University of Glasgow

Roderic Page

More arm-waving notes on taxonomic databases. I\'ve started to add data
to [ChecklistBank](https://www.checklistbank.org) and this has got me
thinking about the issue of data quality. When you add data to
ChecklistBank you are asked to give a measure of confidence based on the
[Catalogue of Life Checklist
Confidence](https://www.catalogueoflife.org/about/glossary.html#checklist-confidence)
system of one - five stars: ★ - ★★★★★. I\'m scepetical about the notion
of confidence or \"trust\" when it is reduced to a star system (see also
[Can you trust
EOL?](https://iphylo.blogspot.com/2012/06/can-you-trust-eol.html)). I
could literally pick any number of stars, there\'s no way to measure
what number of stars is appropriate. This feeds into my biggest
reservation about the [Catalogue of
Life](https://www.catalogueoflife.org), it\'s almost entirely authority
based, not evidence based. That is, rather than give us evidence for why
a particular taxon is valid, we are (mostly) just given a list of taxa
are asked to accept those as gospel, based on assertions by one or more
authorities. I\'m not necessarly doubting the knowledge of those making
these lists, it\'s just that I think we need to do better than \"these
are the accepted taxa because I say so\" implict in the Catalogue of
Life.

So, is there any way we could objectively measure the quality of a
particular taxonomic checklist? Since I have a long standing interest in
link the primary taxonomic litertaure to names in databases (since
that\'s where the evidence is), I keep wondering whether measures based
on that literture could be developed.

I recently revisited the fascinating (and quite old) literature on rates
of synonymy:

> Gaston Kevin J. and Mound Laurence A. 1993 Taxonomy, hypothesis
> testing and the biodiversity crisisProc. R. Soc. Lond. B.251139--142
> <http://doi.org/10.1098/rspb.1993.0020>

> Andrew R. Solow, Laurence A. Mound, Kevin J. Gaston, Estimating the
> Rate of Synonymy, Systematic Biology, Volume 44, Issue 1, March 1995,
> Pages 93--96, <https://doi.org/10.1093/sysbio/44.1.93>

A key point these papers make is that the observed rate of synonymy is
quite high (that is, many \"new species\" end up being merged with
already known species), and that because it can take time to discover
that a species is a synonym the actual rate may be even higher. In other
words, in diagrams like the one reproduced below, the reason the
proportion of synonyms declines the nearer we get to the present day
(this paper came out in 1995) is not because are are creating fewer
synonyms but because we\'ve not yet had time to do the work to uncover
the remaining synonyms.

::: {.separator style="clear: both;"}
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhgwvBcDUD_IJZyAa0gaqXB--ogJeVooV19I635N_w2OuztDFsy-ZPXEFuW5S1NUxxUEHmN8pbdO9MPljIi5v0A2355kYotL1fKqdewP9kmWu9TfwtIJ3jD04SQjeF3SWK-yMVAx-rNc6TO43GIwmftPk6IghOrcmur6SoHe06ws7fEFAvxA/s400/Screenshot%202022-08-24%20at%2014.59.47.png){border="0"
width="400" original-height="404"
original-width="621"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhgwvBcDUD_IJZyAa0gaqXB--ogJeVooV19I635N_w2OuztDFsy-ZPXEFuW5S1NUxxUEHmN8pbdO9MPljIi5v0A2355kYotL1fKqdewP9kmWu9TfwtIJ3jD04SQjeF3SWK-yMVAx-rNc6TO43GIwmftPk6IghOrcmur6SoHe06ws7fEFAvxA/s621/Screenshot%202022-08-24%20at%2014.59.47.png){style="display: block; padding: 1em 0; text-align: center; "}
:::

Put another way, these papers are arguing that real work of taxonomy is
revision, not species discovery, especially since it\'s not uncommon for
\> 50% of species in a taxon to end up being synonymised. Indeed, if a
taxoomic group has few synonyms then these authors would argue that\'s a
sign of neglect. More revisionary work would likely uncover additional
synonyms. So, what we need is a way to measure the amount of research on
a taxonomic group. It occurs to me that we could use the citation graph
as a way to tackle this. Lets imagine we have a set of taxa (say a
family) and we have all the papers that described new species or
undertook revisions (or both). The extensiveness of that work could be
measured by the citation graph. For example, build the citation graph
for those papers. How many original species decsriptions are not cited?
Those species have been potentially neglected. How many large-scale
revisions have there been (as measured by the numbers of taxonomic
papers those revisions cite)? There are some interesting approaches to
quantifying this, such as using [hubs and
authorities](https://en.wikipedia.org/wiki/HITS_algorithm).

