University of Glasgow

Roderic Page

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I\'ve released a very crude GraphQL endpoint for WikiData. More
precisely, the endpoint is for a subset of the entities that are of
interest to WikiCite, such as scholarly articles, people, and journals.
There is a crude demo at <https://wikicite-graphql.herokuapp.com>. The
endpoint itself is at <https://wikicite-graphql.herokuapp.com/gql.php>.
There are various ways to interact with the endpoint, personally I like
the [Altair GraphQL Client](https://altair.sirmuel.design) by [Samuel
Imolorhe](https://github.com/imolorhe).

As I\'ve [mentioned
earlier](https://iphylo.blogspot.com/2021/04/it-been-while.html) it\'s
taken me a while to see the point of GraphQL. But it is clear it is
gaining traction in the biodiversity world (see for example the [GBIF
Hosted Portals](https://dev.gbif.org/hosted-portals.html)) so it\'s
worth exploring. My take on GraphQL is that it is a way to create a
self-describing API that someone developing a web site can use without
them having to bury themselves in the gory details of how data is
internally modelled. For example, WikiData\'s query interface uses
SPARQL, a powerful language that has a steep learning curve (in part
because of the administrative overhead brought by RDF namespaces, etc.).
In my previous SPARQL-based projects such as
[Ozymandias](https://ozymandias-demo.herokuapp.com) and
[ALEC](http://alec-demo.herokuapp.com) I have either returned SPARQL
results directly (Ozymandias) or formatted SPARQL results as [schema.org
DataFeeds](https://schema.org/DataFeed) (equivalent to RSS feeds)
(ALEC). Both approaches work, but they are project-specific and if
anyone else tried to build based on these projects they might struggle
for figure out what was going on. I certainly struggle, and I wrote
them!

So it seems worthwhile to explore this approach a little further and see
if I can develop a GraphQL interface that can be used to build the sort
of rich apps that I want to see. The demo I\'ve created uses SPARQL
under the hood to provide responses to the GraphQL queries. So in this
sense it\'s not replacing SPARQL, it\'s simply providing a (hopefully)
simpler overlay on top of SPARQL so that we can retrieve the data we
want without having to learn the intricacies of SPARQL, nor how Wikidata
models publications and people.


I've released a very crude GraphQL endpoint for WikiData. More precisely, the endpoint is for a subset of the entities that are of interest to WikiCite, such as scholarly articles, people, and journals. There is a crude demo at https://wikicite-graphql.herokuapp.com. The endpoint itself is at https://wikicite-graphql.herokuapp.com/gql.php.

GraphQL for WikiData (WikiCite)

Last week I submitted a manuscript entitled \"Wikidata and the
bibliography of life\". I\'ve been thinking about the \"bibliography of
life\" (AKA a database of every taxonomic publication ever published)
for a
[while](https://iphylo.blogspot.com/search?q=bibliography+of+life), and
this paper explores the idea that Wikidata is the place to create this
database. The preprint version is on bioRxiv
([doi:10.1101/2021.05.04.442638](https://doi.org/10.1101/2021.05.04.442638)).
Here\'s the abstract:

> Biological taxonomy rests on a long tail of publications spanning
> nearly three centuries. Not only is this literature vital to resolving
> disputes about taxonomy and nomenclature, for many species it
> represents a key source - indeed sometimes the only source - of
> information about that species. Unlike other disciplines such as
> biomedicine, the taxonomic community lacks a centralised, curated
> literature database (the "bibliography of life"). This paper argues
> that Wikidata can be that database as it has flexible and
> sophisticated models of bibliographic information, and an active
> community of people and programs ("bots") adding, editing, and
> curating that information. The paper also describes a tool to
> visualise and explore bibliography information in Wikidata and how it
> links to both taxa and taxonomists.

The manuscript summarises some work I\'ve been doing to populate
Wikidata with taxonomic publications (building on a huge amount of work
already done), and also describes
[ALEC](https://alec-demo.herokuapp.com) which I use to visualise this
content. I\'ve made various (unreleased) knowledge graphs of taxonomic
information (and one that I have actually released
[Ozymandias](https://iphylo.blogspot.com/search?q=Ozymandias)), I\'m
still torn between whether the future is to invest more effort in
Wikidata, or construct lighter, faster, domain specific knowledge graphs
for taxonomy. I think the answer is likely to be \"yes\".

Meantime, one chart I quite like from the submitted version of this
paper is shown below.

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It\'s a chart that is a bit tricky to interpret. My goal was to get a
sense of whether bibliographic items added to Wikidata (e.g., taxonomic
papers) were actually being edited by the Wikidata community, or whether
they just sat there unchanged since they were added. If people are
editing these publications, for example, by adding missing author names,
linking papers to items for their authors, or adding additional
identifiers (such as DOIs, ZooBank identifiers, etc.), then there is
clear value in using Wikidata as a repository of bibliographic data. So
I grabbed a sample of 1000 publications, retrieved their edit history
from Wikidata, and plotted the creation timestamp of each item against
the timestamps for each edit made to that item. If items were never
edited then every point would fall along the diagonal line. If edits are
made, they appear to the right of the diagonal. I could have just
counted edits made, but I wanted to visualise those edits. As the chart
shows, there is quite a lot of editing activity, so there his a
community of people (and bots) curating this content. In many ways this
is the strongest argument for using Wikidata for a \"bibliography of
life\". Any database needs curation, which means people, and this is
what Wikidata offers, a community of people who care about often
esoteric details, and get pleasure from improving structured data.

There are still huge gaps in Wikidata\'s coverage of the taxonomic
literature. Once you move beyond the \"low hanging fruit\" of
publications with CrossRef DOIs the task of adding literature to
Wikidata gets a bit more complicated. Then there is the reconciliation
problem: given an existing taxonomic database with a list of references,
how do we match those references to the corresponding items in Wikidata?
There is still a lot to do.


Last week I submitted a manuscript entitled "Wikidata and the bibliography of life". I've been thinking about the "bibliography of life" (AKA a database of every taxonomic publication ever published) for a while, and this paper explores the idea that Wikidata is the place to create this database.

Preprint on Wikidata and the bibliography of life

![3hhZSGOn
400x400](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5DiKsrPtggAab-1Y1rnEwF8-OL-11mcXqEGwBmRnwcIWYgTx10prrRm2c4wi5fH12gGDpQBHhlmgtAqhXpWMOfWcJ6-CS_owPKONLyzdrhRlKNJ0WCjh9XgkvHKgQ18bP-AtJ/?imgmax=1600 "3hhZSGOn_400x400.jpg"){border="0"
width="128" height="128" style="float:right;"}Last week I was at
[WikiCite 2017](https://meta.wikimedia.org/wiki/WikiCite_2017), a
fascinating three day event in Vienna.
[Wikicite](https://meta.wikimedia.org/wiki/WikiCite) is \"a proposal to
build a bibliographic database in Wikidata to serve all Wikimedia
projects\", and is attracting increasing attention from academics,
librarians, publishers, data geeks, and others. You can get a sense of
the project by following [@WikiCite](https://twitter.com/wikicite) on
Twitter.

I went to the meeting in part to learn more about WikiCite, and also to
spend some time hacking on [Wikispecies](https://species.wikimedia.org).
I\'d been to only one Wiki event before (a [Wiki Science
Conference](http://iphylo.blogspot.com/2015/09/wikidata-wikipedia-and-wikisci.html))
so I\'m still finding my way around this community. I spent the first
two days listening to talks while coding away (more on this below), but
on Wednesday put my own coding aside to join a bunch of people hacking
the [CrossRef event API](https://www.crossref.org/services/event-data/)
in a great session led by [Joe Wass](https://twitter.com/joewass). I\'ve
put some notes and code in
[GitHub](https://github.com/rdmpage/crossref-event-hackathon). The event
API tracks what people do with DOIs, including adding them to Wikipedia
pages when citing a source in support of an assertion. A significant
fraction of DOI resolutions are from Wikipedia pages, which is one
reason why CrossRef was present at WikiCite.

