[Taxacom] Automated monitoring of the taxonomic literature

Sat Dec 4 11:56:33 CST 2021

Hi Rod,
Five more cents for BioRSS.
There is some summary data for new Myriapoda and Onychophora taxa for the
year 2020 here (
https://www.researchgate.net/publication/356598842_Some_summary_data_and_metrics_on_Myriapoda_Onychophora_for_the_year_2020).
In total, there were 204 Myriapoda & Onychophora new taxonomic names
recorded for 2020, of which 7 names were in Onychophora and 197 names were
in Myriapoda (including Euthycarcinoidea). The names were published by 102
authors, in 63 publications. I have now shortlisted the 18 journals in
which those publications appeared, with the hope that you will manage to
track most of them for BioRSS.
List of journals, in alphabetical order:
Annales de la Société entomologique de France (N.S.), Arthropoda Selecta,
Biologia Serbica, Bulletin de la Société d'Histoire naturelle de Toulouse,
Cretaceous Research, European Journal of Taxonomy, Invertebrate
Systematics, Journal of Paleontology, Opuscula Zoologica, Proceedings of
the Royal Society of Victoria, Revista de Biología Tropical, Revue suisse
de Zoologie, Royal Society Open Science, Subterranean Biology, The Raffles
Bulletin of Zoology Supplement, Transactions of the American Entomological
Society, ZooKeys, Zootaxa.

Dear Taxacomers,
>From the group of journals mentioned above, the top three poorest
performers in the subgroup of "paywalled and hybrid journals" regarding
individual article pricing are listed below:
1) First prize goes to the Société entomologique de France and its
partnership with Taylor & Francis, publishing the hybrid journal *Annales
de la Société entomologique de France (N.S.)*, and pricing individual
articles at 46.00 EUR (at least from my location / IP address);
2) Shared second prize goes to Elsevier, publishing the hybrid journal
*Cretaceous
Research*, and pricing individual articles at 37.95 USD; and to
3) CSIRO Publishing, a not-for-profit, publishing the hybrid journal *
Invertebrate Systematics*, and pricing individual articles at 60.00 AUD.
With those prices, the generous not-for-profit actors will be the buyers. I
hope that they are getting a commensurable tax deduction for their
generosity every time they purchase an article.

Gentle reminders:
1) The hybrid open access pricing model is the worst of all, because it
creates "double-dipping".
2) Elsevier and Taylor & Francis are part of the oligopoly of 5 publishers
that control more than half of academic publishing, and thus the market
prices. When authors, societies, institutions, and national-level consortia
(especially the latter) choose to publish with them, they (we) are not
exempt from social responsibility.
3) Taylor & Francis is publicly circulating an advertisement containing a
misleading statement, made intentionally to promote the sale of services to
the public: "The article publishing charge supports a range of services
which help ensure the trust, quality and impact of your published research.
When you publish open access with us, you’ll get: Robust peer review: your
paper benefits from thorough review by experts in your field, with
objective and constructive evaluation ahead of publication. (...)" (see
https://authorservices.taylorandfrancis.com/publishing-open-access/open-access-cost-finder/).
The statement is misleading because there is nothing to claim from the
publisher's side if the mentioned "experts" conducting the "robust peer
review" don't receive an amount of the APC as payment. This sort of false
advertising can be reported to the UK Advertising Standards Authority (ASA).

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/>

El jue, 25 nov 2021 a las 10:55, Carlos Alberto Martínez Muñoz (<
biotemail at gmail.com>) escribió:

> Hi Rod,
> Just one quick note: GBIF's classification does not have "Myriapoda", so I
> will have to look for the myriapod classes in BioRSS until that is solved
> on GBIF's side.
> Thanks to you too for your work!
> 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/>
>
>
>
>
> El jue, 25 nov 2021 a las 7:26, Roderic Page (<Roderic.Page at glasgow.ac.uk>)
> escribió:
>
>> Hi Carlos,
>>
>> Thanks for the detailed response. This gives me a sense of the
>> expectations for such a service.
>>
>> In a sense I’ve gone about this the opposite way to what you suggest. The
>> classification in BioRSS is being assembled as the literature collection
>> grows, and it follows GBIF’s classification. That is, the treemap diagram
>> on the left summarises what taxa are in the database so far (based on
>> taxonomic names found in the title and/or abstract). As new papers are
>> added this diagram will expand to include more taxa.
>>
>> Regarding integration with a virtual research environment, this is a good
>> point. At the moment I have focussed on RSS as the API, that is, each
>> combination of taxon and geography has a corresponding RSS feed, the idea
>> being that one could simply grab the URL to a feed of interest and poll
>> that for publications.
>>
>> The desire to have access to the data in a bibliographic format such as
>> BibTex or RSS has also been mentioned by Tony Rees. Initially I was
>> avoiding this as the RSS feeds I use typically lack bibliographic details,
>> but there are ways around this. The data could be stored in BioRSS, or
>> elsewhere such as Wikidata (which is rapidly becoming a repository of a lot
>> of taxonomic literature).
>>
>> Any automated service will have limitations, and the taxonomic literature
>> is particularly challenging given how many journals publish taxonomy.
>> Zootaxa dominates animal taxonomy making it an obvious source, but there is
>> a very long tail of other publications. I am looking at adding Google
>> Scholar as a source, which brings its own challenges.
>>
>> Regarding taxonomic databases as a source, this is something I am
>> thinking about, especially databases that regularly get updated (ZooBank
>> being an obvious one). But I guess the real proof of utility for BioRSS
>> would be that people find references in BioRSS to add to those databases,
>> not the other way around.
>>
>> Thanks again for the feedback, I’ve clearly got a lot of work to do.
>>
>> Regards,
>>
>> Rod
>>
>>
>> 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
>>
>>