[Taxacom] Species Cite: linking scientific names to publications and taxonomists

Tue Aug 3 02:19:06 CDT 2021

Hi Rod,

But of course both (citation of the literature source and citation of a
particular treatment) are useful moreover they can be used for different
purposes. The two ways of citations are linked to each other, as treatments
come always from the published literature and hence they always bear their
respective article / book metadata. Going deeper, a treatment can not only
"cite" a specimen used to support that treatment but also link directly to
the specimen's metadata in a collection, from there one can get the link to
the sequence data of that specimen and so on. That said, I fully understand
that you are not the person we should try to explain the importance of this
cascade of linkages, as many of these ideas have been formulated in your
early blogs and papers.

I think what Donat wanted to stress upon is that  linking of taxon names to
the DOIs of PDFs where a particular taxon name has been mentioned is only a
very basic first step which actually differs from what taxonomists have
been doing for centuries only in scale and accessibility thanks to the
Internet. There are already tools and workflows that provide a far more
granular linking between FAIR data and their further development and
adoption by the biodiversity community is the main goal of the starting
BiCIKL <http://bicikl-project.eu> project.

Best regards,
Lyubo

-----
Prof. Dr. Lyubomir Penev
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On Tue, Aug 3, 2021 at 9:43 AM Roderic Page via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> Hi Donat,
>
> I’ll leave it to John to decide whether the links you provide are the sort
> of thing he was after.
>
> If we think of all these interconnected facts as nodes and edges in  a
> “knowledge graph”, then we’re all working on the same thing, just focussing
> on different nodes, based on a combination of what we think matters and
> what our skills and resources are.
>
> Obviously we may view the same things differently. If the goal is to
> provide article level citations then the often cryptic treatment-style
> citations in taxonomy are an obstacle (what article does  "Molec. Phylogen.
> Evol. 59(2): 328” refer to?). If treatment citations are the goal, then a
> citation like:
>
> Coughenour, J. M., Simmons, M. P., Lombardi, J. A., Yakobson, K., &
> Archer, R. H. (2011). Phylogeny of Celastraceae subfamily Hippocrateoideae
> inferred from morphological characters and nuclear and plastid loci.
> Molecular Phylogenetics and Evolution, 59(2), 320–330.
> doi:10.1016/j.ympev.2011.02.017
>
> is the wrong level of granularity. I think both are useful.
>
> Regards,
>
> Rod
>
>
>
>
> On 2 Aug 2021, at 18:18, Donat Agosti <agosti at amnh.org<mailto:
> agosti at amnh.org>> wrote:
>
> Hi John
>
> A species does only indirectly cite an article. It cites a taxonomic
> treatment, a section of the text the author explicitly created to talk
> about the respective species (taxon; see also slide 4 here
> https://doi.org/10.5281/zenodo.5052458 ). The articles are the carriers
> or containers of the treatments, traditionally published as book or
> article. This tradition has been started already by Linnaeus in 1753 and
> 1758 respectively. At that time it was an efficient way to convey this
> information, whilst today it is a prison and hampering the development of
> our biodiversity knowledge, because the data therein is not open, digitally
> accessible knowledge.
>
> Whilst still a large amount of taxonomic work is not accessible because of
> closed access increasingly treatments, ie over 500,000 alone through
> TreatmentBank, are available in a format that is open, accessible, citable
> and can easily be reused, including those from closed access publications.
> Most of Pensoft Publications, EJT, or those published by the Museum
> nationale d'Histoire Naturelle Paris are now published in a way so that the
> data, e.g. taxonomic treatments, figures and material citations can
> directly be reused. A new collaboration between BHL and Plazi will provide
> further access to and disseminate data in taxonomic publications to
> aggreagators, such as GBIF.
>
> For example there are now treatments liberated from over 35,500 taxonomic
> publications reused and accessible through GBIF, and the data has been
> reused by over 400 scientific publications.
> The Biodiversity Literature Repository
> https://zenodo.org/communities/biosyslit/search?page=1&size=20&q=&sort=mostrecent
> now includes 324,000 images
> https://zenodo.org/communities/biosyslit/search?page=1&size=20&q=&type=image&sort=mostrecentliberatedfrom
> over 50,000 taxonomic publications. It includes an increasing amount of
> taxonomic treatments
> https://zenodo.org/communities/biosyslit/search?page=1&size=20&q=&sort=mostrecent&subtype=taxonomictreatment
> all as FAIR data with extensive metadata, persistent identifiers (DOI) so
> it can easily be discovered.
>
> All the data is accessible through the Plazi Treatment Collection
> Statistics. For example, for 2020 alone treatments for 7,900 new species
> and 570 new genera published in this year have been liberated, as part of
> 42,000 treatments published in 2020. http://tb.plazi.org/GgServer/srsStats
>
> There is even considerable support by Arcadia Fund or grants from EU
> Horizon 2020 (BiCIKL) or Swissuniversities (eBioDiv) to make literature
> based data accessible, citable and linked to specimens, genes, taxonomic
> names.
>
> You can explore your taxa in GBIF, where there is a chance to find
> treatments, images, material citations for your species; you can explore
> BLR, TreatmentBank, or experimental applications such as Synospecies (
> https://synospecies.plazi.org/) or Ocellus (https://ocellus.info/) or the
> BLR Website (https://www.biolitrepo.org/). It might also be possible to
> find the data about your species via Wikidata in the source treatments.
>
> Most importantly, we are well ahead to make the taxonomic treatments not
> only citable, but provide access to all the data used by the author when
> writing it up.
>
> This essentially allows to add to each identification the reference
