A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/bpbm-ent

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/bpbm-ent/issues

2024-04-29

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/bpbm-ent, is 151MiB in size and contains 26,374 interaction with 3 unique types of associations (e.g., adjacentTo) between 8,288 primary taxon (e.g., Fungi) and 14,722 associated taxon (e.g., rocks). 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:

Bernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology https://github.com/globalbioticinteractions/bpbm-ent/archive/c085398dddd36f8a1169b9cf57de2a572229341b.zip 2024-04-19T23:04:38.943Z 9264ad319d6c8052f783ad98d00a0ea3b0d4731204be42f9e232db02d911714c

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/bpbm-ent 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.  151MiB) under review 
elton pull globalbioticinteractions/bpbm-ent

# generate review notes
elton review globalbioticinteractions/bpbm-ent\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/bpbm-ent\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/bpbm-ent\
 | 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/bpbm-ent, is 151MiB in size and contains 26,374 interaction with 3 unique types of associations (e.g., adjacentTo) between 8,288 primary taxon (e.g., Fungi) and 14,722 associated taxon (e.g., rocks).

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
Portulaca pilosa subsp. pilosa adjacentTo rock wall 704fb80e-c15a-4740-b8cf-0007cb58bb00
Pneophyllum minutula adjacentTo Valonia dac03d2c-b339-4bf3-a451-0007d1720242
Neraudia ovata adjacentTo dry scoria. 6aba83fd-07a5-4b43-b590-000919dfde70
Morinda latibractea adjacentTo islet cliffs 3bc0f2b6-75b2-43f9-8f17-000b77fd5c55
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
adjacentTo 25094
interactsWith 1139
hasHost 141
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Fungi 320
Bryophyta 174
Korthalsella complanata 149
Padina 110
Halimeda opuntia 100
Gracilaria salicornia 92
Lepisorus thunbergianus 81
Sargassum 80
Turbinaria ornata 79
Hydroclathrus clathratus 72
Pandanus tectorius 71
Cassytha filiformis 71
Psilotum complanatum 60
Polypodium pellucidum 59
Lobophora variegata 58
Asplenium nidus 58
Psilotum nudum 57
Dictyota 57
Sida fallax 55
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
rocks 359
rocks. 237
ground 180
tree trunk 178
trees 176
rocks in the subtidal zone. 137
dead coral rock. 135
tree 128
Metrosideros 125
reef 112
rock 105
tree trunks 90
mossy tree trunk 88
ridge 81
shaded 73
shrub 72
coral 60
rocks in the lower tidal zone. 59
aa 56
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Bryophyta adjacentTo shrub 65
Turbinaria ornata adjacentTo reef. 27
Coccodiella nuda hasHost Cibotium chamissoi 19
Padina adjacentTo reef 18
Bryophyta adjacentTo branch of tree 16
Sargassaceae adjacentTo granitic rock. 15
Korthalsella complanata adjacentTo Acacia koa 14
Stypopodium adjacentTo reef 13
Lyngbya adjacentTo volcanic rocks 11
Pteris warburghii adjacentTo streambed. 11
Fungi adjacentTo leaves. 11
Korthalsella remyana adjacentTo Metrosideros 10
Gracilariopsis longissima adjacentTo rocks in sand. 10
Ulva compressa adjacentTo coral in shallow water 10
Halimeda opuntia interactsWith reef with sandy-muddy substratum near shore to sandy-rocky at the reef edge. 10
Metrosideros polymorpha var. incana adjacentTo aa lava flow. 10
Joinvillea plicata adjacentTo bank above small stream 10
Hepaticae adjacentTo lichen 9
Sarcothalia papillosa adjacentTo rocks 9

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 Plantae Plantae Animalia->Plantae Plantae->Animalia Plantae->Animalia Plantae->Plantae Plantae->Plantae Chromista Chromista Plantae->Chromista Bacteria Bacteria Bacteria->Plantae Bacteria->Bacteria Bacteria->Chromista Chromista->Plantae Chromista->Chromista Fungi Fungi Fungi->Plantae Fungi->Plantae
interactions Acrochaetiaceae Acrochaetiaceae Cladophoraceae Cladophoraceae Acrochaetiaceae->Cladophoraceae Liagoraceae Liagoraceae Acrochaetiaceae->Liagoraceae Sargassaceae Sargassaceae Acrochaetiaceae->Sargassaceae Adelanthaceae Adelanthaceae Hydrangeaceae Hydrangeaceae Adelanthaceae->Hydrangeaceae Myrtaceae Myrtaceae Adelanthaceae->Myrtaceae Pinaceae Pinaceae Hydrangeaceae->Pinaceae Amphorogynaceae Amphorogynaceae Amphorogynaceae->Myrtaceae Annonaceae Annonaceae Sapindaceae Sapindaceae Annonaceae->Sapindaceae Poaceae Poaceae Sapindaceae->Poaceae Apocynaceae Apocynaceae Combretaceae Combretaceae Apocynaceae->Combretaceae Cupressaceae Cupressaceae Apocynaceae->Cupressaceae Moraceae Moraceae Apocynaceae->Moraceae Orchidaceae Orchidaceae Combretaceae->Orchidaceae Meliaceae Meliaceae Moraceae->Meliaceae Sapotaceae Sapotaceae Moraceae->Sapotaceae Aquifoliaceae Aquifoliaceae Aquifoliaceae->Myrtaceae Aristolochiaceae Aristolochiaceae Euphorbiaceae Euphorbiaceae Aristolochiaceae->Euphorbiaceae Aspleniaceae Aspleniaceae Cycadaceae Cycadaceae Aspleniaceae->Cycadaceae Nyctaginaceae Nyctaginaceae Aspleniaceae->Nyctaginaceae Pandanaceae Pandanaceae Aspleniaceae->Pandanaceae Asteliaceae Asteliaceae Asteliaceae->Myrtaceae Asterinaceae Asterinaceae Asterinaceae->Nyctaginaceae Ebenaceae Ebenaceae Asterinaceae->Ebenaceae Athyriaceae Athyriaceae Athyriaceae->Aquifoliaceae Blenniidae Blenniidae Agariciidae Agariciidae Blenniidae->Agariciidae Brachytheciaceae Brachytheciaceae Brachytheciaceae->Nyctaginaceae Bromeliaceae Bromeliaceae Betulaceae Betulaceae Bromeliaceae->Betulaceae Teiidae Teiidae Bromeliaceae->Teiidae Bryaceae Bryaceae Cibotiaceae Cibotiaceae Bryaceae->Cibotiaceae Cactaceae Cactaceae Asteraceae Asteraceae Cactaceae->Asteraceae Goodeniaceae Goodeniaceae Cactaceae->Goodeniaceae Lindsaeaceae Lindsaeaceae Cactaceae->Lindsaeaceae Lythraceae Lythraceae Cactaceae->Lythraceae Rubiaceae Rubiaceae Cactaceae->Rubiaceae Verbenaceae Verbenaceae Cactaceae->Verbenaceae Rubiaceae->Rubiaceae Rhizophoraceae Rhizophoraceae Rubiaceae->Rhizophoraceae Caliciaceae Caliciaceae Caliciaceae->Pandanaceae Fabaceae Fabaceae Caliciaceae->Fabaceae Fabaceae->Myrtaceae Fabaceae->Rhizophoraceae Samoidae Samoidae Fabaceae->Samoidae Callithamniaceae Callithamniaceae Codiaceae Codiaceae Callithamniaceae->Codiaceae Calymperaceae Calymperaceae Calymperaceae->Myrtaceae Calymperaceae->Combretaceae Calymperaceae->Moraceae Calymperaceae->Cibotiaceae Asparagaceae Asparagaceae Calymperaceae->Asparagaceae Rosaceae Rosaceae Calymperaceae->Rosaceae Santalaceae Santalaceae Calymperaceae->Santalaceae Calypogeiaceae Calypogeiaceae Araucariaceae Araucariaceae Calypogeiaceae->Araucariaceae Campanulaceae Campanulaceae Campanulaceae->Myrtaceae Campanulaceae->Cibotiaceae Blechnaceae Blechnaceae Campanulaceae->Blechnaceae Capnodiaceae Capnodiaceae Anacardiaceae Anacardiaceae Capnodiaceae->Anacardiaceae