OpenCitations Team

[The creation of the ]{style="font-weight: 400"}[[Open Biomedical
Citations in Context Corpus
(CCC)]{style="font-weight: 400"}](https://wellcome.ac.uk/funding/people-and-projects/grants-awarded/open-biomedical-citations-context-corpus)[
is the goal of a one-year project funded by the
]{style="font-weight: 400"}[[Wellcome
Trust]{style="font-weight: 400"}](https://wellcome.ac.uk/)[. The aim is
to create a new open corpus of bibliographic and citation data that
contain detailed information about individual in-text reference pointers
in biomedical journal articles. The project is led by Professor Silvio
Peroni of the ]{style="font-weight: 400"}[[Research Centre for Open
Scholarly
Metadata]{style="font-weight: 400"}](https://openscholarlymetadata.org/)[
(University of Bologna), is being undertaken by Dr Marilena Daquino
(University of Bologna), and actively involves the Oxford e-Research
Centre (University of Oxford), the École de Bibliothéconomie et des
Sciences de l'Information (Université de Montréal), and the Centre for
Science and Technology Studies (CWTS), (Leiden
University).]{style="font-weight: 400"}

[An in-text reference pointer is a textual device (e.g. "\[1\]", or
"(Peroni and Shotton 2012)") that appears in the main text of a citing
work and denotes a bibliographic reference listed in the Bibliography
section of the citing work. While a single in-text reference pointer
uniquely denotes a single bibliographic reference, it can occur together
with one or more other pointers, forming an in-text reference pointer
list that denotes several references (e.g. "\[5-13\]", or "(Peroni and
Shotton 2012; Peroni and Shotton 2019)"). In-text reference pointers may
appear in several places within the same citing publication (e.g.
Introduction, Methods, Discussion), may occur within different document
components (e.g. body text, figure captions, tables), and may address
the cited publication for different purposes (e.g. as the source of an
experimental protocol, as a data source, or for general background
information).]{style="font-weight: 400"}

[Unfortunately, current citation indexes contain no information about
in-text reference pointers, such as the number of times a particular
work is referenced in the citing work, the text of the sentences in
which they occur, or the rhetorical purpose of such
citations.]{style="font-weight: 400"}

[Having data at the level of individual in-text reference pointers
offers many new opportunities, enabling one: (1) to distinguish between
works that are referenced just once in a citing publication and those
that are referenced multiple times, and thereby (potentially) to
distinguish when a citation is fundamental for the understanding or the
development of the citing work, or merely incidental; (2) to see which
in-text reference pointers occur together (e.g. in the same sentence or
the same paragraph), thus, potentially, to infer similarities between
the co-cited publications; and (3) to determine in which specific
sections of the publication these in-text references occur (e.g.
Introduction, Methods, Results), and thus, potentially, by means of
textual analysis of the citation contexts, to retrieve the rhetorical
functions of the citations -- i.e. the reason why an author cites
another work. ]{style="font-weight: 400"}

[The goal of the CCC Project is to provide stakeholders with an exemplar
Linked Open Data corpus, created from the open access biomedical
research literature, that is tailored for such deep citation analyses.
The corpus will be a new member of the collection of OpenCitations
datasets, and will be accompanied by services for accessing and querying
data.]{style="font-weight: 400"}

[In the CCC Project, we have achieved or are currently dealing with the
following developments:]{style="font-weight: 400"}

