University of Glasgow

Roderic Page

![7iUlfzBp](https://lh3.googleusercontent.com/-PFplm7rANV0/V2wIfFwDr5I/AAAAAAAAEOY/Wsgx40sZ8gc/7iUlfzBp.jpg?imgmax=1600 "7iUlfzBp.jpg"){border="0"
width="128" height="128" style="float:right;"}I will be at [ReCon 16 in
Edinburgh](https://reconevent.com) (hashtag
[\#ReCon_16](https://twitter.com/hashtag/ReCon_16?src=hash)), the second
ReCon event I\'ve attended (see [Thoughts on ReCon 15: DOIs, GitHub,
ORCID, altmetric, and transitive
credit](http://iphylo.blogspot.com/2015/06/thoughts-on-recon-15-dois-github-orcid.html)).
For the hack day that follows I\'ve put together some instructions for a
way to glue together annotations made by multiple people using
[hypothes.is](https://hypothes.is). It works by using
[IFTTT](https://ifttt.com) to read a user\'s annotation stream (i.e.,
the annotations they\'ve made) and then post those to a CouchDB database
hosted by [Cloudant](http://cloudant.com).

Why, you might ask? Well, I\'m interested in using hypothes.is to make
machine-readable annotations on papers. For example, we could select a
pair of geographic co-ordinates (latitude and longitude) in a paper, tag
it \"geo\", then have a tool that takes that annotation, converts it to
a pair of decimal numbers and renders it on a map.

![Screenshot 2016 06 23 15 53
07](https://lh3.googleusercontent.com/-PgGXvvkzeBw/V2wIf2JDDgI/AAAAAAAAEOg/U0ksvXQ8jeM/Screenshot%2525202016-06-23%25252015.53.07.png?imgmax=1600 "Screenshot 2016-06-23 15.53.07.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="350"}

Or we could be reading a paper and the literature cited lacks links to
the cited literature (i.e., there are no DOIs). We could add those by
selecting the reference, pasted in the DOI as the annotation, and
tagging it \"cites\". If we aggregate all those annotations then we
could write a query that lists all the DOIs of the cited literature
(i.e., it builds a small part of the citation graph).

By aggregating across multiple users we effectively crowd source the
annotation problem, but in a way that we can still collect those
annotations. For this hack I\'m going to automate this collection by
enabling each user to create an IFTTT recipe that feeds their
annotations into the database (they can switch this feature off at any
time by switching off the recipe).

Manual annotation is not scalable, but it does enable us to explore
different ways to annotate the literature, and what sort of things
people may be interested in. For example, we could flag scientific
names, great numbers, localities, specimens, concepts, people, etc. We
could explore what degree of post-processing would be needed to make the
annotations computable (e.g., converting 8°07′45.73″S, 63°42′09.64″W\'
into decimal latitude and longitude).

If this project works I hope to learn something about people want to
extract from the literature, and to what extent having a database of
annotations can provide useful information. This will also help inform
my thinking about automated annotation, which I\'ve explored in
[Hypothes.is revisited: annotating articles in
BioStor](http://iphylo.blogspot.com/2015/09/hypothesis-revisited-annotating.html).


I will be at ReCon 16 in Edinburgh (hashtag #ReCon_16), the second ReCon event I've attended (see Thoughts on ReCon 15: DOIs, GitHub, ORCID, altmetric, and transitive credit). For the hack day that follows I've put together some instructions for a way to glue together annotations made by multiple people using hypothes.is. It works by using IFTTT to read a user's annotation stream (i.e., the annotations they've made) and then post those to a

Aggregating annotations on the scientific literature: a hack for ReCon 16

Inspired by the forthcoming
[Hack4Knowledge](http://hack4knowledge.eventbrite.com/) I\'ve put
together a service that enables you to assert that you are the author of
a paper using the [Mendeley API](http://dev.mendeley.com).  
  
