University of Glasgow

Roderic Page

![Singlefig 98253
jpg](https://lh3.googleusercontent.com/-U2AGskKg_dU/V8WfP75AcOI/AAAAAAAAERM/nfQ33C_wduM/singlefig_98253.jpg.png?imgmax=1600 "singlefig_98253.jpg.png"){border="0"
width="235" height="128" style="float:right;"} David Schindel and
colleagues recently published a paper in the *Biodiversity Data
Journal*:

> Schindel, D., Miller, S., Trizna, M., Graham, E., & Crane, A. (2016,
> August 26). The Global Registry of Biodiversity Repositories: A Call
> for Community Curation. BDJ. Pensoft Publishers.
> <http://doi.org/10.3897/bdj.4.e10293>

The paper is a call for the community to help grow a database
([GRBio](http://grbio.org)) on biodiversity repositories, a database
that will \"will require community input and curation\".

Reading this, I\'m struck by the lack of a clear sense of what that
community might be. In particular: who is this database for, and who is
most likely to build it? I suspect that these are two different sets of
people.

### Who is it for?

It strikes me that the primary target for GrBio is people who care about
cleaning up and linking data. This is very small set of people. While
cleaned data is nice, and cleaned and linked data is great, by itself
it\'s not much use until it finds its way into useful tools. Why would
taxonomists, curators, and other people working with biodiversity data
care about GrBio? What can it give them? Ultimately, we\'d like things
such as the ability to find any specimen in the world online using
simply it\'s museum collection code. We\'d like to track usage of that
code in other databases, such as GenBank and BOLD, and in the primary
literature. These are all nice things, but they won\'t happen simply
because we have a curated list of natural history collections.

### Who will curate it?

Arguably there are only two active communities who care about the
contents of GrBio on a scale to actually contribute. One is GBIF, which
is building its own registry of collections as more and more natural
history collections move their collections online. GBIF\'s registry is
primarily for digital access points to collection data, which don\'t
necessarily readily map to physical collections listed by GrBio. If GrBo
is to be relevant, it needs to have mappings between its data and GBIF.

But the community that I suspect will really care about this, to the
point that they\'d actively engage in editing the data, is not the
biodiversity community. Rather, it\'s people who edit Wikipedia and
Wikidata.

I was at one of the GrBio workshops and gave a short presentation, which
included this slide:

::: {style="margin-bottom:5px"}
**[GrBio Workshop
talk](//www.slideshare.net/rdmpage/grbio-workshop-talk "GrBio Workshop talk"){target="_blank"}**
de **[Roderic Page](//www.slideshare.net/rdmpage){target="_blank"}**
:::

If you search for a major museum on Google, on the right you will often
see a rich \"knowledge panel\" giving much of the information that GrBio
wants to capture (museum name, location, etc.), often with a link to the
Wikipedia page for that institution (see <http://g.co/kg/m/01t372> for a
detailed view of the knowledge panel for the NHM). GrBio can\'t compete
with Wikipedia for richness of content (just think of all the Wikipedia
pages in languages other than English). Google\'s database is mostly
hidden, but we can get some of the same data from Wikidata, e.g. the
Natural History Museum is [entity
Q309388](https://www.wikidata.org/wiki/Q309388) on Wikidata.

From my perspective, the smart move to make is not to appeal to an
overstretched community of biodiversity researchers, many of whom are
suffering from \"project fatigue\" as yet more acronyms compete for
their attention. Instead, position the project as adding to the already
existing database of natural history institutions that is growing in
Wikidata. GrBio could either link to Wikidata and Wikipedia pages for
institutions, or simply move it\'s data editing efforts to Wikidata and
have GrBio be (at most) a search interface to that data. The notion of
having a separate database for the world\'s collections might not be the
best way to achieve GrBio\'s goals. A lot of people involved in both
Wikipedia and Wikidata care about cultural institutions (of which
natural history museums and herbaria are examples), those are the people
GrBio should be engaging with.