- **Extending the OpenCitations Data Model (OCDM).**[ The OpenCitations
  Data Model has been extended and enriched with new terms and relations
  to represent bibliographic entities related to in-text reference
  pointers, such as the in-text reference pointers themselves, in-text
  reference pointer lists, discourse elements (e.g. sections,
  paragraphs, sentences), and annotations on citations, bibliographic
  references and in-text reference pointers. In addition, the provenance
  layer of the data model has been revised to provide meaningful
  provenance information in a more compact way. A revised version of the
  OCDM including these terms was published on November 8, 2019, and it
  is available on Figshare \[1\].]{style="font-weight: 400"}
- **Extending the OpenCitation harvesting and data re-engineering
  pipeline.**[ The CCC Project leverages existing OpenCitations
  technologies for building this new corpus, using as input articles
  from the Open Access Subset of biomedical literature hosted by Europe
  PubMed Central (EPMC) and encoded in XML. The OpenCitations pipelines
  for knowledge extraction (i.e. the software called BEE) and for data
  re-engineering (i.e. the software called SPACIN) have been enhanced so
  as to harvest relevant information from the full-text of the XML
  sources provided by EPMC, rather than just the reference lists,  and
  to transform these data into RDF according to the revised OCDM. The
  ]{style="font-weight: 400"}[[source
  code]{style="font-weight: 400"}](https://github.com/opencitations/ccc)[
  of the new pipeline is available on GitHub.]{style="font-weight: 400"}
- **Creating InTRePID, a new persistent identifier for in-text reference
  pointers.**[ Different in-text reference pointers denoting the same
  bibliographic reference have distinct logical, rhetorical and textual
  contexts wherein they occur. To permit them to be identified
  individually and handled properly, we have recently developed a new
  persistent identifier, the ]{style="font-weight: 400"}[**In-Text
  Reference Pointer Identifier
  (InTRePID)**](https://doi.org/10.6084/m9.figshare.11674032)[, for
  identifying individual in-text reference pointers relating to an open
  bibliographic citation. The InTRePID is based on the Open Citation
  Identifier (OCI), currently being used to identify the \>624 million
  citations present in the new release of COCI, the OpenCitations Index
  of Crossref open DOI-to-DOI citations, described in the
  ]{style="font-weight: 400"}[[previous blog
  post]{style="font-weight: 400"}](https://opencitations.hypotheses.org/997)[.
  The formal definition of an InTRePID is available on Figshare \[2\].
  In addition, an ]{style="font-weight: 400"}[[InTRePID Resolution
  Service]{style="font-weight: 400"}](http://opencitations.net/intrepid)[
  has been developed (currently in beta-testing) to facilitate the
  retrieval of the metadata relating to in-text reference pointers. At
  the moment, a subset of the CCC corpus is available online for testing
  the InTRePID Resolution Service.]{style="font-weight: 400"}
- **Development of services for accessing and querying the Citations in
  Context Corpus.**[ Along with the development of the CCC itself, we
  are also developing services for querying data within the CCC. In
  particular, we are currently working to extend the RAMOSE software to
  provide an API for accessing the CCC triplestore. This CCC API will
  permit users to access the CCC corpus and retrieve detailed
  information about in-text reference pointers and their related
  annotations in a variety of human- and machine-readable formats. The
  ]{style="font-weight: 400"}[[source
  code]{style="font-weight: 400"}](https://github.com/opencitations/ramose)[
  of the API Manager is available on GitHub. The configuration file for
  querying the CCC corpus is still in the process of
  development.]{style="font-weight: 400"}

[Moreover, we are currently working to evaluate the content data quality
of the CCC corpus and to develop reconciliation activities with
information stored in Crossref. Specifically, by means of new validation
methods, we are testing whether the extracted in-text reference pointers
are complete (i.e. determining that ]{style="font-weight: 400"}***all***
[the in-text reference pointers for a particular bibliographic reference
have been correctly extracted from the text), and that in-text reference
pointer lists (e.g. "\[5-13\]") have been correctly parsed to extract
all the implicit pointers (in this case "\[6\]", "\[7\]", "\[8\]",
"\[9\]", "\[10\]", "\[11\]" and "\[12\]"), and to associate them
correctly with the appropriate bibliographic references that they
denote. This activity is fundamental, in order to address the diverse
citation styles adopted by different journals and to overcome possible
incoherencies in the publishers' XML markup of the articles. Secondly,
whenever a DOI is not specified for the citing or cited publications in
the full-text of the citing publication, a text search using the
]{style="font-weight: 400"}[[Crossref
API]{style="font-weight: 400"}](https://www.crossref.org/services/metadata-delivery/rest-api/)[
is performed in order to match possible candidates and supply the
missing DOI. This reconciliation process itself can be error-prone since
recommended matches are obtained by means of a non-transparent scoring
mechanism. Therefore we are currently testing the application of a
scoring threshold that will eliminate false positives and provide us
only with correct results.]{style="font-weight: 400"}

