2024-02-10
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 interactions dataset of known origin, and discuss their outcome. The dataset under review (aka globalbioticinteractions/ferreira2023) has size 103KiB and contains 13 interactions with 1 unique types of associations (e.g., flowersVisitedBy) between 1 primary taxa (e.g., Citrus) and 10 associated taxa (e.g., Diptera). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple perspectives.
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:
Orange (Citrus sinensis L. Osbeck, var. Pera-rio) insect floral visiting data of orchards in Itaberaí, Goiás, Brasil. file:///home/runner/work/ferreira2023/ferreira2023/./
For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/ferreira2023 and inspect associated metadata files including, but not limited to, README.md, eml.xml, and/or globi.json.
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.
| tool name | version |
|---|---|
| elton | 0.13.2 |
| nomer | 0.5.6 |
| 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. 103KiB) under review
elton pull globalbioticinteractions/ferreira2023
# generate review notes
elton review globalbioticinteractions/ferreira2023\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/ferreira2023\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/ferreira2023\
| nomer append col\
> name-alignment.tsvor visually, in a process diagram.
You can find a recent copy of the full review script at check-data.sh.
In the following sections, the results of the review are summarized 2. Then, links to the detailed review reports are provided.
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/ferreira2023) has size 103KiB and contains 13 interactions with 1 unique types of associations (e.g., flowersVisitedBy) between 1 primary taxa (e.g., Citrus) and 10 associated taxa (e.g., Diptera).
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.
| sourceTaxonName | interactionTypeName | targetTaxonName | referenceCitation |
|---|---|---|---|
| Citrus | flowersVisitedBy | Diptera | interactions.tsv |
| Citrus | flowersVisitedBy | Apis | interactions.tsv |
| Citrus | flowersVisitedBy | Apis | interactions.tsv |
| Citrus | flowersVisitedBy | Apis | interactions.tsv |
| interactionTypeName | count |
|---|---|
| flowersVisitedBy | 58 |
| sourceTaxonName | count |
|---|---|
| Citrus | 58 |
| targetTaxonName | count |
|---|---|
| Diptera | 17 |
| Trigona spinipes | 12 |
| Apis mellifera | 9 |
| Hymenoptera | 6 |
| Apis | 5 |
| Paratrigona lineata | 3 |
| Lepidoptera | 2 |
| Plebeia | 2 |
| Insecta | 1 |
| Tetragona clavipes | 1 |
| sourceTaxonName | interactionTypeName | targetTaxonName | count |
|---|---|---|---|
| Citrus | flowersVisitedBy | Diptera | 17 |
| Citrus | flowersVisitedBy | Trigona spinipes | 12 |
| Citrus | flowersVisitedBy | Apis mellifera | 9 |
| Citrus | flowersVisitedBy | Hymenoptera | 6 |
| Citrus | flowersVisitedBy | Apis | 5 |
| Citrus | flowersVisitedBy | Paratrigona lineata | 3 |
| Citrus | flowersVisitedBy | Lepidoptera | 2 |
| Citrus | flowersVisitedBy | Plebeia | 2 |
| Citrus | flowersVisitedBy | Insecta | 1 |
| Citrus | flowersVisitedBy | Tetragona clavipes | 1 |
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.
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.
As part of the review, all names are aligned against various name catalogs (e.g., col, ncbi, discoverlife, gbif, itis, globi, mdd, tpt, and pbdb). These alignments may serve as a way to review name usage or aid in selecting of a suitable taxonomic name resource to use.
| providedName | relationName | resolvedCatalogName | resolvedName |
|---|---|---|---|
| Apis | HAS_ACCEPTED_NAME | col | Apis |
| Apis mellifera | HAS_ACCEPTED_NAME | col | Apis mellifera |
| Citrus | HAS_ACCEPTED_NAME | col | Citrus |
| Diptera | SYNONYM_OF | col | Saxifraga |
| resolvedCatalogName | resolvedRank | count |
|---|---|---|
| tpt | NA | 10 |
| tpt | species | 1 |
| pbdb | genus | 3 |
| pbdb | order | 3 |
| pbdb | NA | 3 |
| pbdb | species | 1 |
| pbdb | class | 1 |
| ncbi | species | 4 |
| ncbi | genus | 3 |
| ncbi | order | 3 |
| ncbi | class | 1 |
| mdd | NA | 11 |
| itis | species | 4 |
| itis | genus | 3 |
| itis | order | 3 |
| itis | class | 1 |
| globi | NA | 6 |
| globi | genus | 5 |
| globi | species | 4 |
| globi | order | 3 |
| globi | class | 1 |
| globi | phylum | 1 |
| gbif | genus | 4 |
| gbif | species | 4 |
| gbif | order | 3 |
| gbif | class | 1 |
| discoverlife | NA | 7 |
| discoverlife | species | 4 |
| col | genus | 4 |
| col | species | 4 |
| col | order | 3 |
| col | class | 1 |
| resolvedCatalogName | relationName | count |
|---|---|---|
| col | HAS_ACCEPTED_NAME | 11 |
| col | SYNONYM_OF | 1 |
| discoverlife | NONE | 7 |
| discoverlife | HAS_ACCEPTED_NAME | 4 |
| gbif | HAS_ACCEPTED_NAME | 12 |
| gbif | SYNONYM_OF | 1 |
| globi | SAME_AS | 148 |
| itis | HAS_ACCEPTED_NAME | 11 |
| mdd | NONE | 11 |
| ncbi | SAME_AS | 11 |
| pbdb | HAS_ACCEPTED_NAME | 8 |
| pbdb | SYNONYM_OF | 1 |
| pbdb | NONE | 3 |
| tpt | NONE | 10 |
| tpt | HAS_ACCEPTED_NAME | 1 |
| 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) |
| globi | 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) |
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.
| reviewDate | reviewCommentType | reviewComment |
|---|---|---|
| 2024-02-10T19:29:06Z | note | found invalid location: [invalid (latitude, longitude) = (-16,06618,-49,77326)] |
| 2024-02-10T19:29:06Z | note | found invalid location: [invalid (latitude, longitude) = (-16,06618,-49,77326)] |
| 2024-02-10T19:29:06Z | note | found invalid location: [invalid (latitude, longitude) = (-16,06618,-49,77326)] |
| 2024-02-10T19:29:06Z | note | found invalid location: [invalid (latitude, longitude) = (-16,06618,-49,77326)] |
In addtion, you can find the most frequently occurring notes in the table below.
| reviewComment | count |
|---|---|
| found invalid location: [invalid (latitude, longitude) = (-16,06618,-49,77326)] | 34 |
| found invalid location: [invalid (latitude, longitude) = (-16,01645,-49,98505)] | 13 |
| found invalid location: [invalid (latitude, longitude) = (-16,07233,-49,95806)] | 11 |
For addition information on review notes, please have a look at the first 500 Review Notes or the download full csv or tsv archives.
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.
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 5 for badge examples.
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-ness6 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.
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 means that it can be more precisely processed 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 to facilitate seamless data exchanges, i.e., interoperability.
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.