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)

![2etoq0zjwxicokm1woge](http://lh5.ggpht.com/-lgZdE0boCE0/UdwCvwl1N8I/AAAAAAAAC6U/0M-xbAOioEo/2etoq0zjwxicokm1woge.jpeg?imgmax=800 "2etoq0zjwxicokm1woge.jpeg"){border="0"
width="200" height="200" style="float:right;"}  
Jonathan Eisen recently wrote that the [PLOS Hub for Biodiversity is
soon to be
retired](http://phylogenomics.wordpress.com/2013/07/03/plos-hub-for-biodiversity-soon-to-be-retired/),
and sure enough it\'s vanished from the web (the original URL
[hubs.plos.org/web/biodiversity/](hubs.plos.org/web/biodiversity/) now
bounces you straight to <http://www.plosone.org/>, you can still see
what it looked like in the [Wayback
Machine](http://web.archive.org/web/20130430161435/http://hubs.plos.org/web/biodiversity/)).  
  
Like Jonathan, I was involved in the hub, which was described in the
following paper:  

> Mindell, D. P., Fisher, B. L., Roopnarine, P., Eisen, J., Mace, G. M.,
> Page, R. D. M., & Pyle, R. L. (2011). Aggregating, Tagging and
> Integrating Biodiversity Research. (S. A. Rands, Ed.)PLoS ONE, 6(8),
> e19491.
> [doi:10.1371/journal.pone.0019491](http://dx.doi.org/10.1371/journal.pone.0019491)

  
In retrospect PLoS\'s decision to pull the hub is not surprising. The
original proposal imagined a web site looking like this, with the goal
of building a \"dynamic community\".  
  
![Proposal](http://lh4.ggpht.com/-jyti4Rqeoas/UdwCxsLpiwI/AAAAAAAAC6k/1orC_7ICyjs/proposal.png?imgmax=800 "proposal.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="600"}  
  
From my perspective the PLoS HUb failed for two reasons. The first is
that PLoS weren\'t nearly as ambitious as they could have been. The
second is that the biodiversity informatics community simply couldn\'t
(an arguably still can\'t) provide the kind of services that PLoS would
have needed to make the Hubs something worth nurturing.  
  
After a meeting at the California Academy of Science in April 2010 to
discuss the hub idea I wrote a ranty blog post ([Biodiversity
informatics = \#fail (and what to do about
it)](http://iphylo.blogspot.co.uk/2010/04/biodiversity-informatic-fail-and-what.html))
where I expressed my frustration that we had a group of people (i.e.,
PLoS) rock up and express serious interest in doing something with
biodiversity data, and biodiversity informatics collectively failed
them. We could have been aiming for a cool database of \"semantically
enhanced\" publications that we could query taxonomically,
geographically, phylogenetically, etc. (at least, that\'s what I was
hoping PLoS were aiming for). Instead it became clear that most of the
basic services were simply not available (we didn\'t have a simple code
to extract GenBank accession numbers, specimens codes, etc., we
couldn\'t link specimen codes to anything online, and woe betide you if
you asked what a taxon name was).  
  
In fairness, it also became pretty clear that PLoS weren\'t going to go
too far down the line of an all-singing portal to biodiversity data.
They were really looking at a shiny web site that housed a collection of
Open Access papers on biodiversity. But my point is it could have been
so much more than that. We had a chance to build a platform,a knowledge
base for biodiversity data that had an accessible front end (e.g., the
traditional publication) but exploded that into its component parts so
we could spin the data around and ask other questions.  
  
Inspired by the possibilities I spent the next couple of months playing
with some linked data demos (see
[here](http://iphylo.blogspot.com/2010/05/linking-biodiversity-data.html)
and
[here](http://iphylo.blogspot.co.uk/2010/05/linked-data-part-2.html),
the links in these demos have long since died). The idea was to explore
how much of what I imagined the PLoS Hub could be it was possible to
build using RDF and SPARQL. It was fun, but RDF and SPARQL are awful
things to \"play\" with, and the vast bulk of the data had to be wrapped
in custom scripts I wrote because the original data providers didn\'t
supply RDF. As I\'ve written elsewhere, I think the cost of getting to a
place where RDF enables you to do meaningful stuff is just too high. Our
data are too messy, we lack agreed identifiers, and we either have too
many or too few vocabularies (and those we do have invariably spark
lengthy, philosophical debates - vocabularies are taxonomies of data,
need I say more). The RDF approach is also doomed to fail because it
assumes multiple decentralised data repositories are the way forward. In
my experience, these cannot deliver the kinds of things we need. The
data need to be brought together, cleaned, aligned, augmented, and
finally linked together. This is much easier to do if all the data are
in one place.  
  