Carapidae Carapidae Oreasteridae Oreasteridae Carapidae->Oreasteridae Ceramiaceae Ceramiaceae Zosteraceae Zosteraceae Ceramiaceae->Zosteraceae Chordariaceae Chordariaceae Fucaceae Fucaceae Chordariaceae->Fucaceae Cirrhitidae Cirrhitidae Pocilloporidae Pocilloporidae Cirrhitidae->Pocilloporidae Coccodiniaceae Coccodiniaceae Coccodiniaceae->Rubiaceae Collemataceae Collemataceae Collemataceae->Myrtaceae Collemataceae->Pandanaceae Orchidaceae->Myrtaceae Orchidaceae->Apocynaceae Orchidaceae->Aquifoliaceae Orchidaceae->Rubiaceae Orchidaceae->Fabaceae Malvaceae Malvaceae Orchidaceae->Malvaceae Phyllanthaceae Phyllanthaceae Orchidaceae->Phyllanthaceae Gentianaceae Gentianaceae Orchidaceae->Gentianaceae Calophyllaceae Calophyllaceae Orchidaceae->Calophyllaceae Cunoniaceae Cunoniaceae Orchidaceae->Cunoniaceae Nothofagaceae Nothofagaceae Orchidaceae->Nothofagaceae Rutaceae Rutaceae Orchidaceae->Rutaceae Salicaceae Salicaceae Orchidaceae->Salicaceae Convolvulaceae Convolvulaceae Convolvulaceae->Asteraceae Acanthaceae Acanthaceae Convolvulaceae->Acanthaceae Heliotropiaceae Heliotropiaceae Convolvulaceae->Heliotropiaceae Not assigned Not assigned Convolvulaceae->Not assigned Urticaceae Urticaceae Convolvulaceae->Urticaceae Urticaceae->Phyllanthaceae Solanaceae Solanaceae Urticaceae->Solanaceae Corallinaceae Corallinaceae Porolithaceae Porolithaceae Corallinaceae->Porolithaceae Crepidotaceae Crepidotaceae Crepidotaceae->Malvaceae Cucurbitaceae Cucurbitaceae Cucurbitaceae->Apocynaceae Cucurbitaceae->Verbenaceae Cucurbitaceae->Fabaceae Daltoniaceae Daltoniaceae Daltoniaceae->Hydrangeaceae Daltoniaceae->Myrtaceae Davalliaceae Davalliaceae Davalliaceae->Myrtaceae Davalliaceae->Apocynaceae Davalliaceae->Aquifoliaceae Cyatheaceae Cyatheaceae Davalliaceae->Cyatheaceae Delesseriaceae Delesseriaceae Halimedaceae Halimedaceae Delesseriaceae->Halimedaceae Dermocarpaceae Dermocarpaceae Gigartinaceae Gigartinaceae Dermocarpaceae->Gigartinaceae Dicranaceae Dicranaceae Dicranaceae->Fabaceae Dicranellaceae Dicranellaceae Dicranellaceae->Cibotiaceae Dictyotaceae Dictyotaceae Dictyotaceae->Halimedaceae Dryopteridaceae Dryopteridaceae Dryopteridaceae->Myrtaceae Dryopteridaceae->Nyctaginaceae Dryopteridaceae->Ebenaceae Dryopteridaceae->Fabaceae Dryopteridaceae->Cyatheaceae Araliaceae Araliaceae Dryopteridaceae->Araliaceae Dipentodontaceae Dipentodontaceae Dryopteridaceae->Dipentodontaceae Ectocarpaceae Ectocarpaceae Galaxauraceae Galaxauraceae Ectocarpaceae->Galaxauraceae Entophysalidaceae Entophysalidaceae Oscillatoriaceae Oscillatoriaceae Entophysalidaceae->Oscillatoriaceae Ericaceae Ericaceae Ericaceae->Myrtaceae Frullaniaceae Frullaniaceae Frullaniaceae->Myrtaceae Frullaniaceae->Pandanaceae Frullaniaceae->Rubiaceae Frullaniaceae->Asparagaceae Frullaniaceae->Phyllanthaceae Scrophulariaceae Scrophulariaceae Frullaniaceae->Scrophulariaceae Gesneriaceae Gesneriaceae Gesneriaceae->Ericaceae Gobiidae Gobiidae Gobiidae->Halimedaceae Antipathidae Antipathidae Gobiidae->Antipathidae Thorectidae Thorectidae Gobiidae->Thorectidae Acroporidae Acroporidae Gobiidae->Acroporidae Graphidaceae Graphidaceae Graphidaceae->Aquifoliaceae Hymenochaetaceae Hymenochaetaceae Hymenochaetaceae->Myrtaceae Hymenophyllaceae Hymenophyllaceae