Wednesday, August 24, 2022

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

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. When you add data to ChecklistBank you are asked to give a measure of confidence based on the Catalogue of Life 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?). 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, 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
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,

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.

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.

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. 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
Time for some experiments.

Monday, August 22, 2022

Linking taxonomic names to the literature

Just some thoughts as I work through some datasets linking taxonomic names to the literature.

In the diagram above I've tried to capture the different situatios I encounter. Much of the work I've done on this has focussed on case 1 in the diagram: I want to link a taxonomic name to an identifier for the work in which that name was published. In practise this means linking names to DOIs. This has the advantage of linking to a citable indentifier, raising questions such as whether citations of taxonmic papers by taxonomic databases could become part of a taxonomist's Google Scholar profile.

In many taxonomic databases full work-level citations are not the norm, instead taxonomists cite one or more pages within a work that are relevant to a taxonomic name. These "microcitations" (what the U.S. legal profession refer to as "point citations" or "pincites", see What are pincites, pinpoints, or jump legal references?) require some work to map to the work itself (which is typically the thing that has a citatble identifier such as a DOI).

Microcitations (case 2 in the diagram above) can be quite complex. Some might simply mention a single page, but others might list a series of (not necessarily contiguous) pages, as well as figures, plates etc. Converting these to citable identifiers can be tricky, especially as in most cases we don't have page-level identifiers. The Biodiversity Heritage Library (BHL) does have URLs for each scanned page, and we have a standard for referring to pages in a PDF (page=<pageNum>, see RFC 8118). But how do we refer to a set of pages? Do we pick the first page? Do we try and represent a set of pages, and if so, how?

Another issue with page-level identifiers is that not everything on a given page may be relevant to the taxonomic name. In case 2 above I've shaded in the parts of the pages and figure that refer to the taxonomic name. An example where this can be problematic is the recent test case I created for BHL where a page image was included for the taxonomic name Aphrophora impressa. The image includes the species description and a illustration, as well as text that relates to other species.

Given that not everything on a page need be relevant, we could extract just the relevant blocks of text and illustrations (e.g., paragraphs of text, panels within a figure, etc.) and treat that set of elements as the thing to cite. This is, of course, what Plazi are doing. The set of extracted blocks is glued together as a "treatment", assigned an identifier (often a DOI), and treated as a citable unit. It would be interesting to see to what extent these treatments are actually cited, for example, do subsequent revisions that cite work that include treatments cite those treatments, or just the work itself? Put another way, are we creating "threads" between taxonomic revisions?

One reason for these notes is that I'm exploring uploading taxonomic name - literature links to ChecklistBank and case 1 above is easy, as is case 3 (if we have treatment-level identifiers). But case 2 is problematic because we are linking to a set of things that may not have an identifier, which means a decision has to be made about which page to link to, and how to refer to that page.

Wednesday, August 03, 2022

Papers citing data that cite papers: CrossRef, DataCite, and the Catalogue of Life

Quick notes to self following on from a conversation about linking taxonomic names to the literature. There are different sorts of citation:
  1. Paper cites another paper
  2. Paper cites a dataset
  3. Dataset cites a paper
Citation type (1) is largely a solved problem (although there are issues of the ownership and use of this data, see e.g. Zootaxa has no impact factor. Citation type (2) is becoming more widespread (but not perfect as GBIF's #citethedoi campaign demonstrates. But the idea is well accepted and there are guides to how to do it, e.g.:
Cousijn, H., Kenall, A., Ganley, E. et al. A data citation roadmap for scientific publishers. Sci Data 5, 180259 (2018).
However, things do get problematic because most (but not all) DOIs for publications are managed by CrossRef, which has an extensive citation database linking papers to other paopers. Most datasets have DataCite DOIs, and DataCite manages its own citations links, but as far as I'm aware these two systems don't really taklk to each other. Citation type (3) is the case where a database is largely based on the literature, which applies to taxonomy. Taxonomic databases are essentially collections of literature that have opinions on taxa, and the database may simply compile those (e.g., a nomenclator), or come to some view on the applicability of each name. In an ideal would, each reference included in a taxonomic database would gain a citation, which would help better reflect the value of that work (a long standing bone of contention for taxonomists). It would be interesting to explore these issues further. CrossRef and DataCite do share Event Data (see also DataCite Event Data). Can this track citations of papers by a dataset? My take on Wayne's question:
Is there a way to turn those links into countable citations (even if just one per database) for Google Scholar?
is that he's is after type 3 citations, which I don't think we have a way to handle just yet (but I'd need to look at Event Data a bit more). Google Scholar is a black box, and the academic coimmunity's reliance on it for metrics is troubling. But it would be interetsing to try and figure out if there is a way to get Google Scholar to index the citations of taxonomic papers by databases. For instance, the Catalogue of Life has an ISSN 2405-884X so it can be treated as a publication. At the moment its web pages have lots of identifiers for people managing data and their organisations (lots of ORCIDs and RORs, and DOIs for individual datasets (e.g., but precious little in the way of DOIs for publications (or, indeed, ORCIDs for taxonomists). What would it take for taxonomic publications in the Catalogue of Life to be treated as first class citations?