2024-04-22
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/vectorbase, is 4.75MiB in size and contains 2,043 interaction with 1 unique type of association (e.g., parasiteOf) between 84 primary taxa (e.g., Anopheles darlingi) and 82 associated taxa (e.g., human). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple catalogs.
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:
Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., … Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707–D713. doi:10.1093/nar/gku1117. https://github.com/globalbioticinteractions/vectorbase/archive/00d6285cd4e9f4edd18cb2778624ab31b34b23b8.zip 2024-04-20T06:11:11.024Z 97de6d8a4da8cb6b091dcbef550a35d75bc858cf3e647b132ffb6c175b05a287
For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/vectorbase 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 | 0.5.8 |
| 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. 4.75MiB) under review
elton pull globalbioticinteractions/vectorbase
# generate review notes
elton review globalbioticinteractions/vectorbase\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/vectorbase\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/vectorbase\
| 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, named globalbioticinteractions/vectorbase, is 4.75MiB in size and contains 2,043 interaction with 1 unique type of association (e.g., parasiteOf) between 84 primary taxa (e.g., Anopheles darlingi) and 82 associated taxa (e.g., human).
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 |
|---|---|---|---|
| Anopheles funestus | parasiteOf | human | doi:10.1186/s12936-014-0527-9 |
| Anopheles leesoni | parasiteOf | human | doi:10.1186/s12936-014-0527-9 |
| Anopheles arabiensis | parasiteOf | human | doi:10.1186/s12936-014-0527-9 |
| Anopheles gambiae sensu stricto | parasiteOf | human | doi:10.1186/s12936-014-0527-9 |
| interactionTypeName | count |
|---|---|
| parasiteOf | 14374 |
| sourceTaxonName | count |
|---|---|
| Anopheles darlingi | 5635 |
| Anopheles farauti | 1516 |
| Anopheles coustani | 1365 |
| Anopheles maculipalpis | 694 |
| Anopheles squamosus | 670 |
| Anopheles maculipennis sensu lato | 568 |
| Anopheles farauti No. 4 | 544 |
| Anopheles culicifacies BCE subgroup | 435 |
| Anopheles rufipes | 428 |
| Culex cedecei | 347 |
| Anopheles arabiensis | 231 |
| Culiseta annulata | 205 |
| Anopheles punctulatus | 203 |
| Anopheles longirostris | 131 |
| Anopheles mascarensis | 128 |
| Aedes camptorhynchus | 122 |
| Anopheles funestus | 106 |
| Culex pipiens | 100 |
| Anopheles gambiae sensu stricto | 90 |
| targetTaxonName | count |
|---|---|
| human | 6204 |
| cow | 2337 |
| galliformes | 2301 |
| pig | 1256 |
| dog | 473 |
| vertebrate | 454 |
| bovine | 293 |
| european rabbit | 233 |
| hispid cotton rat | 201 |
| rat | 82 |
| chicken | 71 |
| goat | 46 |
| wood pigeon | 44 |
| sheep | 34 |
| blackbird | 33 |
| green anole | 27 |
| house sparrow | 23 |
| animal | 20 |
| white tailed deer | 18 |
| sourceTaxonName | interactionTypeName | targetTaxonName | count |
|---|---|---|---|
| Anopheles darlingi | parasiteOf | human | 3157 |
| Anopheles darlingi | parasiteOf | galliformes | 2301 |
| Anopheles coustani | parasiteOf | cow | 726 |
| Anopheles farauti | parasiteOf | human | 631 |
| Anopheles farauti | parasiteOf | pig | 562 |
| Anopheles maculipalpis | parasiteOf | cow | 482 |
| Anopheles coustani | parasiteOf | human | 454 |
| Anopheles squamosus | parasiteOf | cow | 434 |
| Anopheles maculipennis sensu lato | parasiteOf | human | 281 |
| Anopheles rufipes | parasiteOf | cow | 278 |
| Anopheles farauti No. 4 | parasiteOf | human | 238 |
| Anopheles culicifacies BCE subgroup | parasiteOf | bovine | 220 |
| Anopheles culicifacies BCE subgroup | parasiteOf | human | 215 |
| Anopheles maculipennis sensu lato | parasiteOf | european rabbit | 206 |
| Anopheles farauti No. 4 | parasiteOf | pig | 201 |
| Culex cedecei | parasiteOf | hispid cotton rat | 201 |
| Anopheles farauti | parasiteOf | vertebrate | 195 |
| Culiseta annulata | parasiteOf | human | 187 |
| Anopheles squamosus | parasiteOf | human | 144 |
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.
