University of Glasgow

Roderic Page

I\'ve added an experimental feature to BioStor that uses data from
Wikidata and Wikispecies to augment what information BioStor displays on
authors. This is a crude first step towards the goal of representing all
the data in BioStor as a \"knowledge graph\" where articles, journals,
and authors are all treated as entities, all have identifiers, and we
can explore relationships between those entities (e.g., citation,
co-authorship, etc.). At the moment this is true of articles, which have
Biostor URLs (and in many cases DOIs), and for most journals which are
identified by their ISSN. Using identifiers helps reduce ambiguity,
especially if there are multiple ways to represent the same thing (e.g.,
all the alternative ways to write a journal name can be circumvented by
using the journal\'s ISSN).

However, BioStor doesn\'t have a way to identify authors beyond simply
searching for a name. As a first step to tackling this problem I\'ve
added a little widget that displays information about an author based on
the name you are searching for. For example, searching for [George
Albert
Boulenger](http://biostor.org/?q=author%3A%22George+Albert+Boulenger%22)
will give you a list of publications where the author name is \"George
Albert Boulenger\", as well as a picture of the author and some
identifiers (from sources such as VIAF, ISNI, IPNI, and Wikidata):

![Screenshot 2017 01 11 16 30
57](https://lh3.googleusercontent.com/-X50gPNWBhgM/WHZp0z6AurI/AAAAAAAAEWs/7sDEKYtHWdA/Screenshot%2525202017-01-11%25252016.30.57.png?imgmax=1600 "Screenshot 2017-01-11 16.30.57.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="260"}

For now this widget is independent of the data in BioStor. I don\'t link
an article to its author(s) using identifiers for those authors, nor
have I tackled the problem of clustering all the variations in people\'s
names together into one set of names that share the same identifier (see
[Equivalent author
names](http://iphylo.blogspot.com/2009/01/equivalent-author-names.html))
nor do I attempt to match names to identifiers (see [Reconciling author
names using Open Refine and
VIAF](http://iphylo.blogspot.com/2013/04/reconciling-author-names-using-open.html))
other than by an exact text search (for details see below). At this
stage I just want to get a sense of what identifiers exist for an
author, and what I can learn from those identifiers. I also want to
explore the potential of [Wikispecies](https://species.wikimedia.org/)
as a source of data on people and publications, and how this relates to
[Wikidata](https://www.wikidata.org/) (for earlier thoughts on using
Wikipedia for the same goal see [Thoughts on Wikipedia, Wikidata, and
the Biodiversity Heritage
Library](http://iphylo.blogspot.com/2016/05/thoughts-on-wikipedia-wikidata-and.html)).

#### Wikispecies

I confess I\'ve never really \"got\" Wikispecies (e.g., [Wikispecies is
not a
database](http://iphylo.blogspot.com/2009/08/wikispecies-is-not-database.html)),
it seems to exist in isolation from Wikipedia, which is arguably more
informative about many species. But there are a couple of things
Wikispecies does very well. Firstly, it is building a rich,
crowd-sourced bibliography of papers on the taxonomy of many different
species. Readers of iPhylo will recall how many times I\'ve expressed
frustration at the nearly evidence-free nature of many online taxonomic
databases that simply have lists of names unconnected to the primary
literature. Many Wikispecies pages have long lists of papers, making it
a potential goldmine. Recently there is a lot of interest in extracting
bibliographic data from Wikipedia (see
[WikiCite](https://meta.wikimedia.org/wiki/WikiCite)). Wikispecies could
also be harvested, although a major obstacle any such project faces is
the lack of a consistent format for references in Wikispecies.

The other nice thing about Wikipecies is that it has articles on
taxonomic authorities, and these often list publications by those
authors, and also list external identifiers for those authors, such as
the VIAF and ISNI identifiers used in the library world, IPNI and
ZooBank identifiers used in taxonomic databases, and ORCID which is
becoming the de-facto identifier for academic researchers. This
information also ends up in Wikidata.