### Wikidata

In practice WikiCite\'s goal of building a bibliographic database to
serve all Wikimedia projects means that articles, books, and other
bibliographic items that are cited by Wikimedia projects will each be
added to Wikidata. For example, the *ZooKeys* paper \"Diversity of
manota williston (Diptera, mycetophilidae) in ulu temburong national
park, brunei\" is item
[Q21188431](https://www.wikidata.org/wiki/Q21188431) in Wikidata.
Wikidata stores the key bibliographic metadata, including identifiers
such as the DOI (which many at the WikiCite meeting pronounced \"doy\"
much to my initial confusion). ![Screenshot 2017 05 31 12 46
43](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGtyO7zorQc4LpmvbT-oKKl743_aIcQNZPH_6vAV6IebSSOVZZRzGymhKtCjUqiltqL3ofyOQyp5eHeXxl6Tt2ExB26ouhEfkKvhnrG-emyikhkqFXgF3MaHJYir8E8zAPkqHR/?imgmax=1600 "Screenshot 2017-05-31 12.46.43.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="401"}

This article was published in *ZooKeys*, which itself has a Wikidata
item ([Q219980](https://www.wikidata.org/wiki/Q219980)), so in Wikidata
the article is linked to the journal (i.e., \"ZooKeys\" isn\'t just a
dumb string but a link to another Wikidata item). The article is also
linked to two articles that it cites, and each of these is also a
Wikidata item.

These citation links are one reason people are interested in WikiCite -
it could be the basis of a free and open citation graph (for the
benefits of such a graph see this piece by David Shotton
[doi:10.1038/502295a](http://dx.doi.org/10.1038/502295a), a participant
at the meeting in Vienna). Already some cool tools are being built on
top of citation data in Wikidata, such as
[Scholia](https://tools.wmflabs.org/scholia/) by [Finn Årup
Nielsen](https://twitter.com/fnielsen), [Daniel
Mietchen](https://twitter.com/EvoMRI) and [Egon
Willighagen](https://twitter.com/egonwillighagen). Here, for example, is
my [academic profile based on information in
Wikidata](https://tools.wmflabs.org/scholia/author/Q7356570). It\'s
woefully incomplete, but intriguing. For a more complete example view
[Egon Willighagen\'s
profile](https://tools.wmflabs.org/scholia/author/Q20895241).

To some extent the utility of tools like Scholia will depend on how
complete Wikidata\'s coverage is of the academic literature, which in
turn raises the inevitable question of scope. Does Wikicite want to
include just the literature cited in the various Wikimedia projects, or
does it want to expand to include the total sum of academic literature?

### Wikispecies, Wikidata and the bibliography of life

Wikispecies is one of the Wikimedia projects, and the only one that is
topic-specific (the others are typically global in scope but have
content in different languages, or host different data types such as
images, scanned books, or structured data). As I\'ve sketched out in an
earlier post ([Thoughts on Wikipedia, Wikidata, and the Biodiversity
Heritage
Library](http://iphylo.blogspot.com/2016/05/thoughts-on-wikipedia-wikidata-and.html))
I think Wikicite and Wikidata are potentially very important to projects
such as BHL and the \"bibliography of life\". Much of our knowledge
about the world\'s biodiversity is contained in the academic literature,
and much of this is poorly known with no central database where we can
find it, and much of it is still not digitised. It is tempting to think
that Wikidata might be a platform around which the biodiversity
community could focus its efforts on assembling a global database of
biodiversity literature. Already major taxonomic journals such as
*ZooKeys* are being fed into Wikidata, so it has a significant corpus of
biodiversity literature already.

