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/usnmentflea, is 6.29MiB in size and contains 2,786 interaction with 1 unique type of association (e.g., parasiteOf) between 25 primary taxa (e.g., Echidnophaga gallinacea) and 134 associated taxa (e.g., Rattus norvegicus_Berkenhout 1769). 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:
Data were obtained from specimens belonging to the United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU). https://github.com/globalbioticinteractions/usnmentflea/archive/ce5cb1ed2bbc13ee10062b6f75a158fd465ce9bb.zip 2024-04-20T06:09:41.617Z 0e0edfcc10e00d61725f0c4761322649dd780c0fb5ca0af5f5d2a4efb43fadec
For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/usnmentflea 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. 6.29MiB) under review
elton pull globalbioticinteractions/usnmentflea
# generate review notes
elton review globalbioticinteractions/usnmentflea\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/usnmentflea\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/usnmentflea\
| 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/usnmentflea, is 6.29MiB in size and contains 2,786 interaction with 1 unique type of association (e.g., parasiteOf) between 25 primary taxa (e.g., Echidnophaga gallinacea) and 134 associated taxa (e.g., Rattus norvegicus_Berkenhout 1769).
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 |
|---|---|---|---|
| Echidnophaga gallinacea | parasiteOf | Thallomys paedulcus_Sundevall 1846 | USNM_Flea_and_Associated_Host_Records.tsv |
| Ctenocephalides felis strongylus | parasiteOf | Arvicanthis niloticus_É. Geoffroy 1803 | USNM_Flea_and_Associated_Host_Records.tsv |
| Ctenocephalides felis strongylus | parasiteOf | Arvicanthis niloticus_É. Geoffroy 1803 | USNM_Flea_and_Associated_Host_Records.tsv |
| Ctenocephalides felis strongylus | parasiteOf | Arvicanthis niloticus_É. Geoffroy 1803 | USNM_Flea_and_Associated_Host_Records.tsv |
| interactionTypeName | count |
|---|---|
| parasiteOf | 2786 |
| sourceTaxonName | count |
|---|---|
| Echidnophaga gallinacea | 896 |
| Xenopsylla cheopis | 534 |
| Ctenocephalides felis | 377 |
| Ctenocephalides felis strongylus | 169 |
| Ctenocephalides canis | 168 |
| Oropsylla montana | 134 |
| Polygenis gwyni | 122 |
| Oropsylla hirsuta | 96 |
| Oropsylla tuberculata | 83 |
| Megabothris abantis | 51 |
| Oropsylla tuberculata cynomuris | 46 |
| Oropsylla tuberculata tuberculata | 31 |
| Anomiopsyllus nudatus | 26 |
| Oropsylla bruneri | 16 |
| Thrassis bacchi bacchi | 8 |
| Thrassis bacchi gladiolis | 7 |
| Thrassis bacchi | 6 |
| Oropsylla rupestris | 4 |
| Ctenocephalides felis felis | 4 |
| targetTaxonName | count |
|---|---|
| Rattus norvegicus_Berkenhout 1769 | 419 |
| Canis lupus familiaris_Linnaeus 1758 | 241 |
| Arvicanthis niloticus_É. Geoffroy 1803 | 195 |
| Genetta genetta_Linnaeus 1758 | 190 |
| Cynomys ludovicianus Ord 1815 | 133 |
| Sigmodon hispidus_Say and Ord 1825 | 113 |
| Lepus capensis_Linnaeus 1758 | 112 |
| Spermophilus beecheyi_Richardson 1829 | 111 |
| Suricata suricatta_Schreber 1776 | 111 |
| Spermophilus columbianus_Ord 1815 | 109 |
| Canis mesomelas_Schreber 1775 | 94 |
| Atelerix albiventris_Wagner 1841 | 93 |
| Felis catus_Linnaeus 1758 | 68 |
| Vulpes chama_A. Smith 1833 | 53 |
| Homo sapiens_Linnaeus 1758 | 40 |
| Cerdocyon thous_Linnaeus 1766 | 36 |
| Felis nigripes_Burchell 1824 | 35 |
| Genetta thierryi_Matschie 1902 | 34 |
| Canis latrans_Say 1823 | 33 |
| sourceTaxonName | interactionTypeName | targetTaxonName | count |
|---|---|---|---|
| Xenopsylla cheopis | parasiteOf | Rattus norvegicus_Berkenhout 1769 | 259 |
| Xenopsylla cheopis | parasiteOf | Arvicanthis niloticus_É. Geoffroy 1803 | 182 |
| Echidnophaga gallinacea | parasiteOf | Genetta genetta_Linnaeus 1758 | 175 |
| Ctenocephalides felis | parasiteOf | Canis lupus familiaris_Linnaeus 1758 | 132 |
| Echidnophaga gallinacea | parasiteOf | Rattus norvegicus_Berkenhout 1769 | 131 |
| Polygenis gwyni | parasiteOf | Sigmodon hispidus_Say and Ord 1825 | 111 |
| Echidnophaga gallinacea | parasiteOf | Suricata suricatta_Schreber 1776 | 110 |
| Ctenocephalides canis | parasiteOf | Canis lupus familiaris_Linnaeus 1758 | 98 |
| Echidnophaga gallinacea | parasiteOf | Canis mesomelas_Schreber 1775 | 94 |
| Oropsylla montana | parasiteOf | Spermophilus beecheyi_Richardson 1829 | 94 |
| Echidnophaga gallinacea | parasiteOf | Lepus capensis_Linnaeus 1758 | 88 |
| Oropsylla hirsuta | parasiteOf | Cynomys ludovicianus Ord 1815 | 86 |
| Ctenocephalides felis strongylus | parasiteOf | Atelerix albiventris_Wagner 1841 | 85 |
| Oropsylla tuberculata | parasiteOf | Spermophilus columbianus_Ord 1815 | 74 |
| Ctenocephalides felis | parasiteOf | Felis catus_Linnaeus 1758 | 56 |
| Echidnophaga gallinacea | parasiteOf | Vulpes chama_A. Smith 1833 | 53 |
| Oropsylla tuberculata cynomuris | parasiteOf | Cynomys ludovicianus Ord 1815 | 41 |
| Ctenocephalides felis | parasiteOf | Cerdocyon thous_Linnaeus 1766 | 36 |
| Echidnophaga gallinacea | parasiteOf | Felis nigripes_Burchell 1824 | 35 |
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 |
|---|---|---|---|
| Accipiter striatus | HAS_ACCEPTED_NAME | col | Accipiter striatus |
| Acomys cineraceus | HAS_ACCEPTED_NAME | col | Acomys cineraceus |
| Allactaga tetradactyla | HAS_ACCEPTED_NAME | col | Allactaga tetradactyla |
| Alouatta macconnelli | HAS_ACCEPTED_NAME | col | Alouatta macconnelli |
| resolvedCatalogName | resolvedRank | count |
|---|---|---|
| col | NA | 5 |
| col | family | 3 |
| col | genus | 2 |
| col | order | 1 |
| col | species | 144 |
| col | subspecies | 5 |
| discoverlife | NA | 159 |
| gbif | family | 3 |
| gbif | genus | 2 |
| gbif | order | 1 |
| gbif | species | 144 |
| gbif | subspecies | 10 |
| itis | NA | 21 |
| itis | family | 3 |
| itis | genus | 1 |
| itis | order | 1 |
| itis | species | 132 |
| itis | subspecies | 2 |
| mdd | NA | 159 |
| ncbi | NA | 9 |
| ncbi | family | 3 |
| ncbi | genus | 1 |
| ncbi | order | 1 |
| ncbi | species | 141 |
| ncbi | subspecies | 4 |
| pbdb | NA | 62 |
| pbdb | family | 3 |
| pbdb | order | 1 |
| pbdb | species | 93 |
| tpt | NA | 25 |
| tpt | family | 1 |
| tpt | genus | 1 |
| tpt | species | 132 |
| wfo | NA | 159 |
| resolvedCatalogName | relationName | count |
|---|---|---|
| col | HAS_ACCEPTED_NAME | 147 |
| col | SYNONYM_OF | 9 |
| col | NONE | 5 |
| discoverlife | NONE | 159 |
| gbif | HAS_ACCEPTED_NAME | 154 |
| gbif | SYNONYM_OF | 9 |
| itis | HAS_ACCEPTED_NAME | 132 |
| itis | NONE | 21 |
| itis | SYNONYM_OF | 10 |
| mdd | NONE | 49 |
| mdd | HAS_ACCEPTED_NAME | 110 |
| ncbi | SAME_AS | 140 |
| ncbi | SYNONYM_OF | 10 |
| ncbi | NONE | 9 |
| pbdb | HAS_ACCEPTED_NAME | 90 |
| pbdb | NONE | 62 |
| pbdb | SYNONYM_OF | 7 |
| tpt | HAS_ACCEPTED_NAME | 138 |
| tpt | NONE | 25 |
| tpt | SYNONYM_OF | 2 |
| wfo | NONE | 159 |
| 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 |
|---|---|---|
| 2024-04-22T08:06:29Z | note | found [136] column definitions, but only [119] values: assuming undefined values are empty. |
| 2024-04-22T08:06:29Z | note | found [136] column definitions, but only [18] values: assuming undefined values are empty. |
| 2024-04-22T08:06:29Z | note | source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder |
| 2024-04-22T08:06:29Z | note | target taxon name missing |
In addtion, you can find the most frequently occurring notes in the table below.
| reviewComment | count |
|---|---|
| found [136] column definitions, but only [119] values: assuming undefined values are empty. | 3 |
| found [136] column definitions, but only [18] values: assuming undefined values are empty. | 3 |
| source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder | 3 |
| target taxon name missing | 3 |
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.