Wikipedia as a basic scientific reference

Wikipedia is probably the most current, extensive, and accessible knowledge base available. Currently, there are over 10,000 Wikipedia entries for human genes of interest thanks to the Gene Wiki project and the contributions of the dedicated and altruistic Wikipedia community. Unfortunately, many of these articles are out-of-date or are just stubs in desperate need of content. If you are in science and truly believe in open access, why not contribute?

It may be a bit intimidating to edit a scientific Wikipedia article if you’ve never done it before, but it is actually quite easy! In the interest of encouraging wiki contributions from those in STEM disciplines, here’s a 10 step walk-thru for editing a Wikipedia entry:

1. Register/Login – No, it’s not necessary for you to do this step in order to edit a wiki, but you should just so you can be proud of all the wiki pages you improve in the future
2. Go to a wiki page in need of an update. Look up your favorite gene in wikipedia and help improve it!
3. Click on the ‘edit’ tab in the top, right corner of the page

4. Edit the content of the page. To add a section break, use double equal signs (eg- ==Section== )
5. To add a journal reference, click on ‘cite’ in the navigation bar, click on the ‘templates’ drop-down menu and select ‘cite journal’. Enter the PMID of the article into the ‘PMID’ field and click on the search (magnifying glass) icon to auto-populate the other fields.

6. If you plan on using this reference more than once, assign it a reference name so you can insert it again later.

7. Click ‘insert’ to insert the reference
8. When using a previously inserted/named reference again just use the ‘Named Reference’ (clipboard) icon.

9. Make a note about your changes in the ‘edit summary’ field, and then preview (optional) and save your edits.

10. If you make a mistake, you can easily revert the edits you made. Just go to the ‘view history’ tab. Find the changes you need to revert and click ‘undo’.

That’s it! What are you waiting for?

Need more editing tips? Check out the Gene Wiki portal and learn more ways to help improve Wikipedia as a knowledge base for human genes of interest.

Wikidata can change the way citizen scientists contribute

If you’ve been following discussions on citizen science, you’ve probably realized that researchers are generating so much data, that they need extensive help for parsing the data and making it more useful. For many projects, citizen scientists have answered the call for help–making enormous contributions. Sure, there was a recent study which found that “Most participants in citizen science projects give up almost immediately”, but as Caren Cooper pointed out:

It is the trying, rather than the quitting, that is newsworthy, #citizenscience; my post @plosblogs @naturalsciences http://t.co/lHca4POuSo

— Caren Cooper (@CoopSciScoop) January 12, 2015

Just by trying, citizen scientists made important contributions regardless of whether or not they chose to continue.

But I digress…

What does citizen science have to do with wikidata? On that matter, what the heck is wikidata?

Much of citizen science contributions come in some form of data collection (observations; sample collection; taking measurements, pictures, coordinates, etc) or classification (identification, data entry, etc) but few citizen scientists participate in analyzing the data.

From ‘Surveying the Citizen Science Landscape’ by Andrea Wiggins and Kevin Crowstone (click the figure to read the paper, it’s open access)

Wikidata (a linked, structured database for open data) may serve to change that. Naturally, wikidata relies on the contributions of volunteers; however, the data incorporated into wikidata is open for anyone to use. In fact, wikidata is begging to be used and citizen scientists and citizen data scientists are welcome to use it. An international group of has already put together a grant proposal (open/crowdsourced in the true spirit of wikipedia) to make wikidata an open virtual research environment. Dubbed, Wikidata for Research the proposal aims to establish “Wikidata as a central hub for linked open research data more generally, so that it can facilitate fruitful interactions at scale between professional research institutions and citizen science and knowledge initiatives.”

As exciting as this all is, there is a lot of work that still needs to be done for making wikidata more successful. Although it’s open access, it’s still a bit inaccessible due to the lack of clear documentation for new users. It’s not that the information doesn’t exist–there is a ton of information on wikidata available and a lot of neat tools already available and in development. You just have to look really hard for it. Fortunately, the wikidata community is already aware of the key issues that need to be addressed in order to become more successful.