David Schindel and colleagues recently published a paper in the
<em>
 Biodiversity Data Journal
</em>
:  The paper is a call for the community to help grow a database (GRBio) on biodiversity repositories, a database that will "will require community input and curation".  Reading this, I'm struck by the lack of a clear sense of what that community might be. In particular: who is this database for, and who is most likely to build it? I suspect that

GRBio: A Call for Community Curation - what community?

Given that Wikipedia, Wikidata, and the Biodiversity Heritage Library
(BHL) all share the goal of making information free, open, and
accessible, there seems to be a lot of potential for useful
collaboration. Below I sketch out some ideas.

### BHL as a source of references for Wikipedia

Wikipedia likes to have sources cited to support claims in its articles.
BHL has a lot of articles that could be cited by Wikipedia articles. By
adding these links, Wikipedia users get access to further details on the
topic of interest. BHL also benefits from greater visibility resulting
from visits from Wikipedia readers.

In the short term BHL could search Wikipedia for articles that could
benefit from links to BHL (see below). In the long term as more and more
BHL articles get DOIs this will become redundant as Wikipedia authors
will discover articles via CrossRef.

There are various ways to search Wikipedia to get a sense of what links
could be added. For example, you can search the Wikipedia API for pages
that link to a particular web domain (see
<https://www.mediawiki.org/wiki/API:Lists/All#Exturlusage>). Here\'s a
search for articles linking to biostor.org
<https://en.wikipedia.org/w/api.php?action=query&list=exturlusage&euquery=biostor.org&eulimit=20>.

A quick inspection suggests that many of these links could be improved
(for example, some have outdated links to PDFs and not to the article),
so we can locate Wikipedia articles that could be edited. It is likely
that Wikipedia articles that have one link to BHL or BioStor may have
other citations that could be linked.

### Wikipedia as a source of content

One of the big challenges facing BHL is extracting articles from its
content. My own [BioStor](http://biostor.org) is one approach to
tackling this problem. BioStor takes citation details for articles and
attempts to locate them in BHL - the limiting factor is access to
good-quality citation data. Wikipedia is potentially an untapped source
of citation data. Each page that uses the \"Cite\" template could be
mined for citations, which in turn could be used to locate articles.
Wikipedia pages using the Cite template can be found via the API, e.g.
<https://en.wikipedia.org/w/api.php?action=query&list=embeddedin&eititle=Template:Cite&eilimit=20&format=json>.
Alternatively, we could mine particular types of pages (e.g., those on
taxa or taxonomists), or mine
[Wikispecies](https://species.wikimedia.org/wiki/Main_Page) (which
doesn\'t use the same citation formatting as Wikipedia).

### Wikidata as a data store

If Wikidata aims to be a repository of all structured data relevant to
Wikipedia, then this includes bibliographic citations (see [WikiCite
2016](https://meta.wikimedia.org/wiki/WikiCite_2016) ), hence many
articles in BHL will end up in Wikidata. This has some interesting
implications, because Wikidata can model data with more fidelity than
many other sources of bibliographic information. For example, it
supports multiple languages as well as multiple representations of the
sample language - the journal *Acta Herpetologica Sinica*
<https://www.wikidata.org/wiki/Q24159308> in Wikidata has not only the
Chinese title (兩棲爬行動物學報) but the pinyin transliteration
\"Liangqi baxing dongwu yanjiu\". Rather than attempt to replicate a
community-editable database, Wikidata could be the place to manage
article and journal-related metadata.

### Disambiguating people

As we move from \"strings to things\" we need to associate names for
things with identifiers for those things. I\'ve touched on this already
in [Possible project: mapping authors to Wikipedia entries using lists
of published
works](http://iphylo.blogspot.com/2015/08/possible-project-mapping-authors-to.html).
Ideally each author in BHL would be associated with a globally unique
identifier, such as ORCID or ISNI. Contributors to Wikipedia and
Wikidata have been collecting these for individuals with Wikipedia
articles. If those Wikipedia pages have links to BHL content then we can
semi-automate the process of linking people to identifiers.