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, wfo, mdd, tpt, and pbdb). These alignments can help review name usage or aid in selecting of a suitable taxonomic name resource.
| providedName | relationName | resolvedCatalogName | resolvedName |
|---|---|---|---|
| banded armadillo | NONE | col | banded armadillo |
| Adelaide rosella | NONE | col | Adelaide rosella |
| Aedes aegypti | HAS_ACCEPTED_NAME | col | Aedes aegypti |
| Aedes camptorhynchus | HAS_ACCEPTED_NAME | col | Aedes camptorhynchus |
| resolvedCatalogName | resolvedRank | count |
|---|---|---|
| col | NA | 82 |
| col | genus | 2 |
| col | kingdom | 1 |
| col | order | 3 |
| col | species | 71 |
| discoverlife | NA | 159 |
| gbif | NA | 78 |
| gbif | form | 1 |
| gbif | genus | 3 |
| gbif | kingdom | 1 |
| gbif | order | 3 |
| gbif | species | 74 |
| gbif | subspecies | 1 |
| itis | NA | 79 |
| itis | genus | 1 |
| itis | kingdom | 1 |
| itis | order | 3 |
| itis | species | 74 |
| mdd | NA | 158 |
| ncbi | NA | 61 |
| ncbi | genus | 1 |
| ncbi | kingdom | 1 |
| ncbi | order | 3 |
| ncbi | species | 92 |
| ncbi | subgenus | 1 |
| ncbi | subspecies | 1 |
| pbdb | NA | 152 |
| pbdb | genus | 1 |
| pbdb | kingdom | 1 |
| pbdb | order | 3 |
| pbdb | species | 1 |
| pbdb | unranked clade | 1 |
| tpt | NA | 155 |
| tpt | order | 2 |
| tpt | species | 1 |
| wfo | NA | 157 |
| wfo | genus | 1 |
| resolvedCatalogName | relationName | count |
|---|---|---|
| col | NONE | 83 |
| col | HAS_ACCEPTED_NAME | 81 |
| col | SYNONYM_OF | 58 |
| discoverlife | NONE | 166 |
| gbif | NONE | 79 |
| gbif | HAS_ACCEPTED_NAME | 110 |
| gbif | SYNONYM_OF | 61 |
| itis | NONE | 80 |
| itis | HAS_ACCEPTED_NAME | 84 |
| mdd | NONE | 164 |
| ncbi | NONE | 63 |
| ncbi | SAME_AS | 81 |
| ncbi | SYNONYM_OF | 4 |
| ncbi | COMMON_NAME_OF | 19 |
| pbdb | NONE | 158 |
| pbdb | HAS_ACCEPTED_NAME | 7 |
| pbdb | SYNONYM_OF | 7 |
| tpt | NONE | 161 |
| tpt | HAS_ACCEPTED_NAME | 3 |
| wfo | NONE | 163 |
| wfo | HAS_UNCHECKED_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) |
| 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) |
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 |
|---|---|---|
| 2024-04-22T08:17:26Z | note | issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11” |
| 2024-04-22T08:17:26Z | note | issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11” |
| 2024-04-22T08:17:26Z | note | issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11” |
| 2024-04-22T08:17:26Z | note | issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11” |
In addtion, you can find the most frequently occurring notes in the table below.
| reviewComment | count |
|---|---|
| issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11” | 90 |
| issue handling date range [2019-01/2019-03,2019-04/2019-06]: Invalid format: “2019-03,2019-04/2019-06” is malformed at “,2019-04/2019-06” | 42 |
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 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.
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.
Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes.