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/usnm-ixodes, is 8.03MiB in size and contains 10,199 interaction with 1 unique type of association (e.g., hasHost) between 394 primary taxa (e.g., IXODES SP.) and 2,334 associated taxon (e.g., DRAG). 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:
US National Museum of Natural History Ixodes Records https://github.com/globalbioticinteractions/usnm-ixodes/archive/2c2454bece9307bedc01a5dee5a09e459b879641.zip 2024-04-20T06:09:59.841Z be07d893994692bb9a464c2a290efcc1db75ed2ebd8327a9df90f53210c568b3
For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/usnm-ixodes 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. 8.03MiB) under review
elton pull globalbioticinteractions/usnm-ixodes
# generate review notes
elton review globalbioticinteractions/usnm-ixodes\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/usnm-ixodes\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/usnm-ixodes\
| 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/usnm-ixodes, is 8.03MiB in size and contains 10,199 interaction with 1 unique type of association (e.g., hasHost) between 394 primary taxa (e.g., IXODES SP.) and 2,334 associated taxon (e.g., DRAG).
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 |
|---|---|---|---|
| IXODES (ENDOPALPIGER) | hasHost | PARAMYTHIA MONTIUM | Copy_of_Ixodes_June29_complete.tsv |
| IXODES (ENDOPALPIGER) SP. | hasHost | CRATEROSCELIS ROBUSTA | Copy_of_Ixodes_June29_complete.tsv |
| IXODES (ENDOPALPIGER) SP. | hasHost | PENEOTHELLO SIGILLATUS | Copy_of_Ixodes_June29_complete.tsv |
| IXODES (IXODES) NEAR LORICATUS | hasHost | DIDELPHIS MARSUPIALIS | Copy_of_Ixodes_June29_complete.tsv |
| interactionTypeName | count |
|---|---|
| hasHost | 15845 |
| sourceTaxonName | count |
|---|---|
| IXODES SP. | 3333 |
| IXODES PACIFICUS | 952 |
| IXODES SCAPULARIS | 943 |
| IXODES RICINUS | 810 |
| IXODES ANGUSTUS | 779 |
| IXODES GRANULATUS | 776 |
| IXODES SCULPTUS | 665 |
| IXODES OVATUS | 561 |
| IXODES ARBORICOLA | 408 |
| IXODES COOKEI | 330 |
| IXODES ACUTITARSUS | 319 |
| IXODES URIAE | 251 |
| IXODES SPINIPALPIS | 248 |
| IXODES LORICATUS | 211 |
| IXODES KINGI | 202 |
| IXODES LUCIAE | 197 |
| IXODES DENTATUS | 192 |
| IXODES SORICIS | 160 |
| IXODES TEXANUS | 155 |
| targetTaxonName | count |
|---|---|
| DRAG | 611 |
| HOMO SAPIENS | 490 |
| LUSCINIA LUSCINIA | 428 |
| SPERMOPHILUS RICHARDSONI | 403 |
| PASSER DOMESTICUS | 272 |
| PEROMYSCUS MANICULATUS | 263 |
| DOG | 252 |
| STENOMYS NIOBE | 245 |
| ODOCOILEUS VIRGINIANUS | 212 |
| CATTLE | 196 |
| SYLVILAGUS SP. | 183 |
| GOPHER | 181 |
| MICROTUS CANICAUDUS | 172 |
| PROCYON LOTOR | 151 |
| DIDELPHIS MARSUPIALIS | 137 |
| PUMA CONCOLOR FLORIDANUS | 130 |
| RATTUS MUELLERI | 122 |
| SPERMOPHILUS BEECHEYI | 120 |
| SQUIRREL GROUND | 116 |
| sourceTaxonName | interactionTypeName | targetTaxonName | count |
|---|---|---|---|
| IXODES PACIFICUS | hasHost | DRAG | 539 |
| IXODES RICINUS | hasHost | LUSCINIA LUSCINIA | 412 |
| IXODES ARBORICOLA | hasHost | PASSER DOMESTICUS | 272 |
| IXODES SCULPTUS | hasHost | SPERMOPHILUS RICHARDSONI | 248 |
| IXODES SP. | hasHost | STENOMYS NIOBE | 230 |
| IXODES SCAPULARIS | hasHost | ODOCOILEUS VIRGINIANUS | 185 |
| IXODES SP. | hasHost | GOPHER | 156 |
| IXODES ANGUSTUS | hasHost | MICROTUS CANICAUDUS | 150 |
| IXODES ACUTITARSUS | hasHost | HOMO SAPIENS | 144 |
| IXODES DENTATUS | hasHost | SYLVILAGUS SP. | 120 |
| IXODES GRANULATUS | hasHost | RATTUS MUELLERI | 114 |
| IXODES ANGUSTUS | hasHost | PEROMYSCUS MANICULATUS | 112 |
| IXODES SP. | hasHost | SPERMOPHILUS RICHARDSONI | 106 |
| IXODES SP. | hasHost | MELOMYS PLATYOPS | 104 |
