Science and Web 2.0

Science and Web 2.0 Ian Mulvany, Nature Publishing Group Hi I hope that the the take home message from this short talk will be that web technologies could have an important role for science, that they are in their very early days at the moment, and that over the next few years the outlook is good I’m going to tell you a little bit about myself, about what Web 2.0 is, and why Nature is interested in these approaches After that little overview I''m going to to run you through a short demo of some of the things we have been developing at Nature for scientists My name is Ian Mulvany, and I’m a product development manager with the Web Publishing Group at Nature

Science and Web 2.0

Ian Mulvany, Nature Publishing Group

After that little overview I'm going to to run you through a short demo of some of the things we

have been developing at Nature for scientists

If you want to keep up with what our group is doing we have a public blog at http://

blogs.nature.com/wp/nascent/

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What is Web 2.0?

Historically the term was first used as the name of an O'Reilly Conference held in 2004 that

discussed the post

dot com bubble reemergence of internet business

What has this got to do with science?

We will see that the defining methods that new tech companies use may be applied to issues of

concern to scientists

At the heart of the Web 2.0 approach is getting and using data, so for a scientist it should make perfect sense

Web 2.0 Google AdSense Flickr

BitTorrent Napster Wikipedia blogging upcoming.org and EVDB search engine optimization cost per click

web services participation wikis

tagging (folksonomy) syndication

domain name

publishing CMS

stickiness

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The meme of Web 2.0 was influenced by comparing pre dot com bubble companies and post

dot com bubble companies

What is the difference between the list on the left and the list on the right?

Let’s take the example of Brtiannica vs Wikipedia

The information in Britannica is centrally controlled It has a relatively small number of contributors.The workload per contributor is high

Wikipedia is open to anyone to contribute A collaboration of 1000’s can lead to a work of equal quality to

a more centrally controlled method

Britannica’s revenues decreased from 650M to 50M over a 10 year period!

The new sites make it easy to add information and use that information to

answer or solve problems for people

easy easy

semantic web MicroFormats plain text, emails

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Let’s look at formats for data in the space of how easy it is to create,

and how how easy is it to mine for interesting information

Plain text is the easiest to create, but is very hard to do data-mining on

Text that has been rigorously annotated (semantic-web stuff) is very easy to do data-mining on, but it is hard to get people to make this sort of data in the day to day activity of their lives

(One of the things that helped wikipeida be success was a tool that enabled people to easily add articles that got converted into nice looking web pages)

Unfortunately academic papers are really hard to write, and usually are only available in pdf, the worst of both worlds

Hyperlinks, page views, tags, and possibly academic citations, are easy to create

and are easy to do data-mining on I’ll show you how some people have used these to build

cornerstones

of the web today

Google created their search engine by looking at hyperlinks

If lot’s of pages linked to one particular page then that page is probably important

(the big red ball here)

If that page has a link, that link is important (link from the red ball to the orange ball)

This is a mirror of the academic citation system Sergi Brinn and Larry Page were PhD students at Stanford

when they founded Google

You can see a conference paper that they wrote about their search engine here:

http://infolab.stanford.edu/~backrub/google.html

Amazon use page views and a database of user purchases to find things you might like.

Again, here they are using data that they get for free from people using their site

a buying recommendation (searching for news is very different.)

Google Ad Sense is different

Putting ads on a web page does need almost real time information Where has the person looking atthis page been, where are they physically located? How much time have they spent looking at

different things?

The more accurate your matching based on behavior, the more money you are going to make

We have seen how mining user provided data can help to solve problems about information

on the Internet

Are there any problems in Science that could help with these kinds of approaches?

I think there are lots, and I think they break down into a few different categories Let’s have a look

at a few here

- information management for the individual scientist

- communicating with the public

- mining data

On this slide we have our researcher scanning his favorite journal

How do we get the reader back in control?

Aside from journals, there are also lots of other places that the scientific conversation has

moved to

Discussion Groups and Mailing lists contain a huge amount of information from

from snippets of computer code, to long discussions about topics

Mark Mail, from MarkLogic, have a site that mines this information Here we see

a comparison of a search for FORTRAN vs a search for Java

At the moment these kinds of archives are mainly relevant in the computer science area, but

these kinds of conversations are going on all the time in every field

http://markmail.org/

Science blogs represent another medium where science discussions are happening.