Researchers have already taken considerable effort to make science more accessible by contributing to science-related articles. There are over 10,000 genes already in wikipedia thanks (in part) to the Gene Wiki initiative! It makes sense that wikidata is next. A lot of progress has been made in this arena, but I’ll save that for later.

Neat Science Thursday – Scientific communication is hard

For my dissertation research, I studied the mechanisms of viral persistence in the central nervous system using an in vitro model consisting of picornavirus infections of differentiated and undifferentiated murine neural progenitor and stem cells.

To some of my non-science friends and family, that explanation sounds something like, “I studied blah blah blah, miscellaneous pretentious scientific jargon, blah blah.”

Of course, they would still have no idea what I studied, and any further attempts to explain would be met with that kind, patient look that people give you when they’re bored but are too polite to walk away.

So I would tell non-science people that I studied “how a virus hides in the brain for a long time, and the consequences of having a virus hiding in the brain using mouse stem cells”.

This explanation will elicit much more interest, but can sometimes get distorted when described second-hand to others since it’s not as accurate. Also, there may be some fellow scientists who will think you lack professionalism, or don’t know what you’re talking about if you use this sort of description.

If you think about it, there is so much jargon specific to each field of study, it’s actually pretty impressive how well scientists have been able share information across disciplines. Of course, there is always room for improvement in that arena, especially since researchers primarily disseminate their findings via scholarly articles, keying them for easy search amongst fellow researchers in their discipline. The differences in jargon sets contributes to the difficulty in finding research articles outside your field of research which contain research findings that could have important impacts in your own work. It’s also why there has been a lot of interest in annotating research literature and making it more searchable (Go! Go! Mark2Cure) as well as creating an open database where information contained in research literature can be formally structured around a set of shared ontologies (Go! Go! Wikidata.

It’s also great that these findings are becoming more available as funding agencies help to drive open access policies enabling the public to finally access the research paid by tax/donation dollars. But open access does not mean accessible if we consider the sheer volume of jargon that must be learned in order to read and understand scholarly articles. How can we expect tax payers to support research if they are locked out on so many levels? Now before you argue that ‘people need to take personal responsibility for their own education’ or ‘the articles aren’t really hard to read if you actually put in the effort,’ ask yourself this, ‘Am I dismissive of people science communicators that communicate science via non-traditional channels (ie- non-academic journals)?’ If your answer is ‘yes’, you waive all rights to complain about the scarcity of research funding.

If your answer is ‘no’, consider contributing your expertise to a truly accessible knowledge-base/medium like Wikipedia. Efforts are already under way to make information on every human gene of interest publicly available on Wikipedia (the Gene Wiki initiative), and greater participation is needed from scientific community.

For those of you, researchers or not, who ARE able to communicate science with such elegance, enthusiasm, poignancy, and precision–especially those of you on non-traditional channels like Science 2.0, twitter, etc.–thank you for using your talents to engage the public so they can see how their money is being spent. You are awesome! The rest of us will just have to keep trying.

Neat Science Thursday – Crowdsourcing blues

As evident by a few of the previous posts on crowdsourcing science, wikipedia, and the GENE/Gene Wiki partnership, I think crowdsourcing science and citizen scientists are awesome! The speed with which a lot of interested non-scientists can sift through data is simply astounding!

In spite of all the positive features of crowdsourcing science and information (like wikipedia), there are also some interesting drawbacks. For example, wiki entries have been vandalized as part of a joke/challenge started by a comedian in order to make a joke/commentary on the wisdom of crowds, and more recently, users from government-related ip addresses have been systematically editing pages to reflect a particular political agenda. This kind of vandalism has prompted the banning of government ip addresses in the past.

But issues with crowdsourcing are not limited to just information platforms like wikipedia. Crowdsourcing competitions in order to foster participation and innovation have also been hijacked as covered in a recent (and very interesting) post on Science2.0.

According to the original post found at The Conversation about a new study:
“The research, published today in the Journal of the Royal Society Interface, found the openness of crowdsourced competitions, particularly those with a “winner takes all” prize, made them vulnerable to attack.

The researchers used game theory to analyse the trade-off between the potential for increased productivity from crowdsourcing a project, and the possibility of it being set back by malicious behaviour. They cited the DARPA Network Challenge as an example of a hijacked crowdsourcing competition, in which the organisers were left to sort through many fake submissions, including fabricated pictures of people impersonating DARPA officials….continue to the original post

Or visit the actual study publication (and hope your institution has access to it) if you want to read the original study.