| IXODES ARBORICOLA | hasHost | PASSER DOMESTICUS NILOTICUS | 103 |
| IXODES SCAPULARIS | hasHost | HOMO SAPIENS | 88 |
| IXODES TEXANUS | hasHost | PROCYON LOTOR | 83 |
| IXODES SCULPTUS | hasHost | SPERMOPHILUS BEECHEYI | 82 |
| IXODES SCAPULARIS | hasHost | PUMA CONCOLOR FLORIDANUS | 78 |
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 |
|---|---|---|---|
| Abrocoma bennetti | NONE | col | Abrocoma bennetti |
| Abrothrix longipilis | HAS_ACCEPTED_NAME | col | Abrothrix longipilis |
| Acanthiza ewingii | HAS_ACCEPTED_NAME | col | Acanthiza ewingii |
| Acanthiza pusilla | HAS_ACCEPTED_NAME | col | Acanthiza pusilla |
| resolvedCatalogName | resolvedRank | count |
|---|---|---|
| col | NA | 1161 |
| col | class | 1 |
| col | family | 3 |
| col | genus | 178 |
| col | kingdom | 1 |
| col | species | 1119 |
| col | subfamily | 1 |
| col | subgenus | 25 |
| col | subspecies | 156 |
| discoverlife | NA | 2621 |
| gbif | NA | 1055 |
| gbif | class | 1 |
| gbif | family | 3 |
| gbif | form | 1 |
| gbif | genus | 198 |
| gbif | kingdom | 1 |
| gbif | species | 1202 |
| gbif | subspecies | 162 |
| itis | NA | 1172 |
| itis | class | 1 |
| itis | family | 3 |
| itis | genus | 175 |
| itis | kingdom | 1 |
| itis | order | 1 |
| itis | species | 1108 |
| itis | subfamily | 1 |
| itis | subgenus | 2 |
| itis | subspecies | 157 |
| mdd | NA | 2620 |
| ncbi | NA | 1369 |
| ncbi | class | 1 |
| ncbi | family | 3 |
| ncbi | genus | 171 |
| ncbi | kingdom | 1 |
| ncbi | species | 996 |
| ncbi | subfamily | 1 |
| ncbi | subgenus | 2 |
| ncbi | subspecies | 79 |
| pbdb | NA | 1888 |
| pbdb | class | 1 |
| pbdb | family | 3 |
| pbdb | genus | 165 |
| pbdb | kingdom | 1 |
| pbdb | order | 1 |
| pbdb | species | 555 |
| pbdb | subfamily | 1 |
| pbdb | suborder | 1 |
| pbdb | subspecies | 5 |
| pbdb | unranked clade | 1 |
| tpt | NA | 1522 |
| tpt | family | 3 |
| tpt | genus | 157 |
| tpt | species | 938 |
| wfo | NA | 2616 |
| wfo | genus | 3 |
| wfo | phylum | 1 |
| resolvedCatalogName | relationName | count |
|---|---|---|
| col | NONE | 1222 |
| col | HAS_ACCEPTED_NAME | 1721 |
| col | SYNONYM_OF | 718 |
| discoverlife | NONE | 3110 |
| gbif | NONE | 1110 |
| gbif | HAS_ACCEPTED_NAME | 1756 |
| gbif | SYNONYM_OF | 834 |
| itis | NONE | 1233 |
| itis | HAS_ACCEPTED_NAME | 1648 |
| itis | SYNONYM_OF | 244 |
| mdd | NONE | 2348 |
| mdd | HAS_ACCEPTED_NAME | 757 |
| ncbi | NONE | 1492 |
| ncbi | SAME_AS | 1412 |
| ncbi | SYNONYM_OF | 209 |
| ncbi | COMMON_NAME_OF | 1 |
| pbdb | NONE | 2147 |
| pbdb | HAS_ACCEPTED_NAME | 889 |
| pbdb | SYNONYM_OF | 80 |
| tpt | NONE | 1649 |
| tpt | HAS_ACCEPTED_NAME | 1478 |
| wfo | NONE | 3100 |
| wfo | SYNONYM_OF | 1 |
| wfo | HAS_ACCEPTED_NAME | 3 |
| 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 |
|---|---|---|
| 2024-04-22T08:08:47Z | note | target taxon name missing |
| 2024-04-22T08:08:47Z | note | target taxon name missing |
| 2024-04-22T08:08:47Z | note | target taxon name missing |
| 2024-04-22T08:08:47Z | note | target taxon name missing |
In addtion, you can find the most frequently occurring notes in the table below.
| reviewComment | count |
|---|---|
| target taxon name missing | 846 |
| date [2043-01-01T00:00:00Z] is in the future | 2 |
| failed to parse value [196722–] from column [Host1::FMTDTE2] into column [http://rs.tdwg.org/dwc/terms/eventDate] with datatype: {“base”:“date”,“format”:“YYYYMMdd”,“id”:“string”} | 1 |
| failed to parse value [19690631] from column [Host1::FMTDTE2] into column [http://rs.tdwg.org/dwc/terms/eventDate] with datatype: {“base”:“date”,“format”:“YYYYMMdd”,“id”:“string”} | 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.
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.