiaceae Aristolochiaceae Papilionidae->Aristolochiaceae Crassulaceae Crassulaceae Papilionidae->Crassulaceae Platanaceae Platanaceae Papilionidae->Platanaceae Pieridae Pieridae Pieridae->Asteraceae Pieridae->Lamiaceae Pieridae->Pinaceae Pieridae->Fabaceae Pieridae->Asparagaceae Brassicaceae Brassicaceae Pieridae->Brassicaceae Polemoniaceae Polemoniaceae Pieridae->Polemoniaceae Piophilidae Piophilidae Piophilidae->Asteraceae Piophilidae->Asteraceae Plutellidae Plutellidae Plutellidae->Fagaceae Pompilidae Pompilidae Pompilidae->Asteraceae Pompilidae->Polygonaceae Pompilidae->Polygonaceae Prodoxidae Prodoxidae Prodoxidae->Asparagaceae Pterophoridae Pterophoridae Pterophoridae->Asteraceae Pterophoridae->Rosaceae Pterophoridae->Namaceae Pyralidae Pyralidae Pyralidae->Apidae Reduviidae Reduviidae Reduviidae->Asteraceae Rhopalidae Rhopalidae Rhopalidae->Asteraceae Riodinidae Riodinidae Riodinidae->Asteraceae Riodinidae->Asteraceae Riodinidae->Polygonaceae Sarcophagidae Sarcophagidae Sarcophagidae->Crassulaceae Sarcophagidae->Crassulaceae Saturniidae Saturniidae Saturniidae->Asteraceae Saturniidae->Polygonaceae Saturniidae->Polygonaceae Saturniidae->Rhamnaceae Saturniidae->Salicaceae Saxifragaceae Saxifragaceae Saxifragaceae->Asteraceae Saxifragaceae->Asteraceae Saxifragaceae->Polygonaceae Saxifragaceae->Polygonaceae Saxifragaceae->Asparagaceae Saxifragaceae->Asparagaceae Saxifragaceae->Apiaceae Saxifragaceae->Apiaceae Saxifragaceae->Crassulaceae Saxifragaceae->Crassulaceae Saxifragaceae->Polemoniaceae Saxifragaceae->Polemoniaceae Campanulaceae Campanulaceae Saxifragaceae->Campanulaceae Saxifragaceae->Campanulaceae Scarabaeidae Scarabaeidae Scarabaeidae->Asteraceae Scarabaeidae->Polygonaceae Scarabaeidae->Polygonaceae Amaranthaceae Amaranthaceae Scarabaeidae->Amaranthaceae Scoliidae Scoliidae Scoliidae->Asteraceae Sesiidae Sesiidae Sesiidae->Boraginaceae Sesiidae->Polygonaceae Sesiidae->Polygonaceae Sesiidae->Cucurbitaceae Sphecidae Sphecidae Sphecidae->Asteraceae Sphingidae Sphingidae Apocynaceae Apocynaceae Sphingidae->Apocynaceae Convolvulaceae Convolvulaceae Sphingidae->Convolvulaceae Staphylinidae Staphylinidae Staphylinidae->Asteraceae Syrphidae Syrphidae Syrphidae->Asteraceae Syrphidae->Asteraceae Syrphidae->Nyctaginaceae Syrphidae->Nyctaginaceae Syrphidae->Asparagaceae Syrphidae->Asparagaceae Tephritidae Tephritidae Tephritidae->Asteraceae Thyreocoridae Thyreocoridae Thyreocoridae->Plantaginaceae Thyreocoridae->Plantaginaceae Tingidae Tingidae Tingidae->Asteraceae Tiphiidae Tiphiidae Tiphiidae->Asteraceae Tortricidae Tortricidae Tortricidae->Asteraceae Tortricidae->Rosaceae Tortricidae->Rosaceae Tortricidae->Fagaceae Tortricidae->Euphorbiaceae Tortricidae->Fabaceae Cactaceae Cactaceae Tortricidae->Cactaceae Vespidae Vespidae Vespidae->Polygonaceae Vespidae->Polygonaceae

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
Abaeis nicippe HAS_ACCEPTED_NAME col Abaeis nicippe
Abaeis nicippe SYNONYM_OF ncbi Eurema nicippe
Abaeis nicippe NONE discoverlife Abaeis nicippe
Abaeis nicippe HAS_ACCEPTED_NAME gbif Abaeis nicippe
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 1091
ncbi species 501
ncbi NA 400
ncbi genus 102
ncbi family 44
ncbi subspecies 25
ncbi subfamily 9
ncbi subgenus 4
ncbi order 4
ncbi tribe 2
ncbi cohort 1
ncbi suborder 1
ncbi superfamily 1
mdd NA 1091
itis species 482
itis NA 402
itis genus 87
itis subspecies 53
itis family 44
itis subfamily 9
itis variety 6
itis order 4
itis phylum 1
itis tribe 1
itis superorder 1
itis kingdom 1
itis suborder 1
itis superfamily 1
globi species 700
globi NA 318
globi genus 194
globi subspecies 76
globi family 54
globi subfamily 16
globi variety 12
globi subgenus 6
globi order 5
globi tribe 3
globi superfamily 2
globi form 1
globi phylum 1
globi superorder 1
globi kingdom 1
globi suborder 1
globi infraorder 1
gbif species 615
gbif NA 266
gbif genus 118
gbif subspecies 49
gbif family 46
gbif variety 7
gbif order 4
gbif kingdom 1
discoverlife NA 1079
discoverlife species 12
col species 549
col NA 357
col genus 107
col family 44
col subspecies 19
col subfamily 8
col order 4
col variety 3
col tribe 2
col infraspecific name 1
col subtribe 1
col subgenus 1
col kingdom 1
col superfamily 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 701
col SYNONYM_OF 80
col NONE 357
discoverlife NONE 1079
discoverlife HAS_ACCEPTED_NAME 11
discoverlife SYNONYM_OF 7
gbif HAS_ACCEPTED_NAME 795
gbif SYNONYM_OF 164
gbif NONE 266
globi SAME_AS 7670
globi NONE 157
itis HAS_ACCEPTED_NAME 660
itis NONE 402
itis SYNONYM_OF 31
mdd NONE 1091
ncbi SYNONYM_OF 40
ncbi SAME_AS 655
ncbi NONE 399
ncbi COMMON_NAME_OF 4
tpt NONE 1091
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
2023-09-28T08:52:22Z note found unsupported interaction type with name: [attacked by]
2023-09-28T08:52:24Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2023-09-28T08:52:24Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2023-09-28T08:52:24Z 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 46
found unsupported interaction type with name: [attacked by] 1
found unsupported interaction type with name: [15] 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.

Discussion

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.

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.

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.