[The deployment of the enhanced OpenCitations pipeline for populating
the CCC corpus automatically is planned to start in the next weeks. For
more details and to provide suggestions, please
]{style="font-weight: 400"}[[contact
us]{style="font-weight: 400"}](mailto:marilena.daquino@opencitations.net)[!]{style="font-weight: 400"}

**References**

[\[1\] Marilena Daquino, Silvio Peroni and David Shotton (2019). The
OpenCitations Data Model. Version 2.0. Figshare. DOI: 
​]{style="font-weight: 400"}[[https://doi.org/10.6084/m9.figshare.3443876]{style="font-weight: 400"}[ ]{style="font-weight: 400"}](https://doi.org/10.6084/m9.figshare.3443876)

[\[2\] David Shotton, Marilena Daquino and Silvio Peroni (2020). In-Text
Reference Pointer Identifier: Definition. Figshare.  DOI:
]{style="font-weight: 400"}[[https://doi.org/10.6084/m9.figshare.11674032]{style="font-weight: 400"}](https://doi.org/10.6084/m9.figshare.11674032)


The creation of the Open Biomedical Citations in Context Corpus (CCC) is the goal of a one-year project funded by the Wellcome Trust. The aim is to create a new open corpus of bibliographic and citation data that contain detailed information about individual in-text reference pointers in biomedical journal articles.

The Open Biomedical Citations in Context Corpus: Progress Report

Curtin University

Cameron Neylon

*Consider this yet another commitment to trying to write here a little
more regularly. Lots of thinking has been going on but not much writing!
At least not writing as I'm going...*

Three things colliding over the past few weeks have led me to want to
try and get some ideas down. The first was a conversation -- one of a
set really -- with Titus Brown and Dan Katz relating to the application
of political economy and collective action theory to communities
building research.  

The second was the posting of video of a talk I gave a month or so back
to our research centre, the Centre for Culture and Technology at Curtin
University. In this, I tried to work through the full story of some
recent thinking for the first time. I'm trying to articulate what has
evolved in my thinking from a view driven by network theory that open is
good, more open is better, to an understanding of where and how things
have gone wrong.

The final piece was the publication of a new paper ([preprint version is
also available](http://philsci-archive.pitt.edu/14352/), actually its
what I read so that's what I'll link to) by Sabina Leonelli which
tackles the value of reproducibility as a concept head on. Leonelli's
work has been a big influence on my developing thinking. Two pieces are
particularly relevant. The [idea that data is not a thing, but is a
category defined by
use](https://books.google.co.uk/books?hl=en&lr=&id=i8NADQAAQBAJ&oi=fnd&pg=PR5&dq=sabina+leonelli&ots=iBvrf8uB3L&sig=I5cdiwlIRoZQrm7iX2ksRe70ias&redir_esc=y#v=onepage&q=sabina%20leonelli&f=false).
That is, we can't say whether a particular object *is* data, only that
something is data when it is used in particular ways. This is true of
many things in research, the objectivist in us wants the qualities of
objects like data, methods, and knowledge itself to be eternal platonic
concepts inherent in the objects themselves. In practice however these
qualities only reveal themselves in certain activities.

