2023-09-28
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/unhc-unhc) contains 3,140 interactions with 4 (e.g., interactsWith) unique types of associations between 180 primary taxa (e.g., Bombus impatiens) and 172 associated taxa (e.g., Trifolium repens). 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:
University of New Hampshire Donald S. Chandler Entomological Collection https://github.com/globalbioticinteractions/unhc-unhc/archive/d7668a6bb4545dc4da0645ecc383169ba547b0f5.zip 2023-09-23T11:16:55.704Z e049199519873802caa7c2c74945a902bf6678a0cd603bc5ebe810d1e51957a3
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 | 0.12.7 |
| nomer | 0.5.5 |
| mlr | 6.0.0 |
| pandoc | 3.1.6.1 |
The review process can be described in the form of a script:
# get versioned copy of the dataset under review
elton pull globalbioticinteractions/unhc-unhc
# generate review notes
elton review globalbioticinteractions/unhc-unhc\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/unhc-unhc\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/unhc-unhc\
| 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 1. 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/unhc-unhc) contains 3,140 interactions with 4 (e.g., interactsWith) unique types of associations between 180 primary taxa (e.g., Bombus impatiens) and 172 associated taxa (e.g., Trifolium repens).
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.
| sourceTaxonName | interactionTypeName | targetTaxonName | referenceCitation |
|---|---|---|---|
| Bombus vagans | interactsWith | Rubus sp. | https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511725 |
| Bombus impatiens | interactsWith | Malus sp. | https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511824 |
| Bombus impatiens | interactsWith | Malus sp. | https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511825 |
| Bombus impatiens | interactsWith | Malus sp. | https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511826 |
| interactionTypeName | count |
|---|---|
| interactsWith | 3101 |
| adjacentTo | 18 |
| hasHost | 18 |
| visits | 3 |
| sourceTaxonName | count |
|---|---|
| Bombus impatiens | 917 |
| Halictus ligatus | 246 |
| Bombus vagans | 215 |
| Bombus bimaculatus | 176 |
| Lasioglossum pilosum | 129 |
| Halictus confusus | 71 |
| Xylocopa virginica | 67 |
| Bombus ternarius | 63 |
| Bombus griseocollis | 62 |
| Bombus terricola | 62 |
| Ceratina calcarata | 61 |
| Bombus affinis | 50 |
| Andrena wilkella | 45 |
| Hylaeus modestus | 44 |
| Agapostemon virescens | 37 |
| Lasioglossum versatum | 35 |
| Lasioglossum cressonii | 29 |
| Andrena crataegi | 28 |
| Andrena cressonii | 27 |
| targetTaxonName | count |
|---|---|
| Trifolium repens | 295 |
| Monarda fistulosa | 283 |
| Aster sp. | 163 |
| Trifolium pratense | 148 |
| Fagopyrum esculentum | 130 |
| Heliopsis helianthoides | 108 |
| Solidago speciosa | 101 |
| Rudbeckia hirta | 93 |
| Daucus carota | 72 |
| Solidago canadensis | 68 |
| Barbarea vulgaris | 59 |
| Taraxacum officinale | 56 |
| Rhus glabra | 53 |
| Erigeron annuus | 53 |
| Solidago altissima | 52 |
| Spiraea japonica | 51 |
| Ribes sp. | 50 |
| Solidago sp. | 39 |
| Syringa vulgaris | 38 |
| sourceTaxonName | interactionTypeName | targetTaxonName | count |
|---|---|---|---|
| Bombus impatiens | interactsWith | Trifolium repens | 175 |
| Bombus impatiens | interactsWith | Monarda fistulosa | 116 |
| Bombus impatiens | interactsWith | Aster sp. | 112 |
| Halictus ligatus | interactsWith | Rudbeckia hirta | 80 |
| Bombus impatiens | interactsWith | Solidago speciosa | 67 |
| Bombus impatiens | interactsWith | Trifolium pratense | 52 |
| Lasioglossum pilosum | interactsWith | Fagopyrum esculentum | 46 |
| Bombus impatiens | interactsWith | Solidago canadensis | 42 |
| Xylocopa virginica | interactsWith | Monarda fistulosa | 40 |
| Bombus impatiens | interactsWith | Solidago altissima | 33 |
| Halictus ligatus | interactsWith | Coreopsis lanceolata | 33 |
| Bombus vagans | interactsWith | Aster sp. | 32 |
| Bombus bimaculatus | interactsWith | Monarda fistulosa | 31 |
| Bombus ternarius | interactsWith | Epigaea repens | 29 |
| Hylaeus modestus | interactsWith | Daucus carota | 27 |
| Bombus impatiens | interactsWith | Ribes sp. | 26 |
| Bombus griseocollis | interactsWith | Monarda fistulosa | 25 |
| Lasioglossum pilosum | interactsWith | Monarda fistulosa | 25 |
| Bombus vagans | interactsWith | Trifolium pratense | 24 |
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). 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
: 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.
| catalog name | alignment results |
|---|---|
| col | associated names alignments (csv/tsv/html) |
| ncbi | associated names alignments (csv/tsv/html) |
| discoverlife | associated names alignments (csv/tsv/html) |
| gbif | associated names alignments (csv/tsv/html) |
| itis | associated names alignments (csv/tsv/html) |
| globi | associated names alignments (csv/tsv/html) |
| mdd | associated names alignments (csv/tsv/html) |
| tpt | associated names alignments (csv/tsv/html) |
: List of Available Name Alignment Reports
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 |
|---|---|---|
| 2023-09-28T11:36:07Z | note | found unsupported interaction type with name: [coll. from] |
| 2023-09-28T11:36:08Z | note | found unsupported interaction type with name: [coll. from] |
| 2023-09-28T11:36:08Z | note | found unsupported interaction type with name: [coll. from] |
| 2023-09-28T11:36:08Z | note | found unsupported interaction type with name: [coll. from] |
In addtion, you can find the most frequently occurring notes in the table below.
| reviewComment | count |
|---|---|
| found unsupported interaction type with name: [1] | 16 |
| found unsupported interaction type with name: [coll. from] | 5 |
| found unsupported interaction type with name: [CZ-2] | 2 |
| found unsupported interaction type with name: [2 specimens on one pin] | 2 |
For more exhaustive list of review notes, please have a look at the Review Notes (csv/tsv/html).
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 4 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-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.
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.