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/msb-para, is 4.09GiB in size and contains
90,354 interaction with 4 unique types of associations (e.g.,
parasiteOf) between 1,001 primary taxon (e.g., Acari) and 4,185
associated taxon (e.g., Dipodomys merriami). 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:
For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/msb-para
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.
The review process can be described in the form of the script below
1.
# get versioned copy of the dataset (size approx. 4.09GiB) under review
elton pull globalbioticinteractions/msb-para
# generate review notes
elton review globalbioticinteractions/msb-para\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/msb-para\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/msb-para\
| 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
2. 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, named globalbioticinteractions/msb-para, is
4.09GiB in size and contains 90,354 interaction with 4 unique types of
associations (e.g., parasiteOf) between 1,001 primary taxon (e.g.,
Acari) and 4,185 associated taxon (e.g., Dipodomys merriami).
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
Paragordius varius
hasHost
Physa acuta
http://arctos.database.museum/guid/MSB:Para:24564
Arostrilepis kontrimavichusi
hasHost
Clethrionomys californicus
http://arctos.database.museum/guid/MSB:Para:24566
Cestoda
parasiteOf
Myodes rutilus
http://arctos.database.museum/guid/MSB:Para:24499
Scaphiostomum pancreaticum
hasHost
Tamias triatus
http://arctos.database.museum/guid/MSB:Para:24926
Most Frequently Mentioned Interaction Types (up to 20 most
frequent)
interactionTypeName
count
parasiteOf
47316
hasHost
42967
interactsWith
46
hasParasite
26
Most Frequently Mentioned Primary Taxa (up to 20 most
frequent)
sourceTaxonName
count
Acari
9473
Siphonaptera
6438
Cestoda
4921
Taenia
3653
Nematoda
3649
Toxascaris
3408
Echinococcus multilocularis
3050
Ixodida
2956
Phthiraptera
2206
Echinococcus
1678
Arthropoda
1619
Mastophorus dipodomis
1557
Polyplax borealis
1480
Heteromyoxyuris deserti
1417
Uncinaria
1317
Trematoda
1063
Eimeria chobotari
940
Trichinella
863
Ascarididae
843
Most Frequently Mentioned Associate Taxa (up to 20 most
frequent)
targetTaxonName
count
Dipodomys merriami
5395
Myodes rutilus
4628
Alopex lagopus
4426
Alopex
3973
Microtus oeconomus
2887
Aythya affinis
2423
Peromyscus maniculatus
2386
Dipodomys ordii
2062
Microtus pennsylvanicus
1897
Sorex cinereus
1526
Peromyscus truei
1483
Neotoma albigula
1229
Dipodomys spectabilis
1105
Microtus
1054
Myodes gapperi
1048
Onychomys leucogaster
973
Peromyscus keeni
957
Apodemus peninsulae
944
Perognathus flavus
917
Most Frequent Interactions between Primary and Associate Taxa
(up to 20 most frequent)
sourceTaxonName
interactionTypeName
targetTaxonName
count
Taenia
parasiteOf
Alopex lagopus
1303
Taenia
hasHost
Alopex
1206
Toxascaris
hasHost
Alopex
1177
Toxascaris
parasiteOf
Alopex lagopus
1049
Echinococcus multilocularis
hasHost
Alopex
721
Polyplax borealis
parasiteOf
Myodes rutilus
662
Polyplax borealis
hasHost
Myodes rutilus
662
Echinococcus multilocularis
parasiteOf
Alopex lagopus
574
Echinococcus multilocularis
parasiteOf
Microtus oeconomus
514
Acari
parasiteOf
Sorex cinereus
508
Acari
hasHost
Sorex cinereus
490
Echinococcus
parasiteOf
Alopex lagopus
471
Mastophorus dipodomis
hasHost
Dipodomys merriami
454
Uncinaria
hasHost
Alopex
451
Eimeria chobotari
hasHost
Dipodomys merriami
450
Mastophorus dipodomis
parasiteOf
Dipodomys merriami
440
Eimeria chobotari
parasiteOf
Dipodomys merriami
429
Uncinaria
parasiteOf
Alopex lagopus
415
Siphonaptera
hasHost
Peromyscus maniculatus
382
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 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, 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
Ticks flea
NONE
col
Ticks flea
Fleas mit
NONE
col
Fleas mit
A7114Peromyscus nasutus
NONE
col
A7114Peromyscus nasutus
A99
NONE
col
A99
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
875
col
class
5
col
family
73
col
genus
331
col
infraorder
1
col
nanorder
2
col
order
17
col
parvorder
1
col
phylum
6
col
species
1192
col
subclass
1
col
subfamily
2
col
subgenus
18
col
suborder
1
col
subspecies
103
col
superfamily
10
col
unranked
1
discoverlife
NA
2615
discoverlife
species
1
gbif
NA
656
gbif
class
5
gbif
family
84
gbif
genus
402
gbif
order
13
gbif
phylum
6
gbif
species
1336
gbif
subspecies
121
itis
NA
1164
itis
class
4
itis
family
64
itis
genus
282
itis
order
21
itis
phylum
7
itis
species
969
itis
subclass
4
itis
subfamily
3
itis
subgenus
1
itis
suborder
3
itis
subspecies
94
itis
superfamily
3
mdd
NA
2615
ncbi
NA
889
ncbi
class
4
ncbi
family
79
ncbi
genus
351
ncbi
infraorder
2
ncbi
order
17
ncbi
phylum
7
ncbi
species
1208
ncbi
subclass
4
ncbi
subfamily
2
ncbi
subgenus
2
ncbi
suborder
4
ncbi
subspecies
41
ncbi
superfamily
10
pbdb
NA
1827
pbdb
class
5
pbdb
family
26
pbdb
genus
130
pbdb
order
11
pbdb
phylum
6
pbdb
species
596
pbdb
subclass
1
pbdb
subfamily
1
pbdb
suborder
4
pbdb
subspecies
7
pbdb
subtribe
1
pbdb
superfamily
3
pbdb
superorder
1
pbdb
unranked clade
4
tpt
NA
1761
tpt
family
7
tpt
genus
88
tpt
order
1
tpt
species
758
wfo
NA
2601
wfo
genus
14
worms
NA
1455
worms
class
5
worms
family
71
worms
genus
299
worms
infraorder
1
worms
order
17
worms
phylum
6
worms
species
737
worms
subclass
2
worms
subfamily
1
worms
subgenus
1
worms
suborder
3
worms
subphylum
1
worms
subspecies
7
worms
superfamily
11
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
2024-07-22T21:28:52Z
note
found unresolved reference [10100]
2024-07-22T21:28:52Z
note
found unresolved reference [10101]
2024-07-22T21:28:52Z
note
found unresolved reference [101031]
2024-07-22T21:28:52Z
note
found unresolved reference [101034]
In addtion, you can find the most frequently occurring notes in the
table below.
Most frequently occurring review notes, if any.
reviewComment
count
found unresolved reference [10100]
1
found unresolved reference [10101]
1
found unresolved reference [101031]
1
found unresolved reference [101034]
1
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.
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 ^[At time of writing
(2024-07-23) 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.
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.