The Faulkes telescope does the same with an astronomical telescope.

There are some solutions to these problems that are out there

The Chemical Blogspace, run by Egon Willighagen from Wageningen University, automatically

collects articles from blogs about chemistry and looks for the most popular articles

http://cb.openmolecules.net/

Jean-Claude Bradley from Drexel university does open notebook science.

You can see the data and lab notes for each experiment as it is done is his group through

their blog http://usefulchem.blogspot.com/

A part of his motivation is that all of the data is never gets through to a published paper

can also be very valuable for the community

In arguments about precedence where there is an existent trial of discovery getting

scooped is going to be harder

There do exist senantic-web approaches to science The Crystal Eye project from the University of Cambridge is trying to automate the recognition of crystallographic data in academic papers

Open

Semantic Web

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Though not exactly the same, web 2.0, Open science and the semantic web work well together

and they share some common traits, namely sharing and openness of information

This is leading to a brave new world in the space of scientific conversations

So why are nature involved in these kinds of non-journal initiatives, and what are the initiatives that

we are involved with?

• "It is intended, first, to place before

the general public the grand results

of scientific work and scientific discovery"

• "to aid scientific men by affording

them an opportunity of discussing the various scientific questions that arise from time to time"

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This is Norman Lockyer, the first editor of Nature, and these are snippets or our mission statement

One and one way of looking at the whole issue is that journal publication is only one aspect of

communication in science

As we have seen there are a lot of new channels for communication, apart from journals

and if Nature wants to remain relevant then we have to engage with these new emerging

conversation

We have a group in Nature, web publishing, whose goal is to be experimental and try to both keep

up to date with what is going on out there in terms of new developments, as well as trying to create new tools for researchers

Nature Web Publishing

Nature Network is a place for hosting discussions and forums about science related topics.

Second Life Nature

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- lectures in second life

As my colleague Jo who works on second life likes to say, SL is a platform that offers a lot

of potential, however not many people know what the best way to use it is We have been hosting

a

couple of scientific projects there,

UCL CENTRE FOR ADVANCED SPATIAL ANALYSIS

Drexel Chemical Reactions

and I'll be happy to answer questions about these later, but

But so far the most successful thing we have done is use it as a location for hosting talks for the general public

Scintilla is like the Chemical Blogspace in that it aggregates content from over 700 science relatedblogs.

You can tag, share and rate stories that you like on this site

Precedings is a preprint server for the life sciences

If you have a presentation or a poster that you have presented that will not be submitted later

to a journal you could place it here for people to access When an item is uploaded to precedings it receives a digital object identifier (DOI) which can be used to cite the material later

Connotea is the tool that I am responsible for It is a citation and bookmark management service

The best thing to do is to probably just create an account and start using the site, if you are

interested

in finding out how it works and play with it a bit, it's pretty easy to use, and I'll give you a quick demo of how it works

Social bookmarking sites are often write only -> By making collections public and tagged you

provide a resource -> For example I read what my boss is tagging

This is kind of an orthogonal use case for these kinds of services, even before we add in more

complex algorithms

for example I'll show you later a tool that joins folksonomies with ontologies, (entity decsriber)

In a social environment you create a collection that might represent your interest, by adding some intelligence to the back end we hope that we can aid the presence of serendipity by

highlighting related things like related tags, users, and related content

It might also provide a means to keep track of the scientific conversation around a topic, outside of just the

citations in the literature, for example by tying blog comments to doi's of papers

The Chemical Blogspace can read tags in connotea for items that have a specific chemical tag This way we can begin to automate the aggregation of social information around scientific pieces of

information

Mirko Gontek at the university of Colonge

information visualisation of links in connotea

These social links can create networks of information on top of the basic information.

This is what we want to use to start building collaborative intelligence into these systems.

Text Text Text Graph Analysis?

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This is the graph of items for one user in connotea

There are also other tools out there that are doing the same kind of thing, but I’m partial.

A frequent complaint that I get is that people have no time to investigate new ways of working,

however if you look at how you manage your information now a small investment in, for example, posting your talks to a community site, or having all of your bookmarks in one location, could begin

to make a difference

Thank you!