A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/yale-peabody

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/yale-peabody/issues

2024-11-18

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/yale-peabody, is 457MiB in size and contains 281,386 interaction with 9 unique types of associations (e.g., adjacentTo) between 8,002 primary taxon (e.g., undet. Foraminiferida) and 139,000 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:

Botany Division, Yale Peabody Museum - Version 396.3157 http://ipt.peabody.yale.edu/archive.do?r=ypm-bot 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Entomology Division, Yale Peabody Museum - Version 395.3063 http://ipt.peabody.yale.edu/archive.do?r=ypm-ent 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Invertebrate Paleontology Division, Yale Peabody Museum - Version 395.3095 http://ipt.peabody.yale.edu/archive.do?r=ypm-ip 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Invertebrate Zoology Division, Yale Peabody Museum - Version 395.3162 http://ipt.peabody.yale.edu/archive.do?r=ypm-iz 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Paleobotany Division, Yale Peabody Museum - Version 395.3140 http://ipt.peabody.yale.edu/archive.do?r=ypm-pb 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Vertebrate Paleontology Division, Yale Peabody Museum - Version 395.3162 http://ipt.peabody.yale.edu/archive.do?r=ypm-vp 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Vertebrate Zoology Division - Herpetology, Yale Peabody Museum - Version 395.3126 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-her 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Vertebrate Zoology Division - Ichthyology, Yale Peabody Museum - Version 395.3080 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-ich 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Vertebrate Zoology Division - Mammalogy, Yale Peabody Museum - Version 397.3137 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-mam 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb Vertebrate Zoology Division - Ornithology, Yale Peabody Museum - Version 395.3111 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-orn 2024-11-16T19:16:48.851Z 7bde287a1fbb7bd2f487a506b9059a9f3bf6da9281cef0f5c033cb3d0f5a63eb

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/yale-peabody 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 0.13.9
nomer 0.5.13
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.  457MiB) under review 
elton pull globalbioticinteractions/yale-peabody

# generate review notes
elton review globalbioticinteractions/yale-peabody\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/yale-peabody\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/yale-peabody\
 | 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/yale-peabody, is 457MiB in size and contains 281,386 interaction with 9 unique types of associations (e.g., adjacentTo) between 8,002 primary taxon (e.g., undet. Foraminiferida) and 139,000 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
Aegithalos caudatus macedonicus interactsWith ORN.113916 http://collections.peabody.yale.edu/search/Record/YPM-ORN-065637
Erithacus rubecula rubecula interactsWith ORN.140511.001 http://collections.peabody.yale.edu/search/Record/YPM-ORN-140507.001
Molothrus ater ater hasHost ORN.142308 http://collections.peabody.yale.edu/search/Record/YPM-ORN-142309
Doricha enicura interactsWith ORN.142510.001 http://collections.peabody.yale.edu/search/Record/YPM-ORN-142516
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
adjacentTo 153485
interactsWith 125907
hasHost 1726
hasParasite 384
symbiontOf 50
preysOn 12
visits 7
preyedUponBy 7
eats 3
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
undet. Foraminiferida 22854
Limopsis striatopunctatus 20122
undet. Bivalvia 16736
undet. Mollusca 13874
undet. Rugoglobigerinidae 5778
Protocardia sp. 4603
Hoploscaphites sp. 4431
Diptera 4399
undet. Rotaliida 4256
Protocardia subquadrata 4165
taxon undetermined 3976
Insecta 3611
Bivalvia 3415
undet. Conchostraca 3145
undet. Scaphitidae 2882
Hexapoda 2836
undet. Ammonoidea 2767
Coleoptera 2563
Foraminiferida 2427
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
rocks 1435
same original lot: IP.004851 1158
same slab: IP.850994 774
same slab: IP.076166 713
same slide: IP.856874 704
same slide: IP.856866 654
same slide: IP.856867 635
trees 635
same slide: IP.856873 631
same slide: IP.856871 612
same slab: IP.351960 599
same slide: IP.856872 553
same slab: IP.392287 540
same slide: IP.856903 514
IP.856879 509
same slide: IP.856868 468
same slide: IP.856404 448
same slab: IP.903600 440
same slide: IP.856906 427
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Limopsis striatopunctatus adjacentTo same slab: IP.850994 769
undet. Foraminiferida adjacentTo same slide: IP.856866 653
undet. Foraminiferida adjacentTo same slide: IP.856867 634
undet. Foraminiferida adjacentTo same slide: IP.856871 611
Corbulamella gregaria adjacentTo same slab: IP.076166 601
undet. Foraminiferida adjacentTo same slide: IP.856868 467
undet. Foraminiferida interactsWith IP.856879 411
undet. Rotaliida interactsWith same original lot: IP.004851 389
undet. Foraminiferida adjacentTo same slide: IP.238722 389
undet. Foraminiferida interactsWith same original lot: IP.004851 371
Strophodonta sp. interactsWith same original lot: IP.558034 349
undet. Mollusca adjacentTo same slab: IP.316125 343
undet. Foraminiferida adjacentTo same slide: IP.856388 339
Protocardia subquadrata adjacentTo same slab: IP.392287 332
Protocardia sp. adjacentTo same slab: IP.391866 318
undet. Serpulidae adjacentTo same slab: IP.591512 317
Protocardia sp. adjacentTo same slab: IP.595261 298
undet. Foraminiferida adjacentTo same slide: IP.238721 297
Limopsis striatopunctatus adjacentTo same slab: IP.852383 295

