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Show & Tell from the Open & Citizen Science OKCon Hackathon

- September 19, 2013 in events, Hackday, OKCon

Most hackdays end with “Show and Tell” — each project giving a demo or a report on their progress. Today’s Open Science and Citizen Science Hackathon, anchored in Geneva on the heels of OK Con, included remote participants in France, Germany, the Netherlands and the US, and possibly other places. This did complicate Show and Tell.

The Open Science WikiSprint group in Geneva, photo by

part of the WikiSprint group in Geneva

We will use this post, however to recap the day! Fearless hackathon leaders Stefan Kasberger and Rayna Stamboliyska had previously solicited project proposals and votes on favourites, with which they announced what projects would likely be attempted on the day.

Hackdays don’t always go to plan and that’s intentional, people are welcome to start something unexpected. One unintended, good result of mashing up great people and great ideas was the metabolomics scientist who met Daniel Lombraña-González and got into crowdsourcing, citizen science with CrowdCrafting, run on OKF’s PyBossa.

A particularly active and international group held a WikiSprint to improve Open Science related content at the P2P Foundation and on Wikipedia as detailed in those links. You can still contribute! and please do. Pictured above are some of the participants in Geneva, with the photo taken by project leader, Célya Gruson-Daniel @celyagd. Activities were organized with this Etherpad, where you can find more on who got up to what in the WikiSprint.

@MaliciaRogue!

@MaliciaRogue!

At about the halfway mark, Rayna @MaliciaRogue dropped a few summary tweets:

The Open & Citizen Science workshop is going very nicely: we have an #OpenScienceManifesto coming, an #OpenScienceWiki sprint, (cont) #OKCon

>>> We also have more hardcore statistical stuff going on w friends from OKF Finland organizing R packages for #OpenGov data analysis #OKCon

Last but not least, we have metabolomics scientists interested to involve citizens with #Crowdcrafting cc @teleyinex #OpenScience #OKCon

We will report more soon!

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OKCon Open & Citizen Science hackday: projects

- September 14, 2013 in Announcements, events, Hackday, Members, OKCon, Tools

Join us geeking out Thursday, Sept 19, 10:00 to 17:00 CEST at #OKCon and online! Details are below. See also our announcement of this event and everyone’s votes for favourite projects.

For WikiSprint: Global overview of Open Science initiatives please join us remotely via the coordinating Etherpad (found: https://etherpad.mozilla.org/xpQvKfNv5c) and working either here or on Wikipedia.

For other projects, join us in IRC: #openscience on freenode or via the web at http://webchat.freenode.net/?channels=openscience. Find us on Twitter @MaliciaRogue, @stefankasberger, @openscience, and at #openscience or #OKCon.

okcon_science

Proposal 1

Title: “Open Data in Research: an illusion?”

Details: Despite the dazzling development of the open access movement, open data initiatives in science and research are still trailing in involvement. Additionally, disparities in research data sharing and openness are huge across scientific communities and domains.

Last but not least, formats and licensing terms greatly vary even within specific field. This suggested activity will wrap-up current initiatives and achievements prior to formalizing the challenges ahead. The middle-term goal is to bootstrap connections converging to a true institutional change that leads to more participative, shareable and transparent science: the science of tomorrow.

Support: Open Data enthusiasts, geeks and science nerds welcome.

Comment: Remote participation welcome (IRC, pad). Hashtag: #OpenSciData

Proposal 2

Title: “An inclusive approach to open science”

Details: The discourse in open science often runs along the lines of open vs. closed approaches. In reality though, most researchers act in-between those two extremes. From successful examples such as genomics, we can see that open science is essentially a community effort (cp. Bermuda Principles). Therefore, we (the Austrian chapter of the OKFN) advocate an inclusive approach to open science.

From a community perspective, it is the commitment to openness that matters, and the willingness to promote this openness on editorial boards and program committees. It is therefore important to get as many researchers on board as possible. This approach is _not_ intended to replace existing initiatives but to make researchers aware of these initiatives and helping them with choosing their approach to open science.