I\'m aware that taxonomists have not had the happiest relationship with
citations:

> Pinto ÂP, Mejdalani G, Mounce R, Silveira LF, Marinoni L, Rafael JA.
> Are publications on zoological taxonomy under attack? R Soc Open Sci.
> 2021 Feb 10;8(2):201617. [doi:
> 10.1098/rsos.201617](https://doi.org/10.1098/rsos.201617). PMID:
> 33972859; PMCID: PMC8074659.

Still, I think there is an intriguing possibility here. For this
approach to work, we need to have linked taxonomic names to
publications, and have citation data for those publications. This is
happening on various platforms. Wikidata, for example, is becoming a
repository of the taxonomic literature, some of it with citation links.

> Page RDM. 2022. Wikidata and the bibliography of life. PeerJ 10:e13712
> <https://doi.org/10.7717/peerj.13712>

Time for some experiments.


More arm-waving notes on taxonomic databases. I've started to add data to ChecklistBank and this has got me thinking about the issue of data quality.

Can we use the citation graph to measure the quality of a taxonomic database?

Garnett et al. recently published a paper in PLoS Biology that starts
with the sentence \"Lists of species matter\":

> Garnett, S. T., Christidis, L., Conix, S., Costello, M. J., Zachos, F.
> E., Bánki, O. S., ... Thiele, K. R. (2020). Principles for creating a
> single authoritative list of the world's species. PLOS Biology, 18(7),
> e3000736.
> [doi:10.1371/journal.pbio.3000736](https://doi.org/10.1371/journal.pbio.3000736)

This paper (one of a forthcoming series) is pretty much the kind of
paper I try and avoid reading. It has lots of authors so it is a paper
by committee, those authors all have a stake in particular projects, and
it is an acronym soup of organisations the paper is pitched at. It\'s a
well-worn strategy: write one or more papers outlining making the case
that there is a problem, then get funding based on the notion that
clearly there\'s a problem (you\'ve published papers saying so) and that
you and your co-applicants are best placed to solve it (clearly, because
you wrote the papers identifying the problem in the first place). I\'m
not criticising the strategy, it\'s how you get things done in science.
It just makes for a rather uninspiring read.

From my perspective focussing on \"lists\" is a mistake. Lists don\'t
really matter, it is what is on the list that counts. And I think this
is where the real prize is. As I play with Wikidata I\'m becoming
increasingly aware of the ~~clusterfuck~~ mess the taxonomic database
community has created by conflating taxonomic names with taxa, and by
having multiple identifiers for the same things. We survive this mess by
relying on taxonomic names as somewhat fuzzy identifiers, and the hope
that we can communicate successfully with other people despite this
ambiguity (I guess this is pretty much the basis of all communication).
As [Roger Hyam notes](http://www.hyam.net/blog/archives/1007):

> These taxon names we are dealing with are really just social tags that
> need to be organised in a central place.

Having lots of names (tags) is fine, and Wikidata is busy harvesting all
these taxonomic names and their identifiers (ITIS, IPNI, NCBI, EOL,
iNaturalist, eBird, etc., etc., etc.). For most of these names all we
have is a mapping to other identifiers for the same name, a link to a
parent taxon, and sometimes a link to a reference for the name. But what
happens if we want to attach data to a taxon? Take, for example, the
African Piculet *Verreauxia africana*. This bird has at least two
scientific names, each with a separate entry in Wikidata: *Verreauxia
africana* [Q28123873](https://www.wikidata.org/wiki/Q28123873) and
*Sasia africana* [Q1266812](https://www.wikidata.org/wiki/Q1266812).
These are the same species yet it has two entries in Wikidata. If I want
to add, say, body weight, or population size, or longevity, which
Wikidata item do I add that data too?