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 Plantae Plantae Animalia->Plantae Plantae->Animalia Plantae->Plantae Fungi Fungi Fungi->Animalia Fungi->Plantae Fungi->Fungi
interactions Aneuraceae Aneuraceae Labridae Labridae Aneuraceae->Labridae Antitrichiaceae Antitrichiaceae Sapindaceae Sapindaceae Antitrichiaceae->Sapindaceae Arthoniaceae Arthoniaceae Arthoniaceae->Sapindaceae Anacardiaceae Anacardiaceae Arthoniaceae->Anacardiaceae Aquifoliaceae Aquifoliaceae Arthoniaceae->Aquifoliaceae Juglandaceae Juglandaceae Arthoniaceae->Juglandaceae Lauraceae Lauraceae Arthoniaceae->Lauraceae Nyssaceae Nyssaceae Arthoniaceae->Nyssaceae Ulmaceae Ulmaceae Arthoniaceae->Ulmaceae Brachytheciaceae Brachytheciaceae Brachytheciaceae->Sapindaceae Fagaceae Fagaceae Brachytheciaceae->Fagaceae Brigantiaeaceae Brigantiaeaceae Magnoliaceae Magnoliaceae Brigantiaeaceae->Magnoliaceae Caliciaceae Caliciaceae Caliciaceae->Sapindaceae Caliciaceae->Fagaceae Betulaceae Betulaceae Caliciaceae->Betulaceae Pinaceae Pinaceae Caliciaceae->Pinaceae Cephaloziaceae Cephaloziaceae Pelliaceae Pelliaceae Cephaloziaceae->Pelliaceae Cephaloziellaceae Cephaloziellaceae Cephaloziellaceae->Labridae Coccocarpiaceae Coccocarpiaceae Coccocarpiaceae->Magnoliaceae Collemataceae Collemataceae Burseraceae Burseraceae Collemataceae->Burseraceae Cupressaceae Cupressaceae Collemataceae->Cupressaceae Moraceae Moraceae Collemataceae->Moraceae Crambidae Crambidae Poaceae Poaceae Crambidae->Poaceae Dacampiaceae Dacampiaceae Salicaceae Salicaceae Dacampiaceae->Salicaceae Erebidae Erebidae Rosaceae Rosaceae Erebidae->Rosaceae Erpodiaceae Erpodiaceae Cactaceae Cactaceae Erpodiaceae->Cactaceae Ethmiidae Ethmiidae Asparagaceae Asparagaceae Ethmiidae->Asparagaceae Frullaniaceae Frullaniaceae Frullaniaceae->Sapindaceae Frullaniaceae->Aquifoliaceae Frullaniaceae->Nyssaceae Frullaniaceae->Fagaceae Frullaniaceae->Magnoliaceae Frullaniaceae->Betulaceae Frullaniaceae->Cupressaceae Frullaniaceae->Salicaceae Frullaniaceae->Rosaceae Cannabaceae Cannabaceae Frullaniaceae->Cannabaceae Cornaceae Cornaceae Frullaniaceae->Cornaceae Malvaceae Malvaceae Frullaniaceae->Malvaceae Pandanaceae Pandanaceae Frullaniaceae->Pandanaceae Graphidaceae Graphidaceae Graphidaceae->Sapindaceae Graphidaceae->Magnoliaceae Graphidaceae->Betulaceae Bovidae