The idea of this hackathon is to create a manifesto/declaration for such an inclusive approach. A draft and a first discussion can be found here: http://science20.wordpress.com/2013/06/25/an-inclusive-approach-to-open-science/
We invite contributions from researchers in various disciplines on their experiences with advocating and implementing open science practices. This could be in the form of presentations, lightning talks, or focused discussions.

Support: We mainly need creative minds; designers, illustrators, and animators are welcome as we could produce a short video about the idea.

Comment: N/A

Proposal 3

Title: “Wikisprint: Global overview of OpenScience initiatives”

Details: A few months ago an event was organised to agregate links and knowledge about P2P initiatives. http://codigoabiertocc.wordpress.com/2013/08/07/globalp2p-the-wind-that-shook-the-net/
In partnership with Michel Bauwens of the P2P Foundation and HackYourPhd I’d like to organize a similar event for OpenScience initiative. The P2P Foundation aims to promote and document peer to peer practices in a very broad sense. The collective HackYourPhd federate numerous students, researchers and citizens interested in the production and the sharing of knowledge. Being an administrator on the French Wikipedia, I will likely get support from the Wikimedia communities.

This “wikisprint” will be set up as follow:

  1. The idea will be to announce the event a few days ago and invite people on twitter and other plateform to share their initiative with us.
  2. We could for exemple use the hashtag #OpenScienceWiki
  3. During the hackathon People in Geneva but also elsewhere could help to agregate the links in a wiki, interact with people all around the world and invite them to share their initiatives.
    We can use the P2Pwiki: http://p2pfoundation.net/Spanish_P2P_WikiSprint
    We could also map this OpenSciene initiative in a map http://maps.ubimix.com/hyphdus/
  4. We could also visualize all the interaction with the hashtag
    Here is an example of what people have done during the #GlobalP2P event: http://demos.outliers.es/wikiSprint/
  5. Once the broad mapping is done on the P2Pwiki, it could serve to enhance several Wikipedia articles on Open Science. The content is currently rather poor: see for instance http://en.wikipedia.org/wiki/Open_knowledge and to a lesser extent http://en.wikipedia.org/wiki/Open_Science. Wikidata — the growing open data repository of the Wikimedia Foundation — could also use some contributions to the topic https://www.wikidata.org/wiki/Q2251455 and https://www.wikidata.org/wiki/Q309823 are empty.
  6. Illustrations and dataviz might also be welcome: for instance, graphics of academic publishing economics (figures are rather hard to get).

Support: Designer and programmer are welcome for the visualisation

Comment: Here are some guidelines given by Michel Bauwens to help us organize this workshop.

  • it’s important to give some basic how to advice at the beginning of the process
  • in each locale, it’s good to have a person that can just wander around and help and stimulate the other people (this makes a big difference)
  • we had a permanent rolling hangout, with every hour a different topic to be discussed (it went on for 15 hours or so during the hispanic wikisprint)
  • it makes it much more easy if there is a pre-established form, with the tickable tags etc.
  • clear delimitation of subject matter, not anything goes , make sure you specify what open science is inclusive of, perhaps some geographic limitation (say Europe) etc..
  • choice of tags: one for the event itself, say [[Category:OpenScience Wikisprint]]; one for the topic, so that it continues to live on after the event, say [[Category:Open Science]]
    this can be combined for example with country tags, [[Category:France]] etc.
    (the p2pfoundation.net wiki already has http://p2pfoundation.net/Category:Science for the broader p2p/commons aspects of science, this would allow a more specialized focus)
    I will be also present during this workshop to help the interaction with Wikipedia and the wikipedia community.
  • Including Wikipedia within the wikisprint could stimulate global contribution by attracting experienced wiki user. We can create a parallel contribution project (an example: http://en.wikipedia.org/wiki/Wikipedia:GLAM/MonmouthpediA )

Proposal 4

Title: “rOpenGov – R ecosystem for social and political science”

Details: With the avalanche of open government data and other fields relevant to computational social science, new algorithms are needed to take full advantage of these new information resources – to access, analyse and communicate such information in a fully transparent and reproducible manner as part of scientific inquiry or citizen science projects.

