University of Glasgow

Roderic Page

Here\'s a sketch of my vision of how to make something like the original
PLoS Hubs vision (see [The demise of the @PLoS Biodiversity Hub: what
lessons can we
learn?](http://iphylo.blogspot.com/2013/07/the-demise-of-plos-biodiversity-hub.html)
for background). In the blog post explaining the vision behind PLoS Hubs
([Aggregating, tagging and connecting biodiversity
studies](http://blogs.plos.org/plos/2010/10/aggregating-tagging-and-connecting-biodiversity-studies/)),
David Mindell wrote:  
  

> The Hub is a work in progress and its potential benefits are many.
> These include enhancing information exchange and databasing efforts by
> adding links to existing publications and adding semantic tagging of
> key terms such as species names, making that information easier to
> find in web searches. Increasing linkages and synthesizing of
> biodiversity data will allow better analyses of the causes and
> consequences of large scale biodiversity change, as well as better
> understanding of the ways in which humans can adapt to a changing
> world.

  
So, first up, some basic principles. The goal (only slightly tongue in
cheek) is for the user to never want to leave the site. Put another way,
I want something as engaging as Wikipedia, where almost all the links
are to other Wikipedia pages (more on this below). This means object
(publication, taxon name, DNA sequence, specimen, person, place) gets a
\"page\". Everything is a first class citizen.  
  
It seems to me that the fundamental problem faced by journals that
\"semantically enhance\" their content by adding links is that those
links go somewhere else (e.g., to a paper on another journal\'s site, to
an external database). So, why would you do this? Why actively send
people away?. Google can do this because you will always come back.
Other sites don\'t have this luxury. In the case of citations (i.e.,
adding DOIs to the list of literature cited) I guess the tradeoff is
that because all journals are in this together, you will receive traffic
from your \"rivals\" if papers they publish papers that cite your
content. So you are building a network that will (potentially) drive
traffic to you (as well as send people away). You are building a network
across which traffic can flow (i.e., the \"citation graph\").  
  
If we add other sorts of links (say to GenBank, taxon databases,
specimen databases like [GBIF](http://data.gbif.org), locality databases
such as [Protected Planet](http://protectedplanet.net), etc.) then that
traffic has no obvious way of coming back. This also has a deeper
consequence, those databases don\'t \"know\" about these links, so we
loose the reverse citation information. For example, a semantically
marked-up paper may know that it cites a sequence, but that sequence
doesn\'t know that it has been cited. We can\'t build the equivalent
citation graphs for data.  
  
One way to tackle this is to bring the data \"in house\", and this is
what [Pensoft](http://www.pensoft.net/) are doing with their markup of
ZooKeys. But they are basically creating mashups of external data
sources (a bit like [iSpecies](http://ispecies.org)). We need to do
better.  
  
**Prototyping**  
  
One way to make this more concrete is to think how a hub could be
prototyped. Let\'s imagine we start with a platform like [Semantic
MediaWiki](http://semantic-mediawiki.org/). I\'ve an on-again/off-again
relationship with Semantic MediaWiki, it\'s powerful but basically a
huge, ugly hack on top off a huge piece of software that wasn\'t
designed for this purpose, but it\'s a way to conceptualise what can be
done. So, I\'m not arguing that Semantic MediaWiki is how to do this for
real (trust me, I\'m really, really not), but that it\'s a way to
explore the idea of a hub.  
  
OK, let\'s say we start with a paper, say an Open Access paper from
PLoS. We parse the XML, extract every entity that matters (authors,
cited articles, GenBank accessions, taxon names, georeferenced
localities, specimen codes, chemical compounds, etc.) and then create
pages for each entity (including the article itself). Each page has a
URL that uses an external id (where available) as a \"slug\" (e.g., the
URL for the page for a GenBank sequence includes the accession
number).  
  
Now we have exploded the article into a set of pages, which are linked
to the source article (we can use Semantic MediaWiki to specify the type
of those links), and each entity \"knows\" that it has a relationship
with that article.  
  
Then we set about populating each page. The article page is trivial,
just reformat the text. For other entities we construct pages using data
from external databases wherever possible (e.g., metadata about a
sequence from GenBank).  
  