Bovidae Graphidaceae->Bovidae Cladoniaceae Cladoniaceae Graphidaceae->Cladoniaceae Fabaceae Fabaceae Graphidaceae->Fabaceae Haematommataceae Haematommataceae Meliaceae Meliaceae Haematommataceae->Meliaceae Lecanoraceae Lecanoraceae Lecanoraceae->Nyssaceae Lecanoraceae->Fagaceae Lecanoraceae->Pinaceae Lecanoraceae->Cupressaceae Lecanoraceae->Malvaceae Lejeuneaceae Lejeuneaceae Lejeuneaceae->Anacardiaceae Lejeuneaceae->Aquifoliaceae Lejeuneaceae->Lauraceae Lejeuneaceae->Nyssaceae Lejeuneaceae->Fagaceae Lejeuneaceae->Magnoliaceae Lejeuneaceae->Betulaceae Lejeuneaceae->Cupressaceae Lejeuneaceae->Pandanaceae Lejeuneaceae->Fabaceae Arecaceae Arecaceae Lejeuneaceae->Arecaceae Dryopteridaceae Dryopteridaceae Lejeuneaceae->Dryopteridaceae Ericaceae Ericaceae Lejeuneaceae->Ericaceae Euphorbiaceae Euphorbiaceae Lejeuneaceae->Euphorbiaceae Hymenophyllaceae Hymenophyllaceae Lejeuneaceae->Hymenophyllaceae Myricaceae Myricaceae Lejeuneaceae->Myricaceae Myrtaceae Myrtaceae Lejeuneaceae->Myrtaceae Orchidaceae Orchidaceae Lejeuneaceae->Orchidaceae Primulaceae Primulaceae Lejeuneaceae->Primulaceae Rhizophoraceae Rhizophoraceae Lejeuneaceae->Rhizophoraceae Rubiaceae Rubiaceae Lejeuneaceae->Rubiaceae Urticaceae Urticaceae Lejeuneaceae->Urticaceae Leucodontaceae Leucodontaceae Leucodontaceae->Magnoliaceae Leucodontaceae->Cupressaceae Limoniidae Limoniidae Limoniidae->Fagaceae Lobariaceae Lobariaceae Lobariaceae->Sapindaceae Lobariaceae->Ulmaceae Lobariaceae->Fagaceae Lobariaceae->Magnoliaceae Oleaceae Oleaceae Lobariaceae->Oleaceae Metzgeriaceae Metzgeriaceae Metzgeriaceae->Sapindaceae Metzgeriaceae->Magnoliaceae Metzgeriaceae->Betulaceae Microcaliciaceae Microcaliciaceae Psilolechiaceae Psilolechiaceae Microcaliciaceae->Psilolechiaceae Mycocaliciaceae Mycocaliciaceae Mycocaliciaceae->Anacardiaceae Hymenochaetaceae Hymenochaetaceae Mycocaliciaceae->Hymenochaetaceae Polyporaceae Polyporaceae Mycocaliciaceae->Polyporaceae Naetrocymbaceae Naetrocymbaceae Naetrocymbaceae->Betulaceae Neckeraceae Neckeraceae Neckeraceae->Sapindaceae Neckeraceae->Fagaceae Neckeraceae->Cupressaceae Neckeraceae->Oleaceae Nephromataceae Nephromataceae Garryaceae Garryaceae Nephromataceae->Garryaceae Orthotrichaceae Orthotrichaceae Orthotrichaceae->Sapindaceae Orthotrichaceae->Magnoliaceae Orthotrichaceae->Salicaceae