Cameron Neylon

So [Ian Mulvaney
asked](http://friendfeed.com/e/843063fc-1a40-e206-e18b-3178f1577d18/we-are-having-a-serious-think-about-Connotea-What/),
and as my solution [did not fit into the
margin](http://friendfeed.com/e/843063fc-1a40-e206-e18b-3178f1577d18/we-are-having-a-serious-think-about-Connotea-What/)
I thought I would post here. Following on from the
[two](http://cameronneylon.net/blog/facebooks-for-scientists-theyre-breeding-like-rabbits/)
[rants](http://cameronneylon.net/blog/an-open-letter-to-the-developers-of-social-network-and-%E2%80%98web-20%E2%80%99-tools-for-scientists/)
of a few weeks back and many discussions at Scifoo I have been thinking
about how scientists might be persuaded to make more use of social web
based tools. What does it take to get enough people involved so that the
network effects become apparent. I had a discussion with [Jamie
Heywood](http://en.wikipedia.org/wiki/James_Heywood) of [Patients Like
Me](http://www.patientslikeme.com/) at Scifoo because I was interested
as to why people with chronic diseases were willing to share detailed
and very personal information in a forum that is essentially public. His
response was that these people had an ongoing and extremely pressing
need to optimise *as far as is possible* their treatment regime and
lifestyle and that by correlating their experiences with others they got
to the required answers quicker. Essentially successful management of
their life required rapid access to high quality information sliced and
diced in a way that made sense to them and was presented in as efficient
and timely a manner as possible. Which obviously left me none the wiser
as to why scientists don't get it....

Nonetheless there are some clear themes that emerge from that
conversation and others looking at uptake and use of web based tools. So
here are my 5 thoughts. These are framed around the idea of reference
management but the principles I think are sufficiently general to apply
to most web services.

1.  Any tool must fit within my existing workflows. Once adopted I may
    be persuaded to modify or improve my workflow but to be adopted it
    has to fit to start with. For citation management this means that it
    must have one click filing (ideally from any place I might find an
    interesting paper)Â  but will also monitor other means of marking
    papers by e.g. shared items from Google reader, 'liked' items on
    Friendfeed, or scraping tags in del.icio.us.
2.  Any new tool must clearly outperform all the existing tools that it
    will replace in the relevant workflows *without the requirement for
    network or social effects*. Its got to be absolutely clear on first
    use that I am going to want to use this instead of e.g. Endnote.
    That means I absolutely have to be able to format and manage
    references in a word processor or publication document. Technically
    a nightmare I am sure (you've got to worry about integration with
    Word, Open Office, GoogleDocs, Tex) but an absolute necessity to get
    widespread uptake. And this has to be absolutely clear the first
    time I use the system, before I have created any local social
    network and before you have a large enough user base for theseto be
    effective.
3.  It must be near 100% reliable with near 100% uptime. Web services
    have a bad reputation for going down. People don't trust their
    network connection and are much happier with local applications
    still. Don't give them an excuse to go back to a local app because
    the service goes down. Addendum -- make sure people can easily
    backup and download their stuff in a form that will be useful even
    if your service dissappears. Obviously they'll never need to but it
    will make them feel better (and don't scrimp on this because they
    will check if it works).
4.  Provide at least one (but not too many) really exciting new feature
    that makes people's life better. This is related to \#2 but is
    taking it a step further. Beyond just doing what I already do better
    I need a quick fix of something new and exciting. My wishlist for
    Connotea is below.
5.  Prepopulate. Build in publically available information before the
    users arrive. For a publications database this is easy and this is
    something that [BioMedExperts](http://www.biomedexperts.com/) got
    right. You have a pre-existing social network and pre-existing
    library information. Populate 'ghost' accounts with a library that
    includes people's papers (doesn't matter if its not 100% accurate)
    and connections based on co-authorships. This will give people an
    idea of what the social aspect can bring and encourage them to bring
    more people on board.

So that is so much motherhood and applepie. And nothing that Ian didn't
already know (unlike some other developers who I shan't mention). But
what about those cool features? Again I would take a back to basics
approach. What do I actually want?

Well what I want is a service that will do three quite different things.
I want it to hold a library of relevant references in a way I can search
and use and I want to use this to format and reference documents when I
write them. I want it to help me manage the day to day process of
dealing with the flood of literature that is coming in (real time
search). And I want it to help me be more effective when I am
researching a new area or trying to get to grips with something (offline
search). Real time search I think is a big problem that isn't going to
be solved soon. The library and document writing aspects I think are a
given and need to be the first priority. The third problem is the one
that I think is amenable to some new thinking.