Hymenophyllaceae->Myrtaceae Hymenophyllaceae->Pandanaceae Hymenophyllaceae->Cyatheaceae Hymenophyllaceae->Araliaceae Hymenophyllaceae->Phyllanthaceae Hymenophyllaceae->Gentianaceae Hysteriaceae Hysteriaceae Hysteriaceae->Cupressaceae Lamiaceae Lamiaceae Lamiaceae->Myrtaceae Lamiaceae->Asteraceae Lamiaceae->Araliaceae Lamiaceae->Ericaceae Lejeuneaceae Lejeuneaceae Lejeuneaceae->Myrtaceae Lejeuneaceae->Rubiaceae Lejeuneaceae->Asparagaceae Lejeuneaceae->Anacardiaceae Lejeuneaceae->Malvaceae Lejeuneaceae->Gesneriaceae Polypodiaceae Polypodiaceae Lejeuneaceae->Polypodiaceae Polypodiaceae->Myrtaceae Polypodiaceae->Apocynaceae Polypodiaceae->Cupressaceae Polypodiaceae->Moraceae Polypodiaceae->Aquifoliaceae Polypodiaceae->Pandanaceae Polypodiaceae->Rubiaceae Polypodiaceae->Fabaceae Polypodiaceae->Asparagaceae Polypodiaceae->Malvaceae Polypodiaceae->Araliaceae Polypodiaceae->Cunoniaceae Cordiaceae Cordiaceae Polypodiaceae->Cordiaceae Melastomataceae Melastomataceae Polypodiaceae->Melastomataceae Lembophyllaceae Lembophyllaceae Lembophyllaceae->Myrtaceae Lembosinaceae Lembosinaceae Menispermaceae Menispermaceae Lembosinaceae->Menispermaceae Menispermaceae->Verbenaceae Lepidoziaceae Lepidoziaceae Lepidoziaceae->Myrtaceae Lepidoziaceae->Cupressaceae Lepidoziaceae->Aquifoliaceae Leucobryaceae Leucobryaceae Leucobryaceae->Myrtaceae Primulaceae Primulaceae Leucobryaceae->Primulaceae Primulaceae->Myrtaceae Primulaceae->Rubiaceae Lophocoleaceae Lophocoleaceae Lophocoleaceae->Araliaceae Loranthaceae Loranthaceae Loranthaceae->Myrtaceae Loranthaceae->Euphorbiaceae Lycopodiaceae Lycopodiaceae Lycopodiaceae->Myrtaceae Lycopodiaceae->Fabaceae Lycopodiaceae->Malvaceae Lycopodiaceae->Cyatheaceae Lycopodiaceae->Araliaceae Lycopodiaceae->Dipentodontaceae Megalosporaceae Megalosporaceae Megalosporaceae->Myrtaceae Megalosporaceae->Rubiaceae Meliolaceae Meliolaceae Theaceae Theaceae Meliolaceae->Theaceae Meliolinaceae Meliolinaceae Meliolinaceae->Myrtaceae Meteoriaceae Meteoriaceae Meteoriaceae->Myrtaceae Meteoriaceae->Rubiaceae Meteoriaceae->Verbenaceae Microthyriaceae Microthyriaceae Thymelaeaceae Thymelaeaceae Microthyriaceae->Thymelaeaceae Mystropetalaceae Mystropetalaceae Griseliniaceae Griseliniaceae Mystropetalaceae->Griseliniaceae Neckeraceae Neckeraceae Neckeraceae->Myrtaceae Neckeraceae->Rubiaceae Nephrolepidaceae Nephrolepidaceae Nephrolepidaceae->Myrtaceae Nephrolepidaceae->Ebenaceae Nephrolepidaceae->Fabaceae Octoblepharaceae Octoblepharaceae Octoblepharaceae->Moraceae Octoblepharaceae->Pandanaceae Onagraceae Onagraceae Onagraceae->Blechnaceae Ophioglossaceae Ophioglossaceae Ophioglossaceae->Cibotiaceae Ophioglossaceae->Asparagaceae Orthotrichaceae Orthotrichaceae Orthotrichaceae->Myrtaceae Orthotrichaceae->Euphorbiaceae Orthotrichaceae->Pandanaceae Orthotrichaceae->Rubiaceae Orthotrichaceae->Fabaceae Orthotrichaceae->Asparagaceae Orthotrichaceae->Ericaceae Elaeocarpaceae Elaeocarpaceae Orthotrichaceae->Elaeocarpaceae Lauraceae Lauraceae Orthotrichaceae->Lauraceae Parmeliaceae Parmeliaceae Parmeliaceae->Euphorbiaceae Parmeliaceae->Pandanaceae Parmeliaceae->Primulaceae Fagaceae Fagaceae Parmeliaceae->Fagaceae Peltigeraceae Peltigeraceae Peltigeraceae->Ericaceae Peyssonneliaceae Peyssonneliaceae Peyssonneliaceae->Halimedaceae