So far we have just one article. But that article is linked to a bunch
of other articles (those that it cites), and there may be other less
direct links (e.g., GenBank sequences are linked to the article that
publishes them, taxonomic names may be linked to articles that publish
the name, etc.). We could add all these articles to a queue and process
each article in the same way. In a sense we are now crawling a graph
that includes the citation graph, but it includes links the citation
graph misses (such as articles that cite the same data, see [Enhanced
display of scientific articles using extended
metadata](http://hdl.handle.net/10101/npre.2009.3173.1) for more on
this).  
  
The first hurdle we hit will be that many articles are not open access,
in which case they can\'t be exploded into full text and associated
entities. But that\'s OK, we can create article pages that simply
display the article metadata, and link(s) to articles in the citation
graph. Furthermore, we can get some data citation links for closed
access articles, e.g. from GenBank.  
  
So now we let the crawler loose. We could feed it a bunch of articles to
start with (e.g., those in the original Hub (if that list still exists),
those from various RSS feeds (e.g., PLoS, ZooKeys, BMC, etc.).  
  
**Entry points**  
  
Users can enter the hub in various ways. Via an article would be the
traditional way (e.g., via a link from the article itself on the PLoS
site). But let\'s imagine we are interested in a particular organism,
such as Macaroni Penguins. PLoS has an interesting article on their
feeding \[Studying Seabird Diet through Genetic Analysis of Faeces: A
Case Study on Macaroni Penguins (Eudyptes chrysolophus)
[doi:10.1371/journal.pone.0000831](http://dx.doi.org/10.1371/journal.pone.0000831)\].
This article includes sequence data for prey items. If we enhance this
article we build connections between the bird and its prey. In the
simple level, the hub page for the crustacea and fish it feed on would
include citations to this article, enabling people to follow that
connection (with more sophistication the nature of the relationship
could also be specified). This article refers to a specific locality and
penguin colony, which is in a marine reserve ([Heard Island and McDonald
Islands Marine
Reserve](http://protectedplanet.net/sites/Heard_Island_And_Mc_Donald_Islands_Marine_Reserve)).
Extract these entities, and other papers relevant to this are would be
linked as they are added (e.g., using a geospatial query). Hence people
interested in what we now about the biology of organisms in specific
localities would dive in via the name (or URL) of the locality.  
  
**Summary**  
  
The core idea here is taking an article, exploding it, and treating
every element as a first class citizen of the resulting database. It is
emphatically not about a nice way to display a bunch of articles, it\'s
not a \"collection\", and articles aren\'t privileged. Nor are articles
from any particular publisher privileged. One consequence of this is
that it may not appeal to an individual publisher because it\'s not
about making a particular publisher\'s content look better than
another\'s (although having Open Access content in XML makes it much
easier to play this game).  
  
The real goal of an approach like this is to end up with a database (or
\"knowledgebase\") that is much richer than simply a database of
articles (or sequences, or specimens), and which moves from being a
platform for repurposing article text to a platform for facilitating
discovering.  
  


Here's a sketch of my vision of how to make something like the original PLoS Hubs vision (see The demise of the @PLoS Biodiversity Hub: what lessons can we learn? for background). In the blog post explaining the vision behind PLoS Hubs (Aggregating, tagging and connecting biodiversity studies), David Mindell wrote:So, first up, some basic principles. The goal (only slightly tongue in cheek) is for the user to never want to leave the site.

The challenge of semantically marking up articles (more thoughts on PLoS Hubs)

Yesterday I fired off a stream of tweets, starting with:  

> OK, I\'m back to hatin\' on the wikis. It\'s just way to hard to do
> useful queries (e.g., anything that requires a path linking some
> entities)
> \[[10991434609](http://twitter.com/rdmpage/status/10991434609)\]

  
Various people commented on this, either on twitter or in emails,
e.g.:  

> @rdmpage hatin\' wikis is irrational - all methods have pros and cons,
> so wikis are an essential resource among others
> \[[@stho002](http://twitter.com/stho002/status/10996965111)\]