One way to grow this corpus is to focus on Wikispecies. In a post before
the Wikicite meeting ([Notes for WikiCite 2017: Wikispecies reference
parsing](http://iphylo.blogspot.com/2017/03/notes-for-wikicite-2017-wikispecies.html))
I elaborated on this idea. There are two stumbing blocks, one specific
to Wikispecies, one a more general Wikidata issue.

The first issue is that Wikispecies bibliographic data is relatively
unstructured, which makes converting it into structured data something
of a challenge. I spent much of Wikicite hacking some code to do this on
Glitch (more on Glitch later), you can see the results here:
<https://acoustic-bandana.glitch.me>. This web site takes a Wikispecies
reference and tries to convert it into CSL-JSON. Still very much a work
in progress, but I\'ve started building tools that use this web site as
a service and process larger numbers of Wikispecies citations.

The second issue is how you get data into Wikidata, and this is
something that\'s never been entirely clear to me. There are tools for
adding an article using its DOI
([sourcemd](http://tools.wmflabs.org/sourcemd)) but this isn\'t
scalable, and doesn\'t handle the case of articles that don\'t have
DOIs. This is still a [\"How do you Snapchat? You just
Snapchat\"](https://twitter.com/wittertainment/status/578910842923687936)
moment. Wikidata desparately needs tools and a clear procedure whereby
people like me with lots of bibliographic data can contribute.

### Wikispecies

Another reason for my interest in Wikispecies (and other sources of
bibliographic data such as the listed of cited literature being made
available by CrossRef, see [The Initiative for Open
Citations](https://opencitations.wordpress.com/2017/04/06/the-initiative-for-open-citations/#fn1))
is that this data can be fed into BHL to locate more articles in that
archive. Once these articles have been located they are stored in
[BioStor](http://biostor.org) and BHL itself, but it makes sense to have
them more accessible, and Wikidata looks to be an obvious candidate.
Given that Wikispecies is essentially a crowd-source taxonomic database
there is considerable overlap in content between Wikispecies and BHL.
The Wikidata data model also allows for some of things that taxonomists
care about, such as linking dates of publication to evidence relative to
those dates (in older publications determining the publication date
often requires quite extensive research).

### Summary

Leaving aside the specific issues about how to get bibliographic data
into Wikidata, I guess the question to ask is whether it makes sense to
be developing large databases of bibliographic data without either using
Wikidata as the platform to hold that data, or at least linking to
Wikidata. Projects such as Gene Wiki are migrating from Wikipedia to
Wikidata (see \"Wikidata as a semantic framework for the Gene Wiki
initiative\"
[doi:10.1093/database/baw015](http://dx.doi.org/10.1093/database/baw015)),
perhaps those of us interested in biodiversity literature could use
projects like Gene Wiki as role models for how we could both contribute
and benefit from Wikidata and Wikicite.

I\'ve barely scratched the surface of what was discussed at Wikicite,
for more details see the
[program](https://meta.wikimedia.org/wiki/WikiCite_2017/Program). It is
a very different sort of meeting in that the participants come from
pretty diverse backgrounds, which helps shake up your own assumptions
about what matters and how things should be done. It\'s also great that
it\'s a meeting at which people write code or otherwise hack stuff
together, so things actually get done. I\'ve come away with lots to
think about, and renewed enthusiasm about the role Wikimedia is playing
in structuring our knowledge about the world.


Last week I was at WikiCite 2017, a fascinating three day event in Vienna. Wikicite is "a proposal to build a bibliographic database in Wikidata to serve all Wikimedia projects", and is attracting increasing attention from academics, librarians, publishers, data geeks, and others. You can get a sense of the project by following @WikiCite on Twitter.