Phyllachoraceae Phyllachoraceae Phyllachoraceae->Cibotiaceae Physciaceae Physciaceae Physciaceae->Moraceae Physciaceae->Nyctaginaceae Physciaceae->Fabaceae Piperaceae Piperaceae Piperaceae->Myrtaceae Piperaceae->Apocynaceae Piperaceae->Moraceae Piperaceae->Aquifoliaceae Piperaceae->Fabaceae Piperaceae->Malvaceae Piperaceae->Cyatheaceae Piperaceae->Araliaceae Piperaceae->Phyllanthaceae Piperaceae->Gentianaceae Podocarpaceae Podocarpaceae Piperaceae->Podocarpaceae Plagiochilaceae Plagiochilaceae Plagiochilaceae->Aquifoliaceae Plagiochilaceae->Rubiaceae Pleuroziaceae Pleuroziaceae Pleuroziaceae->Fabaceae Phyllocladaceae Phyllocladaceae Pleuroziaceae->Phyllocladaceae Pluteaceae Pluteaceae Pluteaceae->Urticaceae Polystomellaceae Polystomellaceae Polystomellaceae->Rubiaceae Porellaceae Porellaceae Porellaceae->Fagaceae Pottiaceae Pottiaceae Pottiaceae->Ericaceae Psilotaceae Psilotaceae Psilotaceae->Myrtaceae Psilotaceae->Cibotiaceae Psilotaceae->Araliaceae Psilotaceae->Dipentodontaceae Pteridaceae Pteridaceae Pteridaceae->Myrtaceae Pteridaceae->Nyctaginaceae Pteridaceae->Rubiaceae Pteridaceae->Fabaceae Pteridaceae->Malvaceae Pteridaceae->Melastomataceae Asilidae Asilidae Pteridaceae->Asilidae Dipterocarpaceae Dipterocarpaceae Pteridaceae->Dipterocarpaceae Pucciniastraceae Pucciniastraceae Pucciniastraceae->Ericaceae Pyrenulaceae Pyrenulaceae Pyrenulaceae->Rubiaceae Racopilaceae Racopilaceae Racopilaceae->Pandanaceae Ramalinaceae Ramalinaceae Ramalinaceae->Myrtaceae Ramalinaceae->Fabaceae Arecaceae Arecaceae Ramalinaceae->Arecaceae Casuarinaceae Casuarinaceae Ramalinaceae->Casuarinaceae Rhodomelaceae Rhodomelaceae Rhodomelaceae->Ceramiaceae Rhodomelaceae->Dictyotaceae Rivulariaceae Rivulariaceae Rivulariaceae->Chordariaceae Cystocloniaceae Cystocloniaceae Rivulariaceae->Cystocloniaceae Hormosiraceae Hormosiraceae Rivulariaceae->Hormosiraceae Nemaliaceae Nemaliaceae Rivulariaceae->Nemaliaceae Saccotheciaceae Saccotheciaceae Saccotheciaceae->Myrtaceae Schizothyriaceae Schizothyriaceae Schizothyriaceae->Malvaceae Scytonemataceae Scytonemataceae Scytonemataceae->Fabaceae Scytonemataceae->Galaxauraceae Sematophyllaceae Sematophyllaceae Sematophyllaceae->Euphorbiaceae Sematophyllaceae->Pandanaceae Sematophyllaceae->Cibotiaceae Proteaceae Proteaceae Sematophyllaceae->Proteaceae Seynesiopeltidaceae Seynesiopeltidaceae Seynesiopeltidaceae->Araliaceae Smilacaceae Smilacaceae Smilacaceae->Myrtaceae Smilacaceae->Araliaceae Smilacaceae->Scrophulariaceae Smilacaceae->Primulaceae Smilacaceae->Theaceae Stereaceae Stereaceae Stereaceae->Betulaceae Stereaceae->Fagaceae Teloschistaceae Teloschistaceae Teloschistaceae->Fabaceae Trichothyriaceae Trichothyriaceae Trichothyriaceae->Apocynaceae Trypetheliaceae Trypetheliaceae Trypetheliaceae->Primulaceae Viscaceae Viscaceae Viscaceae->Myrtaceae Viscaceae->Sapindaceae Viscaceae->Apocynaceae Viscaceae->Aquifoliaceae Viscaceae->Euphorbiaceae Viscaceae->Ebenaceae Viscaceae->Rubiaceae Viscaceae->Fabaceae Viscaceae->Campanulaceae Viscaceae->Araliaceae Viscaceae->Ericaceae Viscaceae->Phyllanthaceae Viscaceae->Gesneriaceae Viscaceae->Primulaceae Viscaceae->Elaeocarpaceae Viscaceae->Solanaceae Bovidae Bovidae Viscaceae->Bovidae Oleaceae Oleaceae Viscaceae->Oleaceae