What we need is an identifier for the species, an identifier that
remains unchanged even if the name changes, or if that species moves in
the taxonomic hierarchy. Some databases do this already. For example the
eBird identifier for *Verreauxia africana*/*Sasia africana* is
[afrpic1](https://ebird.org/species/afrpic1). Because the identifier
remains unchanged we can do things such as \"diffs\" between successive
classifications showing how the species has moved between different
genera (see [Taxonomic publications as patch files and the notion of
taxonomic
concepts](https://iphylo.blogspot.com/2018/10/taxonomic-publications-as-patch-files.html)):

![45759416 c9c5ed80 bc1f 11e8 98ca
5f4554ddca42](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEht_pXf61_1l-VVNhxy1Zl9AsOh4DHsWShv4vTrt4Mz09570UpwWBp-u9RFxNV36SHqFOUFt7SKPrz0U-riq1Is3nQWfXuRaMgMGSZqJoHPtaWLaVG5Rr4aHVKG2OvsJY4qO7v1/s0/45759416-c9c5ed80-bc1f-11e8-98ca-5f4554ddca42.png "45759416-c9c5ed80-bc1f-11e8-98ca-5f4554ddca42.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="560" height="478"}

Ironically it seems that for birds the common name (in this case
\"African Piculet\") is a more stable identifier than the scientific
name (although that [may well
change](http://bit.ly/RequestAOSChangeBirdNames)). By having stable
taxon identifiers we can then decide what entity to attach biological
data to. Taxonomic names have failed to do this, but are still vital as
well known tags. The actual taxon identifiers should be opaque
identifiers (like \"afrpic1\" - not really opaque but close enough - or
Avibase\'s
[C4DFB5E31495AE94](https://avibase.bsc-eoc.org/species.jsp?avibaseid=C4DFB5E31495AE94)).
Make each opaque identifier a DOI, use existing taxonomic names as
formalised tags so we aren\'t disconnected from the literature, use
timestamped versions to track changes in species classification over
time, and we have something useful.

This, I think, is the real prize. Rather than frame the task as making a
list of species so that organisations can have a checklist they can all
share, why not frame it as providing a framework that we can hang trait
data on? We have vast quantities of data residing in siloed databases,
spreadsheets, and centuries of biological literature. The argument
shouldn\'t be about what is on a list, it should be how we group that
information together and enable people to do their science. By providing
stable identifiers that are resistant to name changes we can confidently
associate trait data with taxa. Taxonomy could then actually be what it
should be, the organisational framework for biological information (see
[Taxonomy as Information
Science](https://biostor.org/reference/250587)).


Garnett et al. recently published a paper in PLoS Biology that starts with the sentence "Lists of species matter":  This paper (one of a forthcoming series) is pretty much the kind of paper I try and avoid reading.

Lists of species don't matter: thoughts on "Principles for creating a single authoritative list of the world’s species"

Few things have annoyed be as much as the [following post on
TAXACOM](http://markmail.org/thread/piqil5tsjntvzne7):  
  

> The Global Names project will host a workshop to explore options and
> to make recommendations as to issues that relate to Attribution,
> Rights and Licensing of names and compilations of names. The aim of
> the workshop is a report that clarifies if and how we share names.  
>   
> We seek submissions from all interested parties - nomenclaturalists,
> taxonomists, aggregators, and users of names. Let us know what (you
> think) intellectual property rights apply or what rights should be
> associated with names and compilations of names. How can those who
> compile names get useful attribution for names, and what
> responsibilities do they have to ensure that information is
> authoritative. If there are rights, what kind of licensing is
> appropriate.  
>   
> Contributions can be submitted
> [http://names-attribution-rights-and-licensing.wikia.com/wiki/Main_Page](Contributions%20can%20be%20submitted%20http://names-attribution-rights-and-licensing.wikia.com/wiki/Main_Page,%20where%20you%20will%20find%20more%20information%20about%20this%20event.),
> where you will find more information about this event.

  
I\'m trying to work out why this seemingly innocuous post made me so
mad. I think this is because I think this fundamentally framing the
question the wrong way. Surely the goal is to have a list of names that
is global in scope, well documented, and freely usable by all without
restriction? Surely we want open and free access to fundamental
biodiversity data? In which case, can we please stop having meetings and
get on with making this so?  
  
If you frame the discussion as one of \"Attribution, Rights and
Licensing of names and compilations of names\" then you\'ve already lost
sight of the prize. You\'ve focussed on the presumed \"rights\" of name
compilers instead.  
  
