A Review of Biotic Interactions and Taxon Names Found
in globalbioticinteractions/ku-semc
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/ku-semc) contains 120,010 interactions with 2
(e.g., interactsWith) unique types of associations between 5,326 primary
taxa (e.g., Eucerini) and 3,223 associated taxa (e.g., Salix). 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:
University of Kansas Natural History Museum
https://github.com/globalbioticinteractions/ku-semc/archive/a9c7cb81050eef68b4428667206a219da458f517.zip
2023-09-23T04:11:48.901Z
2af46dc3e7ffef08e376a516f9c35ff4246428ced3686119f2eaba6645aa8506
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.
The review process can be described in the form of a script:
# get versioned copy of the dataset under review
elton pull globalbioticinteractions/ku-semc
# generate review notes
elton review globalbioticinteractions/ku-semc\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/ku-semc\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/ku-semc\
| nomer append col\
> name-alignment.tsv
or visually, in a process diagram.
Review Process Overview
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
Biotic Interaction Data
Model
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/ku-semc)
contains 120,010 interactions with 2 (e.g., interactsWith) unique types
of associations between 5,326 primary taxa (e.g., Eucerini) and 3,223
associated taxa (e.g., Salix).
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
Anthophora (Heliophila) phenax
interactsWith
Lycium berlandieri
1721fbd3-1ed6-11e3-bfac-90b11c41863e
Megachile (Xanthosarus) mucida
interactsWith
Tephrosia virginiana
172203a5-1ed6-11e3-bfac-90b11c41863e
Andrena (Larandrena) miserabilis
interactsWith
Prunus
172204ef-1ed6-11e3-bfac-90b11c41863e
Protandrena (Pterosarus) albitarsus innuptus
interactsWith
Gaillardia
17220e48-1ed6-11e3-bfac-90b11c41863e
Most Frequently Mentioned Interaction Types (up to 20 most
frequent)
interactionTypeName
count
interactsWith
119965
adjacentTo
45
Most Frequently Mentioned Primary Taxa (up to 20 most
frequent)
sourceTaxonName
count
Eucerini
3877
Colletes
1870
Perdita
1562
Bombus
1483
Ceratina
1372
Melissodes (Eumelissodes) tristis
1143
Lasioglossum (Dialictus)
1103
Andrena (Micrandrena) illinoiensis
1068
Ashmeadiella
927
Megachile
924
Nomada
869
Halictus (Odontalictus) ligatus
858
Andrena (Andrena)
817
Augochlorella persimilis
777
Melissodes (Eumelissodes) agilis
769
Augochlora
743
Osmia
656
Perdita (Perdita) salicis imperialis
653
Melissodes (Eumelissodes) coreopsis
652
Most Frequently Mentioned Associate Taxa (up to 20 most
frequent)
targetTaxonName
count
Salix
3389
Cucurbita foetidissima
2747
Helianthus annuus
2337
Helianthus petiolaris
2268
Gaillardia
2027
Larrea tridentata
1713
Prosopis
1415
Sphaeralcea
1375
Opuntia
1351
Helianthus
1283
Eucalyptus
1117
Phacelia
1104
Melilotus officinalis
1062
Heterotheca subaxillaris
1025
Melilotus alba
962
Cleome serrulata
904
Aster
896
Vaccinium
841
Cassia
840
Most Frequent Interactions between Primary and Associate Taxa
(up to 20 most frequent)
sourceTaxonName
interactionTypeName
targetTaxonName
count
Eucerini
interactsWith
Cucurbita foetidissima
2598
Bombus
interactsWith
Vaccinium
689
Perdita (Perdita) salicis imperialis
interactsWith
Salix
653
Andrena (Micrandrena) illinoiensis
interactsWith
Salix
619
Eucerini
interactsWith
Cucurbita
554
Abroteles beaumonti
interactsWith
Nasutitermes peruanus
533
Perdita (Perdita) sexmaculata
interactsWith
Quincula lobata
446
Perdita (Pygoperdita) nevadensis nevadensis
interactsWith
Holodiscus discolor
393
Perdita (Cockerellia) albipennis albipennis
interactsWith
Helianthus petiolaris
388
Eucerini
interactsWith
Cucurbita digitata
367
Melissodes (Eumelissodes) agilis
interactsWith
Helianthus annuus
352
Augochlorella persimilis
interactsWith
Aster
335
Perdita (Perdita) zebrata flavens
interactsWith
Cleome serrulata
332
Euryglossina (Euryglossina) fuscescens
interactsWith
Eucalyptus tereticornis
309
Perdita (Perdita) gerhardi dallasiana
interactsWith
Monarda citriodora
305
Chelonus
interactsWith
Cassia
301
Perdita (Cockerellia) coreopsidis obscurior
interactsWith
Gaillardia
290
Perdita (Perdita) zebrata zebrata
interactsWith
Cleome serrulata
287
Perdita (Perdita) wilmattae miricornis
interactsWith
Stanleya pinnata
267
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 on taxonomic kingdom rank as
interpreted by the Catalogue of Life download
svgInteractions on the taxonomic family rank
as interpreted by the Catalogue of Life. download
svg
Another way to discover the dataset under review is by searching for
it on the GloBI
website.