### Caveats

There are a couple of potential \"gotchas\" concerning Wikipedia and
BHL. The licenses used for content are different, BHL is typically
CC-BY-NC whereas Wikipedia is CC-BY. The \"non commercial\" restriction
used by BHL is a deal-breaker for sharing content such as page images
with Wikicommons.

Wikipedia and Wikidata are communities, and I\'ve often found this makes
it challenging to find out how to get things done. Who do you contact to
make a decsioon about some new feature you\'d like to add? It\'s not at
all obvious (unless you\'re a part of that community). Existing
communities with accepted practices can be resistant to change, or may
not be convinced that what you\'d like to do is a benefit. For example,
I think it would be great to have a Wikipedia page for each journal.
[Not everyone agrees with
this](https://en.wikipedia.org/wiki/Talk:Entomologica_Americana_(New_York_Entomological_Society)#Proposed_merge_with_Journal_of_the_New_York_Entomological_Society),
and one can expend a lot of energy debating the pros and cons. The last
time I got seriously engaged with Wikipedia I ended up getting so
frustrated I went off in a huff and [built my own
wiki](http://iphylo.org/linkout). This is where a [\"Wikipedian in
residence\"](https://en.wikipedia.org/wiki/Wikipedian_in_residence)
might be helpful.


Given that Wikipedia, Wikidata, and the Biodiversity Heritage Library (BHL) all share the goal of making information free, open, and accessible, there seems to be a lot of potential for useful collaboration. Below I sketch out some ideas. BHL as a source of references for Wikipedia   Wikipedia likes to have sources cited to support claims in its articles. BHL has a lot of articles that could be cited by Wikipedia articles.

Thoughts on Wikipedia, Wikidata, and the Biodiversity Heritage Library

Last week I attended the [Wikipedia Science
Conference](https://wikimedia.org.uk/wiki/Wikipedia_Science_Conference)
(hashtag:
[\#wikisci](https://twitter.com/search?f=tweets&vertical=default&q=%23wikisci&src=typd))
at the Wellcome Trust in London. it was an interesting two days of talks
and discussion. Below are a few random notes on topics that caught my
eye.

#### What is Wikidata?

> Slides for my upcoming
> [\#wikisci](https://twitter.com/hashtag/wikisci?src=hash) talk on how
> to build a repository of all citations with
> [@wikidata](https://twitter.com/wikidata) <http://t.co/pzfAFrfnXc>
>
> --- Dario Taraborelli (@ReaderMeter) [September 3,
> 2015](https://twitter.com/ReaderMeter/status/639401662055059456)

A recurring theme was the emergence of
[Wikidata](https://www.wikidata.org), although it never really seemed
clear what role Wikidata saw for itself. On the one hand, it seems to
have a clear purpose:

> Wikidata acts as central storage for the structured data of its
> Wikimedia sister projects including Wikipedia, Wikivoyage, Wikisource,
> and others.

At other times there was a sense that Wikidata wanted to take any and
all data, which it doesn\'t really seemed geared up to do. The English
language Wikipedia has nearly 5 million articles, but there are lots of
scientific databases that dwarf that in size (we have at least that many
taxonomic names, for example). So, when Dario Taraborelli suggests
building a repository of all citations with Wikidata, does he really
mean ALL citations in the academic literature? CrossRef alone has 75M
DOIs, whereas Wikidata currently has 14.8M pages, so we are talking
about greatly expanding the size of Wikidata with just one type of data.

The sense I get is that Wikidata will have an important role in (a)
structuring data in Wikipedia, and (b) providing tools for people to map
their data to the equivalent topics in Wikipedia. Both are very useful
goals. What I find less obvious is whether (and if so, how) Wikidata
aims to be a more global database of facts.

#### How do you Snapchat? You just Snapchat

As a relative outsider to the Wikipedia community, and having had a
sometimes troubled experience with Wikipedia, it struck me that how
opaque things are if your are an outsider. I suspect this is true of
most communities, if you are a member then things seem obvious, if
you\'re not, it takes time to find out how things are done. Wikipedia is
a community with nobody in charge, which is a strength, but can also be
frustrating. The answer to pretty much any question about how to add
data to Wikidata, how to add data types, etc. was \"ask the community\".
I\'m reminded of the American complaint about the European Union \"if
you pick up the phone to call Europe, who do you call?\". In order to
engage you have to invest time in discovering the relevant part of the
community, and then learn engage with it. This can be time consuming,
and is a different approach to either having to satisfy the requirements
of gatekeepers, or a decentralised approach where you can simply upload
whatever you want.

