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

Tue Aug 3 03:43:06 CDT 2021

Hi Rod,

I can only wholeheartedly agree with such a balanced approach and it fully
overlaps with my personal perception. No articles - no treatments,
unless people start to publish treatments outside journals, where they,
however, would look like in a rather similar way, that is containers of
information bearing metadata (who, when, how and where) and identifiers
(most probably same DOIs).

Neglection of citation of articles is the last thing I would like to see as
a publisher and this concerns not only the articles we publish but also all
historical literature and all that by other recent publishers.

Best regards,
Lyubo
-----
Prof. Dr. Lyubomir Penev
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On Tue, Aug 3, 2021 at 11:03 AM Roderic Page <Roderic.Page at glasgow.ac.uk>
wrote:

> Hi Lyubo,
>
> I’m not disputing any of this, although I’d quibble about “only a very
> basic first step”. This depends on what the goals are. If you want to link
> to part of an article then yes, identifying the “container” for that part
> (i.e., a fragment of an article) is only a first step, and one that you
> could argue has been neglected in the past. Taxonomists, obviously, are not
> the only scholars who link to parts of publications and who may feel that
> publication-level linking is inadequate.
>
> But articles are part of the scholarly citation graph, it is how we
> currently track the provenance of ideas, they are how we currently measure
> credit (I realise the scope of credit can be expanded to include other
> things), and they are a common currency linking to other databases (for
> example, nucleotide sequences in GenBank are typically linked to the
> publication of that data).
>
> Hence I think there is value in making the link between a name and a
> publication. Equally, there is value in links between fragments of an
> article and the name, and between fragments from different articles. I
> don’t think either is intrinsically better or more valuable than the other,
> it depends on what the goals are. I look forward to having as many of both
> sorts of links as possible.
>
> Regards,
>
> Rod
>
>
> On 3 Aug 2021, at 08:19, Lyubomir Penev <lyubo.penev at gmail.com> wrote:
>
> 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
> ORCID: http://orcid.org/0000-0002-2186-5033
> WoS ResearcherID: O-9982-2019
> <https://publons.com/researcher/324250/lyubomir-penev/>
> Founder and CEO
> Pensoft Publishers <http://pensoft.net/>
> ARPHA Journal Publishing Platform <http://arphahub.com/>
> 13a Geo Milev Street
> 1111 Sofia, Bulgaria
> Tel +359-2-8704281
> Fax +359-2-8704282
> Publishing services for journals <http://arphahub.com/about/services> I
> Journals <http://journals.pensoft.net/> I Books
> <http://pensoft.net/books-published-by-Pensoft>
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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
>> JBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4noKZSp0Acy1AeUAuzEjilAa
>> uyJaykcbmZW0QISHdyM%3D&reserved=0
>> I happen to be one of hundreds of taxonomical editors for this
>> database Sorry...
>> Best,
>> Lena
>>
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>> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftaxacom.markmail.org%2F&data=04%7C01%7C%7C7ec2aca5eae34e59c4c908d955d0fafd%7Cbe0003e8c6b9496883aeb34586974b76%7C0%7C0%7C637635178340510315%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=zGrsL%2BBTvLKK3n5z8iKHVAdmUBTdGT8musgxDij%2Fjbw%3D&reserved=0
>>
>> Nurturing nuance while assailing ambiguity for about 34 years, 1987-2021.
>>
>> _______________________________________________
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>> The Taxacom email archive back to 1992 can be searched at:
>> http://taxacom.markmail.org
>>
>> Nurturing nuance while assailing ambiguity for about 34 years, 1987-2021.
>>
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