What I would really like to see here is a way of pivoting my view of the
literature around a specific item. This might be a paper, a dataset, or
a blog post. I want to be able to click once and see everything that
item cites, click again and see everything that cites it. Pivot away
from that to look at what GoPubmed thinks the paper is about and see
what it has which is related and then pivot back and see how many of
those two sets are common. What are the papers in this area that this
review isn't citing? Is there a set of *authors* this paper isn't
citing? Have they looked at all the datasets that they should have? Are
there general news media items in this area, books on Amazon, books in
my nearest library, books on *my* bookshelf? Are they any good? Have any
of my trusted friends published or bookmarked items in this area? Do
they use the same tags or different ones for this subject? What exactly
is Neil Saunders doing looking at that gene? Can I map all of my friends
tags onto a controlled vocabulary?

Essentially I am asking for is to be able to traverse the graph of how
all these things are interconnected. Most of these connections are
already explicit somewhere but nowhere are they all brought together in
a way that the user can slice and dice them the way they want. My belief
is that if you can start to understand how people use that graph
effectively to find what they want then you can start to automate the
process and that that will be the route towards real time search that
actually works.

...but you'll struggle with uptake...


So Ian Mulvaney asked, and as my solution did not fit into the margin I thought I would post here. Following on from the two rants of a few weeks back and many discussions at Scifoo I have been thinking about how scientists might be persuaded to make more use of social web based tools. What does it take to get enough people involved so that the network effects become apparent.

How to make Connotea a killer app for scientists

University of Glasgow

Roderic Page

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdjDllhFg2sHxQEkIcDa-rbOUyXvNiltoMziDuBtrVJx1nDV3oDrypR0fXEED24CAckOEemlwibzpELI1AuttmX4CcX5S37Ju6MjaryC-cVVIWZsNEQyjrth-1oDblc7nNV8bD/s200/especies.png){#BLOGGER_PHOTO_ID_5219089762074145122
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdjDllhFg2sHxQEkIcDa-rbOUyXvNiltoMziDuBtrVJx1nDV3oDrypR0fXEED24CAckOEemlwibzpELI1AuttmX4CcX5S37Ju6MjaryC-cVVIWZsNEQyjrth-1oDblc7nNV8bD/s1600-h/especies.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Mauro Cavalcanti has released [e-Species](http://especies.infobio.net/),
\"a taxonomically intelligent biodiversity search engine\" written in
Python that mimics much of the functionality of
[iSpecies](http://ispecies.org). The project is open source, with a
[SourceForge page](http://sourceforge.net/projects/e-species/), although
no files seem to be available yet. This is the second iSpecies clone
I\'ve seen, David Shorthouse having [written a clone that uses only
JSON](http://www.canadianarachnology.org/iSpecies/).  
  
One thing which distinguishes e-Species is the use of [Catalogue of Life
web services](http://webservice.catalogueoflife.org/) to provide some
information on the name. However, it doesn\'t look like e-Species makes
use of synonyms in its searches (i.e., what many refer to as \"taxonomic
intelligence\"). Searching on two alternative names for the sperm whale
(*Physeter catodon* and *P. macrocephalus*) yields different results
(unless the underlying source knows that these names are synonyms, such
as NCBI). Presumably, a taxonomically intelligent search would be able
to merge results from searches using different names, and present those
together.  
  
Merging results requires some thought as to how to merge lists from
different sources (e.g., merging lists of publications and images). This
has been the subject of much study in the context of merging results
from different search engines. Some starting points are:  

- [Rank Aggregation Methods for the
  Web](http://www10.org/cdrom/papers/577/)
- [Aggregation of partial rankings, p-ratings and top-m
  lists](http://portal.acm.org/citation.cfm?id=1283383.1283427&coll=ACM&dl=ACM&type=series&idx=SERIES422&part=series&WantType=Proceedings&title=SODA#abstract)
- [Tadpole: A Meta search
  engine](http://www.stanford.edu/class/archive/cs/cs276a/cs276a.1032/projects/reports/mmahathi-pavan.doc)

  
The last link is a student project and is a Microsoft Word document,
which I\'ve uploaded to Scribd and embedded below.  

::: {style="font-size:10px;text-align:center;width:450"}
[Tadpole: A Meta search
engine](http://www.scribd.com/doc/3816396/Tadpole-A-Meta-search-engine) -
[Upload a Document to Scribd](http://www.scribd.com/upload)
:::

::: {style="display:none"}
Read this document on Scribd: [Tadpole: A Meta search
engine](http://www.scribd.com/doc/3816396/Tadpole-A-Meta-search-engine)
:::


Mauro Cavalcanti has released e-Species, "a taxonomically intelligent biodiversity search engine" written in Python that mimics much of the functionality of iSpecies. The project is open source, with a SourceForge page, although no files seem to be available yet. This is the second iSpecies clone I've seen, David Shorthouse having written a clone that uses only JSON.

Messaggi di Rogue Scholar

How to make Connotea a killer app for scientists

iSpecies clones, and taxonomic intelligence