A scalable solution will require coordinated effort from independent developers. Hence, we are now building up a community-driven ecosystem of R packages dedicated to open government data and computational social and political science, building on lessons learned from analogous and wildly successful projects in other fields. The site already provides open source R tools for open government data analytics for Austria, Finland, and Russia and we are now actively collecting further contributions.

The preliminary project website is at: http://louhos.github.io/en/ropengov.html

Support: In addition to internet access, the project would benefit from contributions from website designers, scientists and R package developers.

Comment: Distant participation to the hackathon through IRC/Skype is also possible.

Proposal 5

Title: “Crowdcrafting Everywhere”

Details: Crowdcrafting is a straightforward, open source handy tool for citizen science. Unfortunately, Crowdcrafting solely speaks English for now. What about translating it into other languages, e.g. French, Spanish, Russian,…?

Support: Multilingual enthusiasts welcome!

Comment: Remote participation welcome.

Hashtag: #CCEverywhere.

Crowdcrafting’s lead developer, Daniel Lombrana-Gonzalez, will also be with us throughout the whole day.

Proposal 6

Title: Open Access Button

Details: Open Access Button is a browser-based tool which tracks every time someone is denied access to a paper. We want to display this, along with the person’s location, profession and story on a real time, worldwide, interactive map of the problem. While creating pressure to open up scholarly and scientific research, we also want to help people work within the current broken system by helping them get access to the paper they need.

That’s the project summed up really briefly. We built a prototype at the start of the summer and are working towards a launch of later in the year.

Support: tbc

Comment: Waiting for confirmation for founders to join in person. Remote participation will be confirmed soon.

Proposal 7

Title: “Booksprint: OpenScience Guidelines for PhD Students and researchers”

Description: Organize a book sprint to write a guide about how to do open science for researchers or PhD students.

No special skills are needed to participate, if you are a PhD student or a students or know the basic of science from another area. We will share our ideas and experience with open science.

Possible chapters:
* What does it mean to publish in open access?
* How do you go about publishing in open access?
* What is an “Open notebook”?
* How do I organize an open notebook?
* Which other tools are available?
* What tools are missing?
* How do we communicate and better support each other?
etc.

To write the book, we will use Fidus Writer ( http://fiduswriter.org ), an open source, webbased editor that typesets academic writing with citations and formulas, and lets us publish PDFs or ebooks of articles and/or journals without any technical skills. The Fidus Writer team will assist via hangout/chat.

Support: Some designers are welcome to help for figures, and other visualisations.
Internet access has to be available and Google Chrome or Chromium installed on the machines.
Artististic minds are also welcome 🙂

Comment: I think it would be a good idea to find a printing solution as well, because to have something in your hands, can be very engaging and it would be great for hackyourpdh to have something to show around. But this could be done afterwards.

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Open and Citizen Science in the heart of Europe – 19 Sep, Geneva

- September 1, 2013 in Announcements, events, Hackday, OKCon

okcon_science

Open and Citizen Science in the heart of Europe – Workshop

Thursday 19 September, 10:00 – 17:00 @ Centre Universitaire d’Informatique Université de Genève, Auditorium, Ground Floor

Coordinators: Stefan Kasberger (Open Knowledge Foundation Austria) and Rayna Stamboliyska (Open Knowledge Foundation France), in collaboration with François Grey (Citizen Cyberscience Center / University of Geneva), Margaret Gold/ Brian Fuchs (Citizen Cyberscience Center / The Mobile Collective)

 

Hacking science makes us happy. If it makes you happy, too, then, this year’s Open Knowledge Conference is the place to be!