Making research accessible with the GENE/Gene Wiki Partnership

Did you know you can update your favorite gene on Wikipedia and get a review article published while you’re at it? Here’s what you need to know about the GENE/Gene Wiki partnership:

1. What is it? The goal of the Gene Wiki is to create a comprehensive Wikipedia article for every human gene. To incentivize authors to improve Wikipedia content, GENE is now soliciting new gene-specific review articles under a new dual-publication model. Authors are invited to create two separate versions of their review (one for the journal, and one in wikipedia). More on the partnership here: Gene Wiki Reviews: Marrying crowdsourcing with traditional peer review.
2. How long should the review article be? The length of the review article is up to you! Since you are the expert on the gene you’re writing about, the length is based on whatever you think is necessary to describe the current state of the field.
3. How long should the wikipedia article be? We are targeting a final length of approximately 1200 words (though longer and more detailed articles are certainly welcome)
4. How are the two versions different? One version is targeted at professional scientists following typical academic and editorial standards. The second version is written for the Wikipedia audience and includes a slightly heavier emphasis on a general audience. Both versions will be peer-reviewed together, but for copyright reasons, these two versions must be separate works that have no substantial similarity. Some examples of review articles and wikipedia entries published under this model include:
   • LIG3: Wikipedia entry and the corresponding pubmed-indexed review article
   • EPHX2: Wikipedia entry and the corresponding pubmed-indexed review article
5. I am busy but intrigued, what is the time line? We generally suggest a 2-3 month deadline, but since this is an ongoing series in the journal, the time line is flexible and can be worked around your schedule. Don’t be discouraged from participating because you are busy now. Make the commitment to submit when your schedule permits.
6. Do I have to go at this alone? Absolutely not! If you have colleagues who would make good co-authors for the review, feel free to solicit their assistance.
7. Do I have to write the wiki article all at once? Nope. Our goal is to incentivize you, the expert, to make your knowledge about your favorite gene accessible. If it’s easier for you to write the wiki article in pieces, go ahead and do so! As long as the wiki entry is complete by the time you submit your manuscript, we will be happy to accept your review article.
8. The gene I work on doesn’t make much sense to write about alone, how should I contribute? Genes that work in concert can be tackled as a pair as with this example:
   • SFTPA1: Wikipedia entry and the corresponding pubmed-indexed review article
9. Why should I do this? By publishing a gene-specific review article, you help your scientific colleagues stay abreast of the current literature on your favorite gene. By publishing under the dual publication model (ie- on wikipedia), you help make your favorite gene more accessible to everyone allowing more people to understand the importance of your field of research. Everyone wins!
10. How do I get in on this? Check to see whether or not your favorite gene could use some serious contributions on wikipedia. If so, contact me. Include your gene of interest in the email, and your preferred deadline for the manuscript submission.

Wikipedia is for reals, Gene Wiki is legit

Professor Murray Jennex is an information systems whiz. He would start his classes on Information Security and Decision Support Systems with an open and frank discussion on relevant current affairs. During one of these discussions he raised a question regarding the accuracy of the information on wikipedia. Yes, it is open so that the entries can be vandalized; yes, Stephen Colbert did prove that point well.

Do not underestimate the knowledgeable Professor Wiki!

Surprisingly, people have done an amazing job in correcting the mistakes on wikipedia and thanks to the power of the crowd, wikipedia remains one of the most current sources of information. In one study, ~73% of vandalist revisions on wikipedia were fixed within 1000 seconds! There! That is the power of crowd sourcing that Prof. Jennex was trying to convey! However, it never crossed my mind that this power could potentially be harnessed in order to keep abreast with biomedical research.

But, it is always on the minds of many people geniuses in the Su Lab. Imagine if every gene in biomedical literature had a wikipedia entry and that each entry was current and thorough. Although it’s quite a lofty dream, it could happen. If researchers were to take five minutes out of their day to add their knowledge to Gene Wiki, it could definitely happen. So, my brilliant, biomedical research buddies…what are you waiting for?