> treatment the person identifying has in mind. Much more, a taxonomic name
> linked to a treatment opens up immediately access to the knowledge about it
> - just because treatments themselves are very rich in implicit citations of
> external resources, all of which are rapidly being digitized. Whilst
> citation of an article in many cases leads to a barrier that can only be
> surmounted with a huge effort and thus hampering taxonomic research and
> access to biodiversity data, citing a treatment does not.
>
> Cheers
>
> Donat
>
>
>
>
> -----Original Message-----
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu<mailto:
> taxacom-bounces at mailman.nhm.ku.edu>> On Behalf Of Roderic Page via Taxacom
> Sent: Monday, August 2, 2021 6:17 PM
> To: John Grehan <calabar.john at gmail.com<mailto:calabar.john at gmail.com>>
> Cc: taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] Species Cite: linking scientific names to
> publications and taxonomists
>
> EXTERNAL SENDER
>
>
> Hi John,
>
> This would be a nice thing to have, and as we link things together we may
> be able to get closer to being able to do this.
>
> There have been various attempts in the past. Dave Remsen had a tool that
> subscribed to journal RSS feeds (basically a news reader) and could give
> you lists of recent papers for a taxonomic group. My old iSpecies tried to
> grab data from various sources to summarise what we knew about a taxon.
> There are others.
>
> I've often found Wikipedia to be useful, but that is highly dependent on
> someone with the time and energy to maintain that page. But it's striking
> how often a single sentence will be so much more informative than a
> database.
>
> I suspect that the way forward will be to "automagically" write summaries
> based on a database like Wikidata. In other words, take a set of facts
> about a taxon (e.g., how many species, when the most recent was found,
> something on ecology, etc.) and convert that to natural language, complete
> with references. I think the Encyclopedia of Life attempted something like
> this.
>
> My sense is that what you ask for is in principle doable, if probably a
> bit harder than it sounds, but at the same time is the sort of thing that
> biodiversity informatics should be capable of doing (i.e., making things
> that people actually find useful, rather than thing we can do because,
> well, we can).
>
> Regards,
>
> Rod
>
>
>
> On 2 Aug 2021, at 16:09, John Grehan <calabar.john at gmail.com<mailto:
> calabar.john at gmail.com><mailto:calabar.john at gmail.com>> wrote:
>
> This current discussion reminds me to ask what is out there that is free
> and comprehensive (as much as one might hope for) in terms of recording new
> taxonomic publications for a particular group (terrestrial family in my
> case) that is comparable to Zoo Record or Biosis (which I don't have access
> to), and perhaps even include publications on other aspects of particular
> taxa (e.g. biology, systematics). Under my circumstances I am currently
> left to random Web searches that are hit or miss.
>
> John Grehan
>
> On Mon, Aug 2, 2021 at 7:15 AM Quentin Groom via Taxacom <
> taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu><mailto:
> taxacom at mailman.nhm.ku.edu>> wrote:
> I imagine marine people are very happy with WoRMS, it is a very rich
> source, but it exists in its own marine bubble with only implicit links
> out. How wonderful it would be if all the people it mentions were
> disambiguated (authors, authorities, editors), because then it could really
> take a strong place in the biodiversity informatics landscape, not just the
> marine section of it.
> Quentin
>
>
>
>
>
> On Mon, 2 Aug 2021 at 11:54, Roderic Page via Taxacom <
> taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu><mailto:
> taxacom at mailman.nhm.ku.edu>> wrote:
>
> Hi Lena,
>
> WoRMS is great, and is something that I plan to add to Species-Cite in
> the future.
>
> From my perspective the thing WoRMS lacks is links to external
> identifiers for the literature (e.g., DOIs, etc.). This means that the
> literature is essentially in a database-specific silo 9this is true of
> most taxonomic databases). Now, for WoRMS users that may be just fine,
> the database meets their needs, the names and citations they are after are
> there.
>
> I'd like things to be less siloed such that, for example, I can go
> from a name in WoRMS to an external identifier for the literature,  to
> the taxonomists who did the work, and the full text for the paper. And
> I'd like to do that all in one place.
>
> I think for anyone aggregating data the challenge is to deliver value
> above and beyond what individual databases can do, otherwise there is
> little point in aggregating the data in the first place. So I guess
> the challenge would be to see if aggregating data from WoRMS can
> create something that adds value on top of what WoRMS itself offers.
> And of course, any such value would be available to WoRMS to
> incorporate if the WoRMS editors felt it added something to their database.
>
> Regards,
>
> Rod
>
>
> On 2 Aug 2021, at 10:37, Elena Kupriyanova
> <Elena.Kupriyanova at Australian.Museum<mailto:
> Elena.Kupriyanova at Australian.Museum><mailto:
> Elena.Kupriyanova at Australian.Museum><mailto:
> Elena.Kupriyanova at Australian.Museum<mailto:
> Elena.Kupriyanova at Australian.Museum><mailto:
> Elena.Kupriyanova at Australian.Museum>>> wrote:
>
> Dear colleagues,
>
> I am not talking about it for a simple reason -  I did not want to
> mention that for marine species we already have WoRMS (World Register
> of Marine
> Species)
> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.m
> arinespecies.org
> <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.marinespecies.org>
> <http://arinespecies.org/
> >%2Findex.php&data=04%7C01%7C%7C7ec2aca5eae34e59c4c
> 908d955d0fafd%7Cbe0003e8c6b9496883aeb34586974b76%7C0%7C0%7C63763517834
> 0500359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLC
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> uyJaykcbmZW0QISHdyM%3D&reserved=0
> I happen to be one of hundreds of taxonomical editors for this
> database Sorry...
> Best,
> Lena
>
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