  
So, to clarify, I\'m not abandoning wikis. I\'m just frustrated with the
limitations of [Semantic Mediawiki](http://semantic-mediawiki.org/)
(SMW). Now, SMW is a great piece of software with some cool features.
For example,  

1.  Storing data in Mediawiki templates (i.e., key-value pairs) makes it
    rather like a JSON database with version control (shades of
    [CouchDB](http://couchdb.apache.org/) et al.).
2.  Having Mediawiki underlying SMW makes lots of nice editing and user
    management features available for free.
3.  The template language makes it relatively easy to format pages.
4.  It is easy to create forms for data entry, so users aren\'t
    confronted with editing Mediawiki templates unless they want to.
5.  Supports basic queries.

  
It\'s the last item on the list that is causing me grief. The queries
are, well, basic. What SMW excels at are queries connecting one page to
another. For example, if I create wiki pages for publications, and list
the author of each publication, the page for an author can contain a
simple query (of the form `{{ #ask: [[maker::Author 1]] | }}`) that
lists all the publications of that author:  
  

::: {style="text-align:center;"}
![q1.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/S6s28Mcd81I/AAAAAAAAAoA/fH70TpGAtVc/q1.png?imgmax=800){border="0"
width="400" height="305"}
:::

  
  
That\'s great, and many of the things are want to do can be expressed in
this simple way (i.e., find all pages of a certain kind that link to the
current page). It\'s when I want to go more than one page away that
things start to go pear shaped. For example, for a given taxon I want to
display a map of where it is found, based things like geoferenced
GenBank sequences, or sequences from georeferenced museum specimens.  
  

::: {style="text-align:center;"}
![q2.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/S6s34SWf94I/AAAAAAAAAoE/vzPBWaJzB2w/q2.png?imgmax=800){border="0"
width="400" height="378"}
:::

This can involve a path between several entities (\"pages\" in SMW), and
this just doesn\'t seem to be possible. I\'ve managed to get [some
queries working via baroque Mediawiki
templates](http://iphylo.blogspot.com/2010/03/progress-on-phylogeny-wiki.html),
but it\'s getting to the point where hours seem to be wasted trying to
figure this stuff out.  
  
So, what tends to happen is I develop something, hit this brick wall,
then go and do something else. I suspect that one way forward is to use
SMW as the tool to edit data and display basic links, then use another
tool to do the deeper queries. This is a bit like what I\'m exploring
with [BioStor](http://biostor.org), where I\'ve written my own interface
and queries over a simple MySQL database, but I\'m looking into [SMW +
Wikisource to handle
annotation](http://iphylo.blogspot.com/2010/03/setting-up-local-wikisource.html).  
  
This leaves the question of how to move forward with
<http://iphylo.org/treebase/>? One approach would be to harvest the SMW
pages regularly (e.g., by consuming the RSS feed, and either pulling off
SMW RDF or parsing the template source code for the pages), use this to
populate a database (say, a key-value store or a triple store) where
more sophisticated queries can be developed. I guess one could either
make this a separate interface, or develop it as a SMW extension, so
results could be viewed within the wiki pages. Both approaches have
merits. Having a complete separate tool that harvests the phylogeny wiki
seems attractive, and in many ways is an obvious direction for
[iSpecies](http://ispecies.org) to take. Imagine iSpecies rebuilt as an
RDF aggregator, where all manner of data about a taxon (or sequences, or
specimen, or publication, or person) could be displayed in one place,
but the task of data cleaning took place elsewhere.  
  
Food for thought. And, given that it seems some people are wondering why
on earth I bother with this stuff, and can\'t I just [finish TreeView
X](http://iphylo.blogspot.com/2010/03/treeview-and-windows-vista.html#comment-41409157),
I could always go back to fussing with C++...  


Yesterday I fired off a stream of tweets, starting with:Various people commented on this, either on twitter or in emails, e.g.:So, to clarify, I'm not abandoning wikis. I'm just frustrated with the limitations of Semantic Mediawiki (SMW). Now, SMW is a great piece of software with some cool features.

Messages de Rogue Scholar

The challenge of semantically marking up articles (more thoughts on PLoS Hubs)

Wiki frustration