#### Using Wikidata to glue things together

Wikidata is an interesting project that, like Wikispecies, I\'ve been in
two minds about (see [Wikidata, Wikipedia, and
\#wikisci](http://iphylo.blogspot.com/2015/09/wikidata-wikipedia-and-wikisci.html)).
However, I\'ve started to make more use of it recently. Inspired by the
[Wikidata:SPARQL query service/2016 SPARQL
Workshop](https://m.wikidata.org/wiki/Wikidata:SPARQL_query_service/2016_SPARQL_Workshop)
I decided to explore the [SPARQL query interface to
Wikidata](https://query.wikidata.org/). I was struck by one of the
example queries involving Wikispecies, and so after a little bit of
messing about came up with a query that takes the name of an author and
returns some identifiers from Wikidata, as well as an image of that
person if one is available. I restrict the results to people that have
an article about them in Wikispecies, because I want start exploring
using those articles to make assertions about authorship. Here is a
query to search for \"George Albert Boulenger\":

    SELECT *
    WHERE
    {
      ?item rdfs:label "George Albert Boulenger"@en .
      ?article schema:about ?item .
      ?article schema:isPartOf  .
      OPTIONAL {
       ?item wdt:P213 ?isni .
        }
      OPTIONAL {
       ?item wdt:P214 ?viaf .
        }
      OPTIONAL {
       ?item wdt:P18 ?image .
        }
      OPTIONAL {
       ?item wdt:P496 ?orcid .
        }
      OPTIONAL {
       ?item wdt:P586 ?ipni .
        }
      OPTIONAL {
       ?item wdt:P2006 ?zoobank .
        }
    }

This query simply asks whether Wikidata has an item on this person,
whether that item is linked to Wikispecies, what identifiers Wikidata
has, and whether there is an image of the person. You can see the query
\"live\" here:

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I\'ve added some code to BioStor to do this query on the fly, and
display the results. So, for Boulenger we get: ![Screenshot 2017 01 11
17 04
16](https://lh3.googleusercontent.com/-gqZTl9iu6FI/WHZp12-alXI/AAAAAAAAEWw/cOa8-N3WDpc/Screenshot%2525202017-01-11%25252017.04.16.png?imgmax=1600 "Screenshot 2017-01-11 17.04.16.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="200" height="192"} Here is the result for noted
carcinologist [Jocelyn
Crane](http://biostor.org/?q=author%3A%22Jocelyn+Crane%22) who currently
lacks identifiers: ![Screenshot 2017 01 11 17 05
32](https://lh3.googleusercontent.com/-Dn_NpZh8D6c/WHZp3ElV9RI/AAAAAAAAEW0/QrQFQ9sxdjM/Screenshot%2525202017-01-11%25252017.05.32.png?imgmax=1600 "Screenshot 2017-01-11 17.05.32.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="168" height="135"} A nice surprise was [Bernard
Landry](http://biostor.org/?q=author%3A%22Bernard+Landry%22):
![Screenshot 2017 01 11 17 07
14](https://lh3.googleusercontent.com/-APTSbPjtlcc/WHZp4Bh6_SI/AAAAAAAAEW4/e-OZbFv4Eak/Screenshot%2525202017-01-11%25252017.07.14.png?imgmax=1600 "Screenshot 2017-01-11 17.07.14.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="206" height="72"} Note the ORCID
[0000-0002-6005-1067](http://orcid.org/0000-0002-6005-1067).
Interestingly, Bernard Landry\'s ORCID profile doesn\'t list any
publications, whereas we can see lists of these in BioStor and
[Wikispecies](https://species.wikimedia.org/wiki/Bernard_Landry).

#### Where next?

There are several obstacles to mapping the names of authors to
identifiers. One is simply the lack of identifiers. This seems to be
rapidly becoming less of a problem with the efforts of the library
community around [VIAF](http://viaf.org), the rise of
[ORCID](http://orcid.org) for living researchers, and the creation of
Wikidata items for every taxonomist in Wikispecies. The next challenge
is clustering the different ways of writing the same person\'s name into
sets that represent the same person. As discussed above, there are tools
for this. Furthermore, with Wikipedia and Wikispecies we have sources of
lists of publications linked to a person and their identifiers, which
should simplify the task considerably. What is nice about this is that
it relies on a crowd-sourcing effort which is already well-established,
namely those people who in adding articles to Wikispecies and Wikipedia
are created a curated database of publications linked to authors. In
many cases those publications are linked to BHL (the source that BioStor
extracts its articles from), so many of the links between publications
and people are essentially lying there, just waiting for some skilful
harvesting.