#### Streams

It seems that everything is becoming a stream. Once the volume of
activity reaches a certain point, people don\'t talk about downloading
static datasets, but instead of consuming a stream of data (very like
the [Twitter firehose](https://dev.twitter.com/streaming/firehose)). The
volume of Wikipedia edits means scissile scientists studying the growth
of Wikipedia are now consuming streams. Geoffrey Bilder of CrossRef
showed some interesting visualisations of real-time streams of DOIs
being as users edited Wikipedia pages [CrossRef DOI Events for
Wikimedia](http://events.labs.crossref.org/events/types/WikipediaCitation),
and Peter Murray-Rust of [ContentMine](http://contentmine.org/) seemed
to imply that ContentMine is going to generate streams of facts (rather
than, say, a query able database of facts). Once we get to the stage of
having large, transient volumes of data, all sorts of issues about
reanalysis and reproducibility arise.

#### CrossRef and evidence

One of the other strking visualisations that CrossRef have is the [DOI
Chronograph](http://chronograph.labs.crossref.org), which displays the
numbers of CrossRef DOI resolutions by the domain of the hosting web
site. In other words, if you are on a Wikipedia page and click on a DOI
for an article, that\'s recorded as a DOI resolution from the domain
\"wikipedia.org\". For the period 1 October 2010 to 1 May 2015 Wikipedia
was the source of 6.8 million clicks on DOIs, see
<http://chronograph.labs.crossref.org/domains/wikipedia.org>. One way to
interpret this is that it\'s a measure of how many people are accessing
the primary literature - the underlying evidence - for assertions made
on Wikipedia pages. We can compare this with results for, say,
biodiversity informatics projects. For example, [EOL](http://eol.org)
has 585(!) DOI clicks for the period 15 October 2010 to 30 April 2015.
There are all sorts of reasons for the difference between these two
sites, such as Wikipedia has vastly more traffic than EOL. But I think
it also reflects the fact that many Wikipedia articles are richly
referenced with citations to the primary literature, and projects like
EOL are very poorly linked to that literature. Indeed, most biodiversity
databases are divorced from the evidence behind the data they display.

#### Diversity and a revolution led by greybeards

> Okay, we got the message - more women should ask questions at
> [\#wikisci](https://twitter.com/hashtag/wikisci?src=hash) No need to
> emphasize after every talk. Sometimes we just don\'t have Q
>
> --- Eva Amsen (@easternblot) [September 3,
> 2015](https://twitter.com/easternblot/status/639384752924008448)

\"Diversity\" is one of those words that has become politicised, and
attempts to promote \"diversity\" can get awkward (\"let\'s hear from
the women\", that homogeneous category of non-men). But the aspect of
diversity that struck me was age-related. In discussions that involved
fellow academics, invariably they looked a lot like me - old(ish),
relatively well-established and secure in their jobs (or post-job). This
is a revolution led not by the young, but by the greybeards. That\'s a
worry. Perhaps it\'s a reflection of the pressures on young or
early-stage scientists to get papers into high-impact factor journals,
get grants, and generally play the existing game, whereas exploring new
modes of publishing, output, impact, and engagement have real risks and
few tangible rewards if you haven\'t yet established yourself in
academia.


Last week I attended the Wikipedia Science Conference (hashtag: #wikisci) at the Wellcome Trust in London. it was an interesting two days of talks and discussion. Below are a few random notes on topics that caught my eye. What is Wikidata? A recurring theme was the emergence of Wikidata, although it never really seemed clear what role Wikidata saw for itself.

Postagens de Rogue Scholar

GRBio: A Call for Community Curation - what community?

Thoughts on Wikipedia, Wikidata, and the Biodiversity Heritage Library

Wikidata, Wikipedia, and #wikisci