Indeed, OKCon 2013 is where an amazing bouquet of insights from Open and Citizen science will converge. But if you thought there would be only food for the brain, you were wrong. A satellite event will take place on 19 September aiming at giving space for everyone to actually get great things done.

With our friends François Grey (Citizen Cyberscience Center/University of Geneva), Margaret Gold and Brian Fuchs (Citizen Cyberscience Center/The Mobile Collective), we have come up with a way allowing everyone to take part to this exciting day.

I have an idea!

We know you do. Hence, we have a dedicated form ready for you to submit a short description of what you are keen to work on. You can also indicate what additional competences you need in order to get your project done.

Idea submission will be running from today until 10 September. Every week, we will be updating everyone (through the Open Science mailing list) telling you about the new ideas submitted. In addition, a community call will be scheduled to discuss and narrow down these ideas so that they actually become feasible within one-day long hands-on sprint.

Working together

The idea of the satellite event is to geek out together. On 11 September, we will be publishing a poll with all ideas so that you can be able to vote for the project you want to work on on Day D. Voting will run until 18 September.

Do not forget to bring your favourite geeking gear (laptop, some flavour of mobile device or a fancy notebook in the perfect 1.0 fashion). We will have WiFi, cookies and fun!

 

The workshop space can accommodate up to 45 people.
To sign-up, express your interest in the topic and get in touch with the coordinators please write to openandcitizenscience@okcon.org.

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Open Access Button Hackday, 7-8 Sep, London, UK

- September 1, 2013 in External Meetings, Guest Post, Hackday, Tools

This is a guest post from Joe and David from the Open Access Button project.

oabutton2608

Millions of people a day are denied access to the research they both need and paid for because of paywalls. It doesn’t have to be like this, but we need your help. We’re two students from the UK making a tool to help change the system – it’s called the Open Access Button. The button is a browser-based tool which tracks every time someone is denied access to a paper. We then display this, along with the person’s location, profession and story on a real time, worldwide, interactive map of the problem.

It gets better though. While creating pressure to open up scholarly and scientific research, we help people work within the current broken system by helping them get access to the paper they need. We started building a prototype at the BMJ Hack Weekend, and came third place. But we’re not finished yet and our launch is coming up fast! To help build it we’re hosting a hackathon on the 7-8th of September in London. If you’re a developer, have an eye for design or both we’d love to see you. Not in the UK? Doesn’t matter! you can join in from anywhere in the world – just sign up below.

If you want any more information about the project- email us oabutton@gmail.com or read more here.

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Citizen Science Hack Day at Medialab-Prado, Madrid

- May 3, 2013 in events, External Meetings, Hackday

Come and join other citizen scientists, humanities folks, technologists, designers, students, scientists, and all who are curious for a two days of Crowdcrafting Citizen Science at Medialab-Prado, Madrid, Spain. We’ll be hacking together apps and projects with various open tools such as Epicollect, PyBossa and/or BOINC.

Registration required.

 

The goal of the hackfest is to show the benefits that Citizen Science gives to citizens as well as professional scientists thanks to the new technologies. At the hackfest you will be able to learn about the tools used in volunteer sensing: data acquisition thanks to smartphones and gadgets for scientific projects, volunteer thinking: problem solving thanks to volunteers that collaborate in scientific projects using the web browser, and volunteer computing: where the volunteer donates his/her computer resources, (CPU idle cycles) to different projects.

foto ciencia ciudadana

Image by Daniel Lombraña (CC BY-SA 2.0)

 

How it works?

  1. The first day, Friday 17, we will start with some short talks (around 10 minutes each) about different Citizen Science Projects and/or the technologies used in these projects.
  2. The second day, Saturday 18, you will be the main protagonists: the participants. In this second day we would like that you propose new projects or ideas around citizen science project that could be developed along the day (basically a prototype). You will have 5 minutes to engage the rest of the participants!
  3. We’ll invite you to ‘team-up’ around the ideas you’d like to help make happen, but feel free to ‘vote with your feet’ and join other teams at any stage of the day.
  4. At the end we’ll do a show and tell to see what folks came up with.