These activities depend in turn on 'repertoires' another concept I've
taken from Leonelli's work, this time from [a paper published with
Rachel Ankeny](https://doi.org/10.1016/j.shpsa.2016.08.003). The concept
here is that research communities are defined by practices and that
these practices are not just learned, but displayed and internalised, in
a similar manner to a musician learning repertoire as a set of hurdles
to be jumped in their development. I first read this paper at the same
time as I was reading [Lave and
Wenger's](https://www.amazon.co.uk/Situated-Learning-Participation-Computational-Perspectives/dp/0521413087/)
*[Situated
Learning](https://www.amazon.co.uk/Situated-Learning-Participation-Computational-Perspectives/dp/0521413087/)*
and the parallel between craft learning (see also
[Ravetz](https://www.amazon.com/Scientific-Knowledge-Its-Social-Problems/dp/1560008512)),
identity making (see also [Hartley and
Potts](https://www.bloomsbury.com/uk/cultural-science-9781849666022/))
and community had a significant resonance for me.

In the new piece Leonelli tackles the range of different, and largely
incommensurate meanings that are ascribed to the concept of
'reproducibility'. The paper tackles a range of disciplinarily bound
practices ranging from computational sciences, where there is 'total
control' (yes I could quibble about machine states and compilers but
this is philosophy, let's accept the abstraction) through to
ethnography, where there is the expectation that the life experience of
the researcher affects the outcome, and that a different researcher
would reach different conclusions.

The article focuses on how the necessity for documentation changes as
different aspects of *accountability* rather than reproducibility are
taken into account. These concepts of responsibility and accountability
for sources of variability that have implications for the claims being
made seems more productive and more readily contextualised and
generalised. The article finishes with a call to value 'epistemic
diversity'. That is, it is through differing kinds of cross referencing,
with different sources of variability, accountability, and reliability
that we can most usefully build knowledge.

All of this resonates for me because I've been working towards a similar
end from a different place. My concern has been thinking about how to
operationalise social models of knowledge production. There are a broad
class of constructivist models of knowledge where validation occurs when
groups come together and contest claims. I have a paper currently in
review that casts this as 'productive conflict'.

In such models the greater the diversity of groups in contact the more
'general' the knowledge that is created. However the more diverse those
groups are, the less likely it is that such contact will be productive.
Indeed it can be harmful â€" and in most cases involving disadvantaged
groups (which is practically everyone in comparison to a professional,
permanently employed, western academic) it is at the very least a
significant burden and frequently significantly damaging.

<figure
class="wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio">
<div class="wp-block-embed__wrapper">
<div class="iframe">
<div id="player">

</div>
<div class="player-unavailable">
<h1 id="ein-fehler-ist-aufgetreten." class="message">Ein Fehler ist
aufgetreten.</h1>
<div class="submessage">
<a href="https://www.youtube.com/watch?v=9wvEh1Rn4-8"
target="_blank">Sieh dir dieses Video auf www.youtube.com an</a> oder
aktiviere JavaScript, falls es in deinem Browser deaktiviert sein
sollte.
</div>
</div>
</div>
</div>
</figure>

In the talk I'm trying to work through the question of how such contacts
can be made safe, while equally privileging the value of closing ranks,
returning to community to regain strength and re-affirm identity. If
diversity is a first order principle in the utilitarian goal of making
knowledge, what are the principles of care that allow us to protect the
communities that contribute that diversity?

Part of the argument I make is that we need to return to the thinking
about network structures. Five years ago I was making the case that
'bigger is better' underpinned by an assumption that even if benefits
flowed to those who were already well connected the new opportunities of
scale would still spread benefits more widely. That seems less and less
to be the case today, and the key problems appear to be ones where the
benefits of locality are reduced or broken, boundaries are too readily
traversed, and groups come into contact in *non-productive* conflict too
frequently.

In the talk I discuss the need to privilege locality. This is the
opposite of what most of our systems do today, both in the wider world
('you need to go viral!') and in academia ('international rankings!
international journals!'). Many social models draw simple lines with
groups inside or outside. Even with a mental view of groups within
groups and overlapping groups this tends to miss the messiness that
results from non-homogenous interactions across group boundaries.
Network structural analysis is harder to do and harder to visualise but
it seems to me crucial to get a view of what the optimal dynamics are.

