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

2024-04-22

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 453MiB in size and contains 279,278 interaction with 9 unique types of associations (e.g., adjacentTo) between 7,893 primary taxon (e.g., undet. Foraminiferida) and 137,584 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 396.2970 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_bot 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Entomology Division, Yale Peabody Museum - Version 395.2876 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_ent 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Invertebrate Paleontology Division, Yale Peabody Museum - Version 395.2907 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_ip 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Invertebrate Zoology Division, Yale Peabody Museum - Version 395.2966 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_iz 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Paleobotany Division, Yale Peabody Museum - Version 395.2960 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_pb 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Vertebrate Paleontology Division, Yale Peabody Museum - Version 395.2966 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_vp 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Vertebrate Zoology Division - Herpetology, Yale Peabody Museum - Version 395.2959 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_vz_her 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Vertebrate Zoology Division - Ichthyology, Yale Peabody Museum - Version 395.2882 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_vz_ich 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Vertebrate Zoology Division - Mammalogy, Yale Peabody Museum - Version 397.2941 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_vz_mam 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98 Vertebrate Zoology Division - Ornithology, Yale Peabody Museum - Version 395.2923 http://ipt.peabody.yale.edu/ipt/archive.do?r=ipt_vz_orn 2024-04-20T19:44:35.908Z f906a192ef79134902b8006964d89ff031c0bb397975f58701c5535574c8af98

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 0.13.2
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.  453MiB) 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 453MiB in size and contains 279,278 interaction with 9 unique types of associations (e.g., adjacentTo) between 7,893 primary taxon (e.g., undet. Foraminiferida) and 137,584 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
Leucothoidae interactsWith same original lot: IZ.057001 http://collections.peabody.yale.edu/search/Record/YPM-IZ-072272
Botrylloides diegensis interactsWith IZAR.000910 http://collections.peabody.yale.edu/search/Record/YPM-IZ-020129
Conchoderma virgatum hasHost IZ.102495 http://collections.peabody.yale.edu/search/Record/YPM-IZ-102496
Characodoma adjacentTo same slide: IZ.089454 http://collections.peabody.yale.edu/search/Record/YPM-IZ-089455
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
adjacentTo 152973
interactsWith 124331
hasHost 1712
hasParasite 379
symbiontOf 50
preysOn 11
preyedUponBy 7
visits 7
eats 3
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
undet. Foraminiferida 23692
Limopsis striatopunctatus 20121
undet. Bivalvia 18969
undet. Mollusca 15357
undet. Rugoglobigerinidae 5875
undet. Diptera 5117
Hoploscaphites sp. 4557
undet. Rotaliida 4270
Protocardia sp. 4212
Protocardia subquadrata 4165
taxon undetermined 3972
undet. Insecta 3767
undet. Ammonoidea 3290
undet. Conchostraca 3150
undet. Scaphitidae 3147
undet. Hexapoda 2819
undet. Coleoptera 2709
Scaphites sp. 2172
Verneuilinoides kansasensis 2065
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
trees 635
same slide: IP.856867 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
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 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, 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
clay over sandstone rock at entrance triangular fault Shaded damp NONE col clay over sandstone rock at entrance triangular fault Shaded 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 7021
col class 37
col family 193
col genus 683
col gigaclass 1
col infraorder 5
col infraphylum 1
col infraspecific name 1
col kingdom 3
col order 62
col parvorder 1
col parvphylum 1
col phylum 13
col section 1
col species 3269
col subclass 10
col subfamily 10
col subgenus 19
col suborder 11
col subphylum 4
col subspecies 186
col subtribe 1
col superclass 1
col superfamily 18
col superorder 2
col tribe 3
col variety 22
discoverlife NA 11513
discoverlife species 13
gbif NA 5285
gbif class 37
gbif family 274
gbif form 9
gbif genus 1237
gbif kingdom 4
gbif order 59
gbif phylum 13
gbif species 4396
gbif subspecies 213
gbif variety 71
itis NA 8278
itis class 38
itis family 165
itis genus 413
itis infraclass 1
itis infraorder 5
itis infraphylum 1
itis kingdom 3
itis order 68
itis phylum 12
itis section 1
itis species 2273
itis subclass 16
itis subfamily 9
itis suborder 23
itis subphylum 10
itis subspecies 175
itis superclass 2
itis superfamily 10
itis superorder 4
itis variety 34
mdd NA 11525
ncbi NA 8680
ncbi clade 12
ncbi class 35
ncbi cohort 2
ncbi family 160
ncbi genus 441
ncbi infraclass 1
ncbi infraorder 6
ncbi kingdom 2
ncbi order 62
ncbi phylum 13
ncbi species 1984
ncbi subclass 14
ncbi subfamily 9
ncbi subgenus 7
ncbi suborder 14
ncbi subphylum 4
ncbi subspecies 69
ncbi superclass 2
ncbi superfamily 15
ncbi superorder 5
ncbi tribe 2
ncbi varietas 1
pbdb NA 8722
pbdb class 60
pbdb family 258
pbdb genus 1020
pbdb informal 1
pbdb infraclass 2
pbdb infraorder 7
pbdb kingdom 5
pbdb order 124
pbdb phylum 16
pbdb species 1212
pbdb subclass 18
pbdb subfamily 16
pbdb suborder 38
pbdb subphylum 7
pbdb subspecies 14
pbdb superclass 3
pbdb superfamily 34
pbdb superorder 5
pbdb superphylum 1
pbdb tribe 2
pbdb unranked clade 30
tpt NA 11333
tpt family 6
tpt genus 13
tpt order 5
tpt species 168
wfo NA 9687
wfo class 1
wfo family 7
wfo genus 135
wfo order 1
wfo phylum 1
wfo section 1
wfo species 1662
wfo subspecies 19
wfo variety 17
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 140472
col SYNONYM_OF 2036
col HAS_ACCEPTED_NAME 3747
discoverlife NONE 145611
discoverlife HAS_ACCEPTED_NAME 12
discoverlife SYNONYM_OF 2
gbif NONE 138539
gbif SYNONYM_OF 3043
gbif HAS_ACCEPTED_NAME 6144
itis NONE 141914
itis HAS_ACCEPTED_NAME 2999
itis SYNONYM_OF 804
mdd NONE 145502
mdd HAS_ACCEPTED_NAME 103
ncbi NONE 142235
ncbi SAME_AS 3021
ncbi SYNONYM_OF 358
ncbi COMMON_NAME_OF 47
pbdb NONE 141976
pbdb HAS_ACCEPTED_NAME 3465
pbdb SYNONYM_OF 542
tpt NONE 145399
tpt HAS_ACCEPTED_NAME 202
tpt SYNONYM_OF 5
wfo NONE 143571
wfo SYNONYM_OF 458
wfo HAS_ACCEPTED_NAME 1327
wfo HAS_UNCHECKED_NAME 366
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
2024-04-22T08:59:21Z summary https://github.com/globalbioticinteractions/yale-peabody/archive/43be869f17749d71d26fc820c8bd931d6149fe8e.zip
2024-04-22T08:59:21Z summary 279473 interaction(s)
2024-04-22T08:59:21Z summary 0 note(s)
2024-04-22T08:59:21Z 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 5 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-ness6 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.