We will provide support for any teams who’d like to continue working on their projects or apps beyond the event!

What do I need to participate?

In principle you will only need a laptop, but feel free to bring any hardware, gadget, device that you think it is relevant for the hackfest and that could help in a citizen science project. For example, bring your own mobile phone (we will try EpiCollect in Android) as we will show how you can help in the acquisition of data, or an Arduino device that you have created, etc. In other words: bring any device that you think it will be useful for a citizen science project.

But if I’m not a scientist or a developer, how can I help?

You are more than welcome! Actually your participation is really important. Why? Because this workshop is about Citizen Science, so we want your participation in the event and the projects. How? Well, it is easy, giving us feedback, ideas, suggestions about the projects and tools that we are presenting. Maybe you know different languages, so you can help translating a project, or maybe you are a designer so you could work with the scientists creating a really nice logo for the project. As you can see, you can help a lot!

What is Citizen Science

Citizen Science is scientific research conducted, in whole or in part, by amateur or nonprofessional scientists, often by crowdsourcing data collection, problem solving & thinking. Formally, citizen science has been defined as “the systematic collection and analysis of data; development of technology; testing of natural phenomena; and the dissemination of these activities by researchers on a primarily avocational basis”. Citizen science is sometimes called “public participation in scientific research.”

Citizen Cyberscience leverages digital tools, mobile technologies and the web to involve citizen around the globe in the ‘formulating’ and ‘doing’ of Science.

Crowdcrafting tools provide online assistance in performing tasks that require human cognition, knowledge or intelligence such as image classification, transcription, geocoding and more.

Open Science means many things, but primarily scientific knowledge that people are free to use, re-use and distribute without legal, technological or social restrictions.

Organizers

Medialab-Prado

Ibercivis

The Citizen Cyberscience Centre

The OKF Open Science Group

Citizen Cyberlab

Socientize
Sponsors

Sloan Foundation

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Crowdsourcing Success: Science Hack Day London

- March 17, 2013 in events, Hackday

Yesterday was our Science Hack Day London event.

I think it’s safe to say it was a roaring success and we’ll likely be having more this year.

We had Daniel Lombraña González jet in from Spain to help us with PyBossa / Crowdcrafting projects and got a working demo of a sound classification app using SoundCloud by the end of the day

ZIzQ
An excellent demo of the potential of Konekta geolocation and polygon drawing
2013-03-17-171304_1029x867_scrot
Lots of brainstorming with the new WAXscience project from France (Aude Bernheim @AudeBer & Flora Vincent @vincentflora). WAXscience aims to do something positive about gender imbalance in science. We talked a lot about potential methods of ‘sampling’ gender balance at scientific meetings & conferences – twitter mining, web mining, and even citizen science self-reporting with mobile apps.
WAXscience

 

There was even wonderful free food & drink provided especially for this hack!

food
 
For more details about the event see the Storify of tweets in full here.

We will let you know as and when we plan the next hack day
🙂

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Open Science Course Sprint: An Education Hackathon for Open Data Day

- February 11, 2013 in External Meetings, Guest Post, Hackday

A blog entry by Billy Meinke cross-posted from the Creative Commons blog.

An Education Sprint

The future of Open is a dynamic landscape, ripe with opportunities to increase civic engagement, literacy, and innovation. Towards this goal, the Science Program at Creative Commons is teaming up with the Open Knowledge Foundation and members of the Open Science Community to facilitate the building of an open online course, an Introduction to Open Science. The actual build will take place during a hackathon-style “sprint” event on Open Data Day on Saturday, February 23rd and will serve as a launch course for the School of Open during Open Education Week (Mar 11-15).

Screen-shot-2013-02-10-at-3.56.45-PM1

Want to help us build this?