One way to frame the question of network and community dynamics is
economically. That is, to ask how the differing groups and communities
in contact are sustained and succeed or fail. This in turn is a question
of exchange (not necessarily purely financial exchange, but there are
limitations to this framing!). Models of club economics and collective
action from political economy are useful here and this leads us back to
the first conversation I mentioned above.

Titus Brown has been working through [a series of
posts](http://ivory.idyll.org/blog/tag/cpr.html), relating to the NIH
Data Commons project looking at the goods produced in open source
projects through the lens of commons and clubs goods. Dan Katz was
raising good questions about issues of time and scale that are not well
captured by the classical analysis of goods.

<figure
class="wp-block-embed is-type-rich is-provider-twitter wp-block-embed-twitter">
<div class="wp-block-embed__wrapper">
<blockquote>
<p>Chatting with @egonwillighagen and <a
href="https://twitter.com/derkarts?ref_src=twsrc%5Etfw">@derkarts</a>
yesterday, drew this diagram of club/public/private goods and they asked
me to tweet it – so here it is! see also <a
href="https://t.co/8pmGIBEak4">https://t.co/8pmGIBEak4</a> <a
href="https://twitter.com/hashtag/commonspilot?src=hash&amp;ref_src=twsrc%5Etfw">#commonspilot</a>
<a href="https://t.co/RbBoTCLGVr">pic.twitter.com/RbBoTCLGVr</a></p>
<p>— Titus Brown (@ctitusbrown) <a
href="https://twitter.com/ctitusbrown/status/1047409685001904134?ref_src=twsrc%5Etfw">October
3, 2018</a></p>
</blockquote>
</div>
</figure>

<figure
class="wp-block-embed is-type-rich is-provider-twitter wp-block-embed-twitter">
<div class="wp-block-embed__wrapper">
https://twitter.com/danielskatz/status/1047442062264717312
</div>
</figure>

<figure
class="wp-block-embed is-type-rich is-provider-twitter wp-block-embed-twitter">
<div class="wp-block-embed__wrapper">
https://twitter.com/danielskatz/status/1047449426564960256
</div>
</figure>

I have quibbles with Brown's analyses and often with others who use this
kind of goods-class analysis. However I only just realised that my issue
was similar to Leonelli's point about data. The question of what is 'the
good' in any particular case is relational, not an absolute. Our
discussion of these models tends to turn on an implicit assumption that
something (prestige, code, knowledge, expert attention) is the specific
good in play, something that in turn surfaces a common assumption in
most classical economics that it is appropriate to assume some kind of
'numeraire good' that allows exchange of all the others (this is what
money is for, and if there's anything wrong with economic analysis, its
money..).

This doesn't leave me with any firm conclusions beyond some possible
routes to analysis. It seems likely that simple analysis based on static
descriptions of community and the environment aren't going to give us
answers. We need to understand dynamics of groups opening up and
enclosing over time, what sustains them, and what they might find
valuable in exchange. We need agent based modelling of the network
structures these occur over, and ways of translating from local
structure in networks to more 'bright-lined' social models of groups. We
need to move beyond the simple 'economic mathematics' that is often
developed from the the club economics of Buchannan and Olson and to
develop much more sophisticated and flexible models that allow the
nature of exchange and goods to change when viewed from different
perspectives.

All in all it emphasises the conclusion I'd reached, that diversity is a
first order principle. All forms of diversity and the more diverse the
better, provided the coordination between groups is principled. There's
a lot to unpack in that word 'principled' but I feel like its the link
to the ethical dimension I've been missing. I need to dig deeper into
notions of 'care' (Moore, Priego) and 'flourishing' (Holbrook) to tease
this out.  


<em>
 Consider this yet another commitment to trying to write here a little more regularly. Lots of thinking has been going on but not much writing! At least not writing as I’m going…
</em>
Three things colliding over the past few weeks have led me to want to try and get some ideas down.

Postagens de Rogue Scholar

The Open Biomedical Citations in Context Corpus: Progress Report

Epistemic diversity and knowledge production