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:
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.
The review process can be described in the form of a script:
# get versioned copy of the dataset under review elton pull globalbioticinteractions/lacm-lacmec # generate review notes elton review globalbioticinteractions/lacm-lacmec\ > review.tsv # export indexed interaction records elton interactions globalbioticinteractions/lacm-lacmec\ > interactions.tsv # export names and align them with the Catalogue of Life using Nomer elton names globalbioticinteractions/lacm-lacmec\ | nomer append col\ > name-alignment.tsv
or 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/lacm-lacmec) contains 0 interactions with 0 (e.g., ) unique types of associations between 0 primary taxa (e.g., ) and 0 associated taxa (e.g., ).
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.
: Sample of Indexed Interaction Claims
: Most Frequently Mentioned Interaction Types (up to 20 most frequent)
: Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
: Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
: Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
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.
|2023-09-28T03:24:44Z||note||no interactions found|
In addtion, you can find the most frequently occurring notes in the table below.
|no interactions found||1|
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.