The course will be open in it’s entirety, the building process and content all available to be worked on, all to help people learn about Open Science. Do you know a thing or two about Open Access? Are you a researcher who’s practicing Open Research? Do you have experience in instructional or visual design? This is an all-hands event and will be facilitated by representatives at CC, OKFN, and others in the Community. Open Science enthusiasts in the Bay Area are invited to the CC Headquarters in Mountain View for the live event. Remote participants will also be able to join and contribute online via Google Hangout.

The day will begin with coffee, refreshments and a check-in call with other Open Data Day Hackathons happening around the globe. The Open Science Community is strengthened by shared interests and connections between people, which we hope will grow stronger through networked events on Open Data Day. The Open Science course sprint at CC HQ will build upon open educational content, facilitate the design of challenges for exploration, and provide easy entry for learners into concepts of Open Access, Open Research, and Open Data. It will be done in a similar fashion to other “sprint-style” content-creation events, with lunch and refreshments provided for in-person participants. We’re literally going to be hacking on education. Sound like something you’d be interested in?

Join us.

For details about the ways you can participate, see the Eventbrite page here.
To see the draft (lightly framed) course site on Peer to Peer University, go here.
For information about other Open Data Day events, see the events wiki here.

Screen-shot-2013-02-10-at-4.17.35-PM-e1360547585923
Opendataday.org/map

Developers

We need you, too! Basic skills for working with open datasets is important, and can be difficult to grasp. Who better to develop great lessons about working with data than you? Similarly, for those interested in building upon apps and projects from other Open Data Events, updated source code and repository information will be posted to a public feed (for now, follow hashtags #ODHD13 and #opendataday on Twitter.

For other information, contact billy dot meinke at creative commons dot org or @billymeinke.

This event is being organized by the Science Program at Creative Commons with support from the Open Knowledge Foundation and members of the Open Science Community.

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#OKFest Open Science and Culture Hackday – Project 2 Louhos

- September 19, 2012 in Hackday, Meetings, OKFest, Tools

Louhos have generated a tool called Sorvi with the aim of making R based statistical computational tools and methods traditionally used by scientists available for people wrangling all sorts of data sets from government and finance to weather and more.

Sorvi combines these resources by providing a centralized collection of general-purpose open-source tools for data manipulation, analysis and and visualization. The project currently focuses on Finnish open data sets, but has far wider applications.

Members of the Louhos team hard at work.

The hackday project focused on formulating documentation that will be easy for newcomers and two use cases for a regular user and developer to illustrate the abilities of the tools.

The team made significant advances in completing and improving documentation during the day, if you’d like to explore, check out the Louhos homepage and have a go with the tools yourself!

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#OKFest Open Science and Culture Hackday – Project 1 pyBOSSA Feynman’s Flowers

- September 19, 2012 in Hackday, Meetings, OKFest, Tools

This morning saw the start of the world’s biggest ever open knowledge meeting and following an inspiring opening session 40 odd hackers descended on the OKFest MAKE space to collaborate on building apps and tools to open up scientific and cultural data sets. The open science crowd was about 15 strong and quickly settled on three projects to focus on throughout the day.

We had our friendly mascot Chuff to help us on the way, sporting his own conference badge:

Creating a pyBOSSA App: Feynman’s Flowers

Daniel Lombraña González and Quentin Mazars-Simon are leading development of Feynman’s Flowers, a pyBOSSA app to crowdsource measurement of how individual molecules stick to surfaces. Read on for more details!

Spintronics with Individual Molecules

Example of a single atom diagram (Helium atom)

Traditional electronic devices work by moving charge around a circuit. This has produced astounding results over the last half century, but we are now at a point where further reducing the size of circuit elements is difficult because it would create too much heat in too small a space.

Our research group is studying magnetic molecules to understand how they can be used to make the smallest possible “spintronic” devices, in which charge (electronic) and spin (magnetic) properties can be used together. In the future, this would allow us to make devices that can do more and also use less energy.