If you are impatient, give it a try at:  
  
<http://iphylo.org/~rpage/hack4knowledge/iwrotethat/>  
  
To use it you need a Mendeley account. When you go to [I wrote
that](http://iphylo.org/~rpage/hack4knowledge/iwrotethat/) you will be
asked to connect to your Mendeley account. Once you\'ve done that, enter
the DOI or PubMed ID of a paper and, if the paper is in your Mendeley
library and flagged as a paper you\'ve authored, you should see
something like this:  
  
![Wrote](http://lh5.ggpht.com/-XXiqJSJt5MQ/Te8mlV884BI/AAAAAAAAA5s/xcrimRbmzYM/wrote.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="500"}  
  
The site can be a little sluggish as it needs to go through all of your
publications one by one until it finds a match.  
  
**Why?**  
Imagine you have a web database that includes publications, and you want
people to join your site as users. If they have publications in your
database, you\'d like your users to be able to say \"I\'m the author of
those papers\" or, more generally, the author you have as \"Roderic D.
M. Page\" is me.  
  
One way to do this would be to enable the users to sign in to your site
using Mendeley (see my blog post [Mendeley
connect](http://iphylo.blogspot.com/2010/09/mendeley-connect.html)).
Once they\'ve done that, the user could select a publication and say
\"that\'s mine\". How do we test this assertion? Well, if the user is
indeed the author it is likely that they will have added it to their
\"My Publications\" section in their [Mendeley
library](http://www.mendeley.com/library/). So, we can use the Mendeley
API to get a list of the author\'s publications and see whether the
publication they claim is, in fact, one of theirs.  
  
The inspiration for this came from tools like Google Analytics, where in
order to add the tool to your web site you need to convince Google that
you own the site. One way to do this is to add some text supplied by
Google to the HTML on for site, on the assumption that only you can do
this (because it\'s your site). In the same way, only you can add papers
to your Mendeley library. Of course, I\'m assuming that Mendeley users
are being trustworthy when they and papers to \"My Publications\" (i.e.,
they\'re not claiming authorship on papers they didn\'t write).  
  
**How?**  
This hack uses Mendeley\'s OAuth support (the same technology used by
Twitter and Facebook to connect to other sites) to enable you to connect
your Mendeley account to the \"I wrote that\" application (note that my
app never sees your account name or password). I use the Mendeley API
[user
authored](http://apidocs.mendeley.com/home/user-specific-methods/user-authored)
method to get a list of your publications, and [user library document
details](http://apidocs.mendeley.com/home/user-specific-methods/user-library-document-details)
to retrieve details of each publication. I then compare the DOI or PMID
you supplied with each publication, until I find one that matches. If
none matches, then I\'ve no evidence you authored that paper.  
  
**Moan**  
No post about the Mendeley API would be complete without a moan about
the state of the API. Apart from the fact that there is no function to
directly find a publication in your library by DOI or PMID (hence I have
to look at them all), there is virtually no support for retrieving any
details about the user. For example, I wanted to brighten the web page
up a little by adding a picture of the Mendeley user once they\'ve
logged in. There is no API function for this, nor a function to retrieve
an identifier or URL for the user. Hence, in order to get a picture I
screen scrape (yes, *screen scrape*) the Mendeley web page for the
reference to get the URL for the linked author of the paper, then scrape
the author\'s profile page and extract the URL for the image. This is
insane. Please, please can we have a better API?


Inspired by the forthcoming Hack4Knowledge I've put together a service that enables you to assert that you are the author of a paper using the Mendeley API.If you are impatient, give it a try at:  http://iphylo.org/~rpage/hack4knowledge/iwrotethat/To use it you need a Mendeley account. When you go to I wrote that you will be asked to connect to your Mendeley account.

Messages de Rogue Scholar

Aggregating annotations on the scientific literature: a hack for ReCon 16

I wrote that: asserting authorship using the Mendeley API