Pannariaceae Pannariaceae Pannariaceae->Fagaceae Parmeliaceae Parmeliaceae Parmeliaceae->Sapindaceae Parmeliaceae->Ulmaceae Parmeliaceae->Fagaceae Parmeliaceae->Magnoliaceae Parmeliaceae->Betulaceae Parmeliaceae->Pinaceae Parmeliaceae->Cupressaceae Parmeliaceae->Salicaceae Parmeliaceae->Rosaceae Parmeliaceae->Fabaceae Parmeliaceae->Meliaceae Parmeliaceae->Ericaceae Platanaceae Platanaceae Parmeliaceae->Platanaceae Pertusariaceae Pertusariaceae Pertusariaceae->Sapindaceae Pertusariaceae->Magnoliaceae Pertusariaceae->Pinaceae Pertusariaceae->Malvaceae Physciaceae Physciaceae Physciaceae->Sapindaceae Physciaceae->Juglandaceae Physciaceae->Ulmaceae Physciaceae->Fagaceae Physciaceae->Betulaceae Plagiochilaceae Plagiochilaceae Plagiochilaceae->Magnoliaceae Plagiotheciaceae Plagiotheciaceae Plagiotheciaceae->Betulaceae Porellaceae Porellaceae Porellaceae->Nyssaceae Porellaceae->Magnoliaceae Porellaceae->Betulaceae Porellaceae->Ericaceae Pottiaceae Pottiaceae Pottiaceae->Betulaceae Ptilidiaceae Ptilidiaceae Ptilidiaceae->Betulaceae Ptilidiaceae->Pinaceae Pylaisiaceae Pylaisiaceae Pylaisiaceae->Cupressaceae Pylaisiaceae->Oleaceae Pyrenulaceae Pyrenulaceae Pyrenulaceae->Sapindaceae Pyrenulaceae->Fagaceae Pyrenulaceae->Magnoliaceae Radulaceae Radulaceae Radulaceae->Betulaceae Radulaceae->Pinaceae Radulaceae->Cupressaceae Radulaceae->Rosaceae Radulaceae->Cornaceae Ramalinaceae Ramalinaceae Ramalinaceae->Juglandaceae Ramalinaceae->Fagaceae Ramalinaceae->Magnoliaceae Ramalinaceae->Betulaceae Ramalinaceae->Pinaceae Ramalinaceae->Cupressaceae Ramalinaceae->Salicaceae Ramalinaceae->Oleaceae Saturniidae Saturniidae Asteraceae Asteraceae Saturniidae->Asteraceae Sclerococcaceae Sclerococcaceae Ochrolechiaceae Ochrolechiaceae Sclerococcaceae->Ochrolechiaceae Stereocaulaceae Stereocaulaceae Stereocaulaceae->Sapindaceae Strigulaceae Strigulaceae Strigulaceae->Magnoliaceae Teloschistaceae Teloschistaceae Teloschistaceae->Betulaceae Teloschistaceae->Cupressaceae Teloschistaceae->Salicaceae Tortricidae Tortricidae Tortricidae->Rosaceae Aristolochiaceae Aristolochiaceae Tortricidae->Aristolochiaceae Geraniaceae Geraniaceae Tortricidae->Geraniaceae Trypetheliaceae Trypetheliaceae Trypetheliaceae->Fagaceae Trypetheliaceae->Meliaceae Verrucariaceae Verrucariaceae Verrucariaceae->Fagaceae