So where does this leave us? In many ways I\'d like to attempt something
like PLoS Hubs again, or perhaps more precisely, think about building a
**platform** so that if a publisher came along and wanted to do
something similar (but more ambitious) we would have the tools in place
that could make it happen. What I\'d like is a way more sophisticated
version of [this](http://iphylo.org/~rpage/challenge), where you could
explore data in various dimensions (geography, taxonomy, phylogeny),
track citation and provenance information (what papers cite this
specimen, what sequences is it a voucher for, what trees are built on
those sequences). If we had a platform that supported these sorts of
queries, not only could we provide great environment upon which we could
embed scientific publications, we could also support the kinds of
queries we can\'t do at the moment (e.g., give me all the molecular
phylogenies for species in Madagascar, locate all the data -
publications, taxonomic identifications, sequences - about a specimen,
etc.).  
  
I\'ll leave you with a [great rant about
platforms](https://gist.github.com/chitchcock/1281611). It\'s long but
it\'s fun, and I think it speaks to where we are now in biodiversity
informatics (hint, we aren\'t Amazon).  


Jonathan Eisen recently wrote that the PLOS Hub for Biodiversity is soon to be retired, and sure enough it's vanished from the web (the original URL hubs.plos.org/web/biodiversity/ now bounces you straight to http://www.plosone.org/, you can still see what it looked like in the Wayback Machine).  Like Jonathan, I was involved in the hub, which was described in the following paper:  In retrospect PLoS's decision to pull the hub is not surprising.

The demise of the @PLoS Biodiversity Hub: what lessons can we learn?

::: {style="text-align:center;"}
![hubs.png](http://lh6.ggpht.com/_Gct8lVAxKqQ/TKpatLNzIEI/AAAAAAAAAxg/eaQpZW4Y1b0/hubs.png?imgmax=800){border="0"
width="387" height="62"}
:::

  
The [PLoS Biodiversity Hub](http://hubs.plos.org/biodiversity) has
launched today. There\'s a [PLoS blog
post](http://blogs.plos.org/plos/2010/10/announcing-plos-hubs-biodiversity/)
explaining the background to the project, as well as a
[summary](http://hubs.plos.org/web/biodiversity/about) on the Hub
itself:  
  

> The vision behind the creation of PLoS Hubs is to show how open-access
> literature can be reused and reorganized, filtered, and assessed to
> enable the exchange of research, opinion, and data between community
> members.  
>   
> PLoS Hubs: Biodiversity provides two main functions to connect
> researchers with relevant content. First, open-access articles on the
> broad theme of biodiversity are selected and imported into the Hub. In
> time, the content will also be enhanced so that the articles are
> connected with data, and we will provide features to make the articles
> easier for people to use. These two functions - aggregation and adding
> value - build on the concept of open access, which removes all the
> barriers to access and reuse of journal article content.

  
  
Readers of iPhylo may recall [my
account](http://iphylo.blogspot.com/2010/04/biodiversity-informatic-fail-and-what.html)
of one of the meetings involved in setting up this hub, in which I began
to despair about the lack of readiness of biodiversity informatics to
provide much of the information needed for projects such as hubs.
Despite this (or perhaps, because of it), I\'ve become a [member of the
steering
committee](http://hubs.plos.org/web/biodiversity/curators#Roderic_Page)
for the Biodiversity Hub. There\'s clearly a lot of interest in
repurposing the content found in scientific articles, and I think we\'re
going to see an increasing number of similar projects from the major
players in science publishing, Open Access or otherwise. One of the
challenges is going to be moving beyond the obvious things (such as
making taxon names clickable) to enable new kinds of ways of reading,
navigating, and querying the literature, and exploring ways to track the
use that is made of the information in these articles. Biodiversity
studies are ideally placed to explore this as the subject is data rich
and much of that data, such as specimens and DNA sequences, persist over
time and hence get reused (data citation gets very boring if the data is
used just once). We also have obvious ways to enrich navigation, such as
spatially and taxonomically.  
  
For now the PLoS Biodiversity Hub is very pretty, but it\'s more a
statement of intent than a real demonstration of what can be done.
Let\'s hope our field gets its act together and seizes the opportunity
that initiatives like the Hub represents. Publishers are desperate to
differentiate themselves from their competitors by providing added value
as part of the publication process, and they provide a real use case for
all the data that the biodiversity projects have been accumulating over
the last couple of decades.


The PLoS Biodiversity Hub has launched today. There's a PLoS blog post explaining the background to the project, as well as a summary on the Hub itself:  Readers of iPhylo may recall my account of one of the meetings involved in setting up this hub, in which I began to despair about the lack of readiness of biodiversity informatics to provide much of the information needed for projects such as hubs.

Messaggi di Rogue Scholar

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

The demise of the @PLoS Biodiversity Hub: what lessons can we learn?

PLoS Biodiversity Hub launches