I would argue that names compilations are somewhat overvalued. They are
basically lists of names, sometimes (all to rarely) with some degree of
provenance (e.g., a citation to the original use of the name). As I\'ve
documented before (e.g., [More fictional taxa and the myth of the expert
taxonomic
database](http://iphylo.blogspot.com/2012/06/more-fictional-taxa-and-myth-of-expert.html)
and [Fictional
taxa](http://iphylo.blogspot.com/2012/06/fictional-taxa.html)) entirely
fictional can end up in taxonomic databases with alarming ease. So any
claims that these are expert-curated lists should be taken with a pinch
of salt.  
  
Furthermore, it is increasingly easy to automate building these lists,
given that we have tools for finding names in text, and an ever
expanding volume of digitised text becoming available. Indeed, in an
ideal world where all taxonomic literature was digitised much of the
rationale for taxonomic name databases would disappear (in the same way
that library card catalogues are irrelevant in the age of Google). We
are fast approaching the point where we can do better than experts. To
give just one example, in a recent [BHL interview with Gary
Poore](http://blog.biodiversitylibrary.org/2012/06/bhl-and-our-users-dr-gary-poore.html)
it was stated that:  
  

> For example, the name widely used name Pentastomida itself was widely
> attributed to Diesing, 1836, but the word did not appear in the
> literature until 1905.

  
  
A quick check of [Google
Ngrams](http://books.google.com/ngrams/graph?content=Pentastomida&year_start=1800&year_end=2000&corpus=0&smoothing=3)
shows this to be simply false:  
  
![Pentastomida](http://lh6.ggpht.com/-Xu8s9oV0UxY/UTnW5jyuL0I/AAAAAAAACgk/jUbCKeodaBc/Pentastomida.png?imgmax=800 "Pentastomida.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="167"}  
  
I don\'t need taxonomic expertise to see this, I simply need decent text
indexing. So, if you have a list of names, you have something that it
will soon be largely possible to recreate using automated methods (i.e.,
text mining). With a little sophistication we could mine the literature
for further details, such as synonymy, etc. Annotation and clarification
of a few \"edge cases\" where things get tricky will always be needed,
but if you want to argue that your lists deserves \"Attribution, Rights
and Licensing\" then you fail to realise that your list is going to be
increasing easy to recreate simply by crawling the web.  
  
It seems to me that most taxonomic databases are little more than
digitised 5x3 index cards, and lack any details on the provenance of the
names they contain. They often don\'t have links to the primary
literature, and if they do cite that literature they typically do so in
a way that makes it hard to find the actual publication. I once [gave a
talk](http://www.slideshare.net/rdmpage/why-arent-we-there-yet) which
included the slide below showing taxonomic databases as being \"in the
way\" between taxonomists and users of taxonomic information:  
  
![Users](http://lh6.ggpht.com/-zWQmGcGADE4/UTnW67qpMyI/AAAAAAAACgs/8zfOicn6YiA/users.png?imgmax=800 "users.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="284"}  
  
In the old days building taxonomic databases required expertise and
access to obscure, hard to find, physical literature. A catalogue of
names was a way to summarise that information (since we couldn\'t share
access). Now we are in an age where more and more primary taxonomic
information is available to all, which removes most of the rationale for
taxonomic databases. Users can go directly to taxonomic information
themselves, which mean they can get the \"good stuff\", and maybe even
cite it (giving us provenance and credit, which I regard as basically
the same thing). In many ways taxonomic databases are transitional
phenomena (like phone directories, remember those), and one could argue
are now in the way of the taxonomists\' Holy Grail, getting their work
cited.  
  
Lastly, any discussion of \"Attribution, Rights and Licensing of names
and compilations of names\" reflects one of the great self inflicted
wounds of biodiversity informatics, namely the reluctance to freely
share data. As we speak terrabytes of genomics data are whizzing around
the planet, people are downloading entire copies of GenBank and creating
new databases. All of this without people fussing over \"Attribution,
Rights and Licensing.\" It\'s time for taxonomic databases to get over
themselves and focus on making biodiversity data as accessible and
available as genomics data.  


Few things have annoyed be as much as the following post on TAXACOM:  I'm trying to work out why this seemingly innocuous post made me so mad. I think this is because I think this fundamentally framing the question the wrong way. Surely the goal is to have a list of names that is global in scope, well documented, and freely usable by all without restriction? Surely we want open and free access to fundamental biodiversity data?

Messaggi di Rogue Scholar

Can we use the citation graph to measure the quality of a taxonomic database?

Lists of species don't matter: thoughts on "Principles for creating a single authoritative list of the world’s species"

On Names Attribution, Rights, and Licensing of taxonomic names