Wikidata, WikiCite,  and the "bibliography of life"

![Wikispecies logo
svg](https://lh3.googleusercontent.com/-bjcWZmsl9yQ/WNURFDAs1uI/AAAAAAAAEag/Wdbj6nlFbo8/Wikispecies-logo.svg.png?imgmax=1600 "Wikispecies-logo.svg.png"){border="0"
width="128" height="149" style="float:right;"} In preparation for
[WikiCite 2017](https://meta.wikimedia.org/wiki/WikiCite_2017) I\'m
looking more closely at extracting bibliographic information from
Wikispecies. The [WikiCite](https://meta.wikimedia.org/wiki/WikiCite)
project \"is a proposal to build a bibliographic database in Wikidata to
serve all Wikimedia projects\". One reason for doing this is so that
each factual statement in WikiData can be linked to evidence for that
statement. Practical efforts towards this goal include tools to add
details of articles from CrossRef and PubMed straight into Wikidata, and
tools to extract citations from Wikipedia (as these are likely to be
sources of evidence for statements made in Wikipedia articles).

[Wikispecies](https://species.wikimedia.org/) occupies a rather
isoldated spot in the Wiikipedia landscape. Unlike other sites which are
essentially comprehensive encyclopedias in different languages,
Wikispecies focusses on one domain - taxonomy. In a sense, it\'s a
prototype of Wikidata in that it provides basic facts (who described
what species when, and what is the classification of those species) that
in principle can be reused by any of the other wikis. However, in
practice this doesn\'t seem to have happened much.

What Wikispecies has become, however, is a crowd-sourced database of the
taxonomic literture. For someone like me who is desparately gathering up
bibliographic data so that I can extract articles from the [Biodiversity
Heritage Library (BHL)](http://biodiversitylibrary.org), this is a
potential goldmine. But, there\'s a catch. Unlike, say, the English
language Wikipedia which has a single widely-used template for
describing a publication, Wikispecies has it\'s own method of
representing articles. It uses a somewhat confusing mix of templates for
author names, and then uses barely standardised formatting rules to mark
out parts of a publication (such as journal, volume, issue, etc.).
Instead of a single template to describe a publication, in Wikispecies a
publication my itself be described by a unique template. This has some
advantages, in that the same reference can be transcluded into multiple
articles (in other words, you enter the bibliographic details once). But
this leaves us with many individual templates with multiple,
idiosyncratic styles of representing bibliographic data. Some have tried
to get the Wikispecies community to adopt the same template as Wikipedia
(see e.g., [this
discussion](https://species.wikimedia.org/wiki/Wikispecies:Village_Pump#Citation_templates))
but this proposal has met with a lot of resistance. From my perspective
as a potential consumer of data, the current situation in Wikispecies is
frustrating, but the reality is that the people who create the content
get to decide how they structure that content. And understandably, they
are less than impressed by requests that might help others (such as data
miners) at the expense of making their own work more difficult.

In summary, if I want to make use of Wikispecies I am going to need to
develop a set of parsers than can make a reasonable fist of parsing all
the myriad citation formats used in Wikispecies (my first attempts are
on [GitHub](https://github.com/rdmpage/wikispecies-cite)). I\'m looking
at parsing the references and converting them to a more standard format
in JSON (I\'ve made some [notes on various bibliographic formats in JSON
such as BibJSON and
CSL-JSON](https://github.com/rdmpage/bibliographic-metadata-json)). One
outcome of this work will be, I hope, more articles discovered in BHL
and hence added to [BioStor](http://biostor.org)), and more links to
identifiers, which could be fed back into Wikispecies. I also want to
explore linking the authors of these papers to identifiers, as already
sketched out in [The Biodiversity Heritage Library meets Wikidata via
Wikispecies: adding author identifiers to
BioStor](http://iphylo.blogspot.co.uk/2017/01/the-biodiversity-heritage-library-meets.html).


In preparation for WikiCite 2017 I'm looking more closely at extracting bibliographic information from Wikispecies. The WikiCite project "is a proposal to build a bibliographic database in Wikidata to serve all Wikimedia projects". One reason for doing this is so that each factual statement in WikiData can be linked to evidence for that statement.

Messaggi di Rogue Scholar

GraphQL for WikiData (WikiCite)

Preprint on Wikidata and the bibliography of life

Wikidata, WikiCite, and the "bibliography of life"

Notes for WikiCite 2017: Wikispecies reference parsing