I've added an experimental feature to BioStor that uses data from Wikidata and Wikispecies to augment what information BioStor displays on authors.

The Biodiversity Heritage Library meets Wikidata via Wikispecies: adding author identifiers to BioStor

![220px Boulenger George 1858
1937](https://lh3.googleusercontent.com/-qCLlGqdFDu0/Vcg0dh8JUuI/AAAAAAAAEAI/Gd1cYKILyVM/220px-Boulenger_George_1858-1937.png?imgmax=800 "220px-Boulenger_George_1858-1937.png"){border="0"
width="128" style="float:right;"}One of the less glamorous but necessary
tasks of data cleaning is mapping \"strings to things\", that is, taking
strings such as \"George A. Boulenger\" and mapping them to identifiers,
such as [ISNI: 0000 0001 0888
841X](http://isni-url.oclc.nl/isni/000000010888841X). In case of authors
such as George Boulenger, one way to do this would be through Wikipedia,
which has entries for many scientists, often linked to identifiers for
those people (see the bottom of the [Wikipedia page for George A.
Boulenger](https://en.wikipedia.org/wiki/George_Albert_Boulenger) and
look at the \"Authority Control\" section).

How could we make these mappings? Simple string matching is one
approach, but it seems to me that a more robust approach could use
bibliographic data. For example, if I search for [George A.
Boulenger](http://biostor.org/search/author:%22George%20A%20Boulenger%22)
in BioStor, I get lots of publications. If at least some of these were
listed on the Wikipedia page for this person, together with links back
to BioStor (or some other external identifier, such as DOIs), then we
could do the following:

1.  Search Wikipedia for names that matched the author name of interest
2.  If one or more matches are found, grab the text of the Wikipedia
    pages, extract any literature cited (e.g., in the {cite} tag), get
    the bibliographic identifiers, and see if they match any in our
    search results.
3.  If we get one or more hits, then it\'s likely that the Wikipedia
    page is about the author of the papers we are looking at, and so we
    link to it.
4.  Once we have a link to Wikipedia, extract any external identifier
    for that person, such as ISNI or ORCID.

For this to work, it requires that the Wikipedia page cites works by the
author in a way that we can harvest, and uses identifiers that we can
match to those in the relevant database (e.g., BioStor, Crossef, etc.).
We might also have to look at Wikipedia pages in multiple languages,
given that English-language Wikipedia may be lacking information on
scholars from non-English speaking countries (this will be a significant
issue for many early taxonomists).

Based on my limited browsing of Wikipedia, there seems to be little
standardisation of entries for people, certainly little in how their
published works are listed (the section heading, format, how many,
etc.). The project I\'m proposing would benefit from a consistent set of
guidelines for how to include a scholar\'s output.

What makes this project potentially useful is that it could help flesh
out Wikipedia pages by encouraging people to add lists of published
works, it could aid bibliographic repositories like my own BioStor by
increasing the number of links they get from Wikipedia, and if the
Wikipedia page includes external identifiers then it helps us go from
strings to things by giving us a way to locate globally unique
identifiers for people.


One of the less glamorous but necessary tasks of data cleaning is mapping "strings to things", that is, taking strings such as "George A. Boulenger" and mapping them to identifiers, such as ISNI: 0000 0001 0888 841X. In case of authors such as George Boulenger, one way to do this would be through Wikipedia, which has entries for many scientists, often linked to identifiers for those people (see the bottom of the Wikipedia page for George A.

Messaggi di Rogue Scholar

The Biodiversity Heritage Library meets Wikidata via Wikispecies: adding author identifiers to BioStor

Possible project: mapping authors to Wikipedia entries using lists of published works