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, pbdb, and worms). 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
Clay over sandstone rock at entrance triangular fault damp NONE col Clay over sandstone rock at entrance triangular fault damp
Balsamea SYNONYM_OF col Commiphora
Bank along an old road NONE col Bank along an old road
Bank NONE col Bank
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 6626
col class 37
col family 195
col genus 692
col gigaclass 1
col infraorder 5
col infraphylum 1
col infraspecific name 1
col kingdom 3
col order 63
col parvorder 1
col parvphylum 1
col phylum 13
col section 1
col species 3303
col subclass 10
col subfamily 10
col subgenus 19
col suborder 11
col subphylum 4
col subspecies 187
col subtribe 1
col superclass 1
col superfamily 19
col superorder 2
col tribe 3
col variety 22
discoverlife NA 11166
discoverlife species 13
gbif NA 4832
gbif class 37
gbif family 276
gbif form 9
gbif genus 1252
gbif kingdom 4
gbif order 60
gbif phylum 13
gbif species 4480
gbif subspecies 214
gbif variety 74
itis NA 7914
itis class 38
itis family 168
itis genus 414
itis infraclass 1
itis infraorder 5
itis infraphylum 1
itis kingdom 3
itis order 69
itis phylum 12
itis section 1
itis species 2283
itis subclass 16
itis subfamily 9
itis suborder 24
itis subphylum 10
itis subspecies 175
itis superclass 2
itis superfamily 11
itis superorder 4
itis variety 34
mdd NA 11178
ncbi NA 8331
ncbi clade 12
ncbi class 35
ncbi cohort 2
ncbi family 162
ncbi genus 439
ncbi infraclass 1
ncbi infraorder 6
ncbi kingdom 2
ncbi order 63
ncbi phylum 13
ncbi species 1984
ncbi subclass 14
ncbi subfamily 9
ncbi subgenus 7
ncbi suborder 15
ncbi subphylum 4
ncbi subspecies 68
ncbi superclass 2
ncbi superfamily 16
ncbi superorder 5
ncbi tribe 2
ncbi varietas 1
pbdb NA 8315
pbdb class 60
pbdb family 260
pbdb genus 1034
pbdb informal 1
pbdb infraclass 2
pbdb infraorder 7
pbdb kingdom 5
pbdb order 127
pbdb phylum 16
pbdb species 1249
pbdb subclass 18
pbdb subfamily 17
pbdb suborder 39
pbdb subphylum 7
pbdb subspecies 15
pbdb superclass 3
pbdb superfamily 35
pbdb superorder 5
pbdb superphylum 1
pbdb tribe 2
pbdb unranked clade 30
tpt NA 10982
tpt family 6
tpt genus 14
tpt order 5
tpt species 171
wfo NA 9334
wfo class 1
wfo family 7
wfo genus 136
wfo order 1
wfo phylum 1
wfo section 1
wfo species 1667
wfo subspecies 19
wfo variety 17
worms NA 9106
worms class 46
worms family 178
worms genus 617
worms gigaclass 1
worms infraclass 5
worms infraorder 6
worms infraphylum 1
worms kingdom 3
worms order 69
worms parvphylum 1
worms phylum 15
worms species 1049
worms subclass 12
worms subfamily 3
worms suborder 22
worms subphylum 9
worms subspecies 16
worms superclass 2
worms superfamily 25
worms superorder 2
worms variety 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 141925
col SYNONYM_OF 2068
col HAS_ACCEPTED_NAME 3796
discoverlife NONE 147138
discoverlife HAS_ACCEPTED_NAME 12
discoverlife SYNONYM_OF 2
gbif NONE 139939
gbif SYNONYM_OF 3122
gbif HAS_ACCEPTED_NAME 6216
itis NONE 143415
itis HAS_ACCEPTED_NAME 3013
itis SYNONYM_OF 813
mdd NONE 147028
mdd HAS_ACCEPTED_NAME 103
mdd SYNONYM_OF 1
ncbi NONE 143771
ncbi SAME_AS 3042
ncbi SYNONYM_OF 374
pbdb NONE 143417
pbdb HAS_ACCEPTED_NAME 3529
pbdb SYNONYM_OF 573
tpt NONE 146921
tpt HAS_ACCEPTED_NAME 206
tpt SYNONYM_OF 6
wfo NONE 145090
wfo SYNONYM_OF 463
wfo HAS_ACCEPTED_NAME 1330
wfo HAS_UNCHECKED_NAME 367
worms NONE 144544
worms HAS_ACCEPTED_NAME 2349
worms SYNONYM_OF 408
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)
worms 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
2024-11-18T10:18:35Z summary https://github.com/globalbioticinteractions/yale-peabody/archive/4525d8b90998b1d3ec3c83a5074839fce5f047f3.zip
2024-11-18T10:18:35Z summary 281581 interaction(s)
2024-11-18T10:18:35Z summary 0 note(s)
2024-11-18T10:18:35Z summary 20 info(s)

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

: Most frequently occurring review notes, if any.

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 (2024-11-18) 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.