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
Rock NONE col Rock
ft vertical rocks NONE col ft vertical rocks
ft flat rocks covered Odonthalia or more usually Rhodomela NONE col ft flat rocks covered Odonthalia or more usually Rhodomela
Boulders NONE col Boulders
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 15017
col class 7
col family 81
col genus 988
col gigaclass 1
col kingdom 2
col order 2
col phylum 9
col section 1
col species 4923
col subfamily 3
col subgenus 1
col subkingdom 1
col subspecies 98
col tribe 1
col variety 49
discoverlife NA 21130
gbif NA 13550
gbif class 8
gbif family 88
gbif form 5
gbif genus 1012
gbif kingdom 2
gbif order 2
gbif phylum 10
gbif species 6256
gbif subspecies 118
gbif variety 188
itis NA 17227
itis class 6
itis division 7
itis family 84
itis genus 700
itis infrakingdom 1
itis kingdom 2
itis order 3
itis phylum 4
itis species 2994
itis subclass 1
itis subkingdom 1
itis subspecies 81
itis superclass 1
itis variety 23
mdd NA 21129
ncbi NA 15626
ncbi clade 3
ncbi class 6
ncbi family 79
ncbi forma 1
ncbi genus 939
ncbi kingdom 1
ncbi order 3
ncbi phylum 9
ncbi section 2
ncbi series 1
ncbi species 4437
ncbi subgenus 6
ncbi subspecies 12
ncbi superclass 1
ncbi varietas 9
pbdb NA 20595
pbdb class 9
pbdb family 71
pbdb genus 377
pbdb informal 1
pbdb kingdom 2
pbdb order 2
pbdb phylum 9
pbdb species 60
pbdb subclass 1
pbdb superclass 1
pbdb superphylum 1
pbdb tribe 1
pbdb unranked clade 5
tpt NA 21122
tpt genus 5
tpt species 2
wfo NA 16142
wfo family 60
wfo form 3
wfo genus 627
wfo order 1
wfo phylum 1
wfo section 1
wfo species 4223
wfo subspecies 45
wfo variety 43
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 16484
col HAS_ACCEPTED_NAME 5262
col SYNONYM_OF 2171
discoverlife NONE 23010
gbif NONE 14964
gbif HAS_ACCEPTED_NAME 7483
gbif SYNONYM_OF 3534
itis NONE 18673
itis HAS_ACCEPTED_NAME 4003
itis SYNONYM_OF 481
mdd NONE 22968
ncbi NONE 17100
ncbi SAME_AS 5353
ncbi SYNONYM_OF 629
ncbi COMMON_NAME_OF 9
pbdb NONE 22223
pbdb HAS_ACCEPTED_NAME 761
pbdb SYNONYM_OF 54
tpt NONE 22959
tpt HAS_ACCEPTED_NAME 9
wfo NONE 17701
wfo HAS_ACCEPTED_NAME 4174
wfo SYNONYM_OF 1258
wfo HAS_UNCHECKED_NAME 299
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
2024-04-28T23:44:42Z note found unsupported interaction type with name: [associates]
2024-04-28T23:44:42Z note found unsupported interaction type with name: [associates]
2024-04-28T23:44:42Z note found unsupported interaction type with name: [WNW aspect. Red-brown clay loam on basalt. Low closed foest]
2024-04-28T23:44:42Z note found unsupported interaction type with name: [WNW aspect. Red-brown clay loam on basalt. Low closed foest]

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: [Vegetation] 1708
found unsupported interaction type with name: [associates include] 503
found unsupported interaction type with name: [Associated vegetation] 375
found unsupported interaction type with name: [Common plants] 208

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 (2024-04-29) 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.