[Taxacom] Automated monitoring of the taxonomic literature

Wed Nov 24 13:36:01 CST 2021

Hi Rod,
I have a similar interest and thus a similar problem to that of Peter Uetz:
Myriapoda & Onychophora are around 15K valid species (very rough number).
Of course, the new works on reptiles are definitely more than those on
multipedes.
When I see new tools, I always ask myself if they could be wrapped in a
virtual research environment (VRE), and not just exist as a standalone
application or web service. That's a good thing to keep in mind when
developing something like BioRSS.
Finding both new and old names is important in the course of a research
workflow. That is one of the reasons why I like that Scratchpads has both
ReFindIt and BHL search integrated with a customizable classification (taxonomic backbone). Because of that, if I were to create something like
BioRSS, the first thing that I would do is to import a classification as
complete as possible, at least down to the family level, but that would
take BioRSS closer to being a virtual research environment, which takes me
back to the idea of rather having the service as a module and adding it to
an existing VRE with a taxonomic backbone. Then something like BioRSS could
be an alternative or addition to integration with ReFindIt.
If I were to use a standalone BioRSS as a broker of other feeds, then I
would very much like it to have "Myriapoda" in the classification. One
issue that I see is deduplication, e.g., a broker should reduce and not add
more reading burden on top of Google Scholar alerts, journal alerts, etc.
If such a broker could deduplicate alerts, then that would already be a
win, as users could subscribe to the broker and unsubscribe from journals +
Google Scholar + other alerts.
Anyway, it seems that there is no replacement for a tight community
committed to recording, as some publications (including new taxa) don't
reach the internet and others do but are not findable by taxon. In the
latter I include articles in technologically advanced journals which do
taxon tagging for the "text" but not for the supplementary data. If authors
(mainly in ecology and molecular biology) are trying to save on pricey page
charges, taxa tend to be relegated to those supplementary files and thus
not marked up. Then recorders have no other option than to take a closer
look at unmatched but "suspicious" articles.
Next in automatically monitoring new literature for databasing purposes is
the possibility to make a bulk download (BibTex, RIS) of the bibliographic
references for closer inspection, or for direct, bulk upload into a
database. It is inefficient to go back to the sources and download a BibTex
or a RIS at the time. That also depends on how frequently one wants / can
update the database. If there are two updates per year and few people,
better to go to the publishers a couple of times, make a search, and export
references in bulk. So, the preferences will depend on the tradeoff between
"daily / weekly aggregated and downloadable references from a broker"
versus "biannual / annual aggregated and downloadable references from a
publisher or journal". If the broker can't provide bulk download, the users
may tend to shift to other services.
Taxonomic databases as a source: In Myriatrix (a Scratchpad) I do try to
add DOIs whenever available. I also try to record publication dates as
exact as possible in a dedicated "Date Published:" field. Additionally,
most bibliographic databases (all?) would try to record the publication
year ("Year of Publication:" in Scratchpads). Those two fields should
facilitate harvesting recent literature from Scratchpads sites, with the
added benefit of the references being exportable in bulk in several
interoperable formats. Combined with taxon search and matching in titles,
abstracts, and keywords, that would make e.g., myriapod-reptile
publications discoverable and downloadable for reuse in the Reptile
Database.
Just my five cents.
Kind regards,
Carlos

Carlos A. Martínez Muñoz
Zoological Museum, Biodiversity Unit
FI-20014 University of Turku
Finland
Myriatrix <http://myriatrix.myspecies.info/>
ResearchGate profile
<https://www.researchgate.net/profile/Carlos_Martinez-Munoz>
Myriapod Morphology and Evolution
<https://www.facebook.com/groups/205802113162102/>