As a simple example, we may be able to use the magnetic orientation of one molecule (the direction in which its internal compass needle points) to store a single bit (0 or 1) of information: this would potentially increase the storage density on hard drives by 100x.

How You Can Help: Measure How Molecules Stick to Surfaces

Using a special kind of “microscope”, operating at close to absolute zero temperature and based on the quantum mechanical principle of tunneling, we can measure single molecules on surfaces.

Many of a molecule’s magnetic properties are determined by how it binds (sticks) to the surface. For example, a group in Japan found that the magnetic stability energy of a molecule could change by 50% just by a 15˚ rotation in its binding angle.

It is therefore crucial for us to measure the distribution of binding angles of a particular molecule on a given surface. This will allow us to compare our results with theoretical predictions to better understand their properties. That’s where you come in …

The App

Data on the centre of attached molecules and their angle must be determined by hand as there is no reliable algorithm. the Feynman’s Flowers app will allow users to determine the centre of the attached molecule and its angle allowing researchers to analyse the data digitally.

What Did We Do?

We’re nearly there! Daniel and Quentin have the app online and with a few tweaks it should be fully up and running within the next day!

You can have a go and also check out the code if you’re keen to see under the bonnet or adapt the code to your own needs.

[Atom diagram from Wikimedia Commons under CC-BY-SA 3.0. All other images under CC-BY]

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#OKFest Open Science and Culture Hackday – Project 3: Investigative Open Bibliography

- September 18, 2012 in Hackday, Meetings, OKFest, Tools

The third hackday project aims to explore the links between corporations and researchers for the areas of organic food, but more widely research into pharmaceuticals, cosmetics, food and other consumer products. By extracting author and funding data from the full text open access literature, funding links become clearer allowing visualisation which can be manipulated into patterns based on study outcomes to identify areas with particularly high positive result publication biases which may be influenced by commercial interests.

How to Do It?


Luckily the OKFN has several tools at its disposal to make this happen:

Our Open Biblio project has developed tools to extract full text literature (PubCrawler) and convert files into bibliographic metadata formats such as BibJSON whereby data can be easily manipulated and facet browsed (BibServer).
Therefore, we are extracting a subset of the open access BioMedCentral articles.

The next step will be to extract author information and affiliation (illustrated using Ahmet et al., 2011), which brings up a new problem of reconciling affiliations where no canonical list of institutions exists. Much discussion ensued about the possibility of using pyBOSSA and merging several publicly available lists of institutions from authoritative sources as a starting point.

We will also require funding data and competing interests sections from the articles, which can be mined using natural language processing tools to extract corporate names (possibly utilising Open Corporates) and references to other funders e.g. research councils and charities.

Once extracted this information would be entered into a database for faceted searching by funder, institution and author along with standard bibliographic metadata e.g. list all articles funded by GlaxoSmithKline and published in UK institutions in 2011.

What Can We Do With It?

This would lay the ground work for linking to other data sets and further elucidating patterns in corporate funding of research. For example, abstracts and key words could be used to browse by topic and a further pyBOSSA app could be generated to type the articles by a positive or negative result, or even graded e.g. relative risk of a new clinical treatment. This could be used to look at positive publishing bias in different areas of science and for work through different funders – which appear to be the worst affected areas? Which funders very rarely publish negative results?

Many studies on publication bias already exist in clinical trials but they are often limited to a few hundred articles e.g. Friedman and Richter, 2004, whereas the automated methodology described above could examine large portions of the literature. There are also different types of publication biases e.g. citation biases for positive articles which could possibly be investigated on a larger scale using these techniques than is currently possible, particularly involving Open Citation tools.

Incorporating geographic information on institutions and keyword analysis could reveal hot spots of research and other useful information for funders and research managers.

Hard at work hacking with the OKF Okapi

What Did We Do?

We completed liberating BMC articles by crawling the site and using parsers from BibTex to BibJSON. By the end of the week we expect to have 140k articles uploaded to BibServer including author, affiliations, abstracts and more.

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