Taxonomic Alignment
As part of the review, all names are aligned against various name
catalogs (e.g., col ncbi discoverlife gbif itis globi mdd tpt). These
alignments may serve as a way to review name usage or aid in selecting
of a suitable taxonomic name resource to use.
Sample of Name Alignments
providedName
relationName
resolvedCatalogName
resolvedName
NONE
ncbi
NONE
discoverlife
NONE
globi
Abedus dilatatus
HAS_ACCEPTED_NAME
col
Abedus dilatatus
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
5060
tpt
genus
6
tpt
species
1
tpt
order
1
ncbi
species
2330
ncbi
NA
1480
ncbi
genus
1005
ncbi
family
125
ncbi
subfamily
52
ncbi
subgenus
31
ncbi
tribe
19
ncbi
subspecies
14
ncbi
varietas
12
ncbi
order
10
ncbi
superfamily
7
ncbi
suborder
2
ncbi
section
2
ncbi
superorder
1
ncbi
class
1
ncbi
clade
1
ncbi
cohort
1
ncbi
subtribe
1
ncbi
species group
1
mdd
NA
5068
itis
species
2648
itis
NA
1134
itis
genus
924
itis
family
130
itis
variety
89
itis
subspecies
71
itis
subfamily
39
itis
tribe
18
itis
order
10
itis
superfamily
7
itis
suborder
2
itis
superorder
2
itis
subgenus
1
itis
class
1
globi
species
3503
globi
genus
1639
globi
NA
1523
globi
subspecies
279
globi
variety
176
globi
family
147
globi
subgenus
63
globi
subfamily
62
globi
tribe
27
globi
order
11
globi
superfamily
7
globi
section
5
globi
subtribe
4
globi
form
4
globi
suborder
3
globi
class
2
globi
superorder
2
globi
infraorder
1
globi
phylum
1
globi
species group
1
gbif
species
3325
gbif
genus
1078
gbif
NA
352
gbif
subspecies
221
gbif
family
135
gbif
variety
105
gbif
order
9
gbif
class
1
gbif
form
1
discoverlife
NA
4396
discoverlife
species
673
col
species
3118
col
genus
1035
col
NA
575
col
subspecies
161
col
family
127
col
variety
69
col
subfamily
29
col
tribe
22
col
subgenus
17
col
order
9
col
superfamily
7
col
subtribe
4
col
section
1
col
form
1
col
subterclass
1
col
class
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).
Elton, Nomer, and other tools may have difficulties interpreting
existing species interaction datasets. Or, they may misbehave, or
otherwise show unexpected behavior. As part of the review process,
detailed review notes are kept that document possibly misbehaving, or
confused, review bots. An sample of review notes associated with this
review can be found below.
First few lines in the review notes.
reviewDate
reviewCommentType
reviewComment
2023-09-28T03:24:18Z
note
found invalid location: [range of latitude [3717] not valid]
2023-09-28T03:24:18Z
note
found invalid location: [range of latitude [3717] not valid]
2023-09-28T03:24:18Z
note
found invalid location: [range of latitude [3717] not valid]
2023-09-28T03:24:18Z
note
found invalid location: [range of latitude [3717] not valid]
In addtion, you can find the most frequently occurring notes in the
table below.
Most frequently occurring review notes, if any.
reviewComment
count
found invalid location: [range of latitude [3717] not valid]
5
found invalid location: [range of latitude [3630] not valid]
1
found invalid location: [range of longitude [3452.516] not
valid]
1
found unsupported interaction type with name: [attacked by]
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.
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.
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.
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.