I am really impressed with Biostar. The quality of the answers here is often so good that it surely will have an influence. In a way Biostar extends the informal helping among peers of which gratitude is often expressed in the acknowledgments.
How does this work with Biostar. Should we acknowledge the system, all contributors, or both? Do you acknowledge Biostar in your output and if so, how?
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Andra Waagmeester
Perhaps the founders and moderators of BioStar could get together and put together a publication on BioStar and their experiences in managing it, get it published. This would provide a publication to be referenced by those who want to acknowledge the site, and would provide some direct academic benefit (a publication and citations) for at least some of those who contribute.
How about giving a DOI to outstanding questions? You would then have a founding paper published by the founders/moderators and a DOI to cite a specific question. This would also be an additional incentive to the biostar community.
Andra: That is a very nice way to provide microcitations. I wasn't aware it was possible to generate DOIs ad-hoc like that. To avoid spamming DOIs perhaps they could be generated only for notable questions/answers at the discretion of moderators.
@gawp: I completely agree. You don't want to give a doi to a question that might get deleted.
Actually you should not give a DOI to anything that may get changed. So either you need to freeze questions when you give them a DOI or we need a versioning system where the DOI relates to a single version. That is for instance what they do at Nature Precedings.
As for using DOI, have a look at this thread on using DOI/Handle on FigShare service http://friendfeed.com/science-2-0/a9ae2d32/does-anyone-have-any-experience-with-handle
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Pawel Szczesny
Published today: :-) !!!
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002216
"BioStar: An Online Question & Answer Resource for the Bioinformatics Community"
Laurence D. Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall'Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S. Pedersen, Mary E. Mangan, Christopher A. Miller, Istvan Albert
congratulations to all, and thank to all the Biostar members that helped make this community so good.
Many thanks for validating my answer Andra, but here, I wasn't alone at all. :-)
I would like to thank the authors of this paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034238 for citing biostar in the acknowledgments section. I will do the same for future papers (if I manage to publish more :-) )
Direct citations feel inappropriate since the people listed as authors of the publication may not be the same that provided the value that was essential for the author in question.
I think the best course of action would be to do two things:
Actually, there is an NLM citation standard that was developed for blogs--maybe that's suitable?
Here's where we talked about it on our blog (which I'm not citing properly here)
:
NLM citation standard…for blogs!
All of our references to BioStar at this point have been in workshops, where we just tell everyone how cool this community is and give them the URL. Sometimes we put the flyer we made in the workshop packets if we have some printed up.
I didn't thank BioStar specifically, but in my latest paper, I included the following line:
We thank the communities at stats.stackexchange.com and stackoverflow.com for useful advice concerning statistics and R.
In my opinion, that's adequate. It's just like if you spent 5 minutes talking to the statistician down the hall about which distribution to use. It probably wasn't a substantial enough contribution to warrant an authorship, but an acknowledgement of their contribution is fitting.
Datacite could be used to assign DOIs to questions. It's relatively easy to mint DOIs using their API (I have code to do so if anyone's interested), once you are authorised to do so (which at the moment is just a matter of asking I believe).
DOIs do not automatically make an object citable, but they do seem to carry a certain cachet among particular circles (ie publishing ones) that a URI simply doesn't (though there is no reason why it shouldn't).
+1 for datacite. I guess it's because you can search for a URI without any ambiguity but you cannot safely do this for a url with a 'GET' query (e.g: http://www.ncbi.nlm.nih.gov/pubmed/21208982 vs http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=21208982&hello=world )
Isn't DataCite for data?
DataCite is for data, yes. We are already 'misusing' them for publication objects on the Knowledgeblog project however (all the articles on http://ontogenesis.knowledgeblog.org/ have DataCite DOIs). I would also argue that the distinction between data and publication is an arbitrary one, that is going to become more and more blurred in the near future.
An instance of this question now has its own DOI: doi:10.1038/npre.2011.6041.1
I had the opportunity to thank Biostar in some presentations: e.g: slide #3 of http://www.slideshare.net/lindenb/20101210-ngscourse , or in my blog.
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Pierre Lindenbaum
Earlier this year we published a short paper on how to give feedback to annotation databases, and what to do when encountering errors in the data.
Dall'Olio GM, Bertranpetit J, Laayouni H. The annotation and the usage of scientific databases could be improved with public issue tracker software. Database (Oxford). 2010 Dec 23;2010:baq035. Print 2010. PubMed PMID: 21186182; PubMed Central PMCID: PMC3011984. Available from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3011984 . During the writing we opened some questions on biostar (example) and followed some discussions on the site, to know what was the opinion of the rest of the scientific community about some of the databases described. These discussions have helped us improving the manuscript, although we could have probably have been able to do it even without them.
At the end, we acknowledged biostar in a generic form without explaining in details which discussions we had opened and why we were acknowledging biostar. This is from the paper:
We would like to thank the community athttp://biostar.stackexchange.com/ for useful discussion.
On a side note, the people who follow the biostar mailing list will already know that a manuscript is currently being prepared for submission to a Bioinformatics related journal. I will leave the description of how I have cited biostar in a paper, as an example of when and how I consider necessary to cite it or acknowledge.
EDIT by @RamRS: http://biostar.stackexchange.com is obsolete now, we're at https://www.biostars.org
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Giovanni M Dall'Olio
What about using WebCite, which is used by BioMedCentral to preserve URLs in reference lists? I think this system gets around the data/webpage and static/dynamic issues discussed in previous posts. As explained here, if you add a WebCite bookmarklet to your browser, WebCite will generate a stably archived version of a BioStar page and send you a link to the cached content. E.g. application to this thread, prior to my original post yields....
Your recent WebCite request has completed. Following are the results from this request:
SUCCESSFULLY CACHED
Please use the URL http://www.webcitation.org/5zlLNPMiQ to access the cached copy of this page
If you have any questions, please feel free to contact the WebCite team at http://www.webcitation.org
Regards,
The WebCite Team
And after my post (but before this edit) yields...
Your recent WebCite request has completed. Following are the results from this request:
SUCCESSFULLY CACHED
Please use the URL http://www.webcitation.org/5zlMCwu64 to access the cached copy of this page
If you have any questions, please feel free to contact the WebCite team at http://www.webcitation.org
Regards,
The WebCite Team
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Casey Bergman
I was just about to ask the same question! For example, the answers in this question literally taught me how to get the data right, and probably saved several hours of work!!!
My choice is to acknowledge the community in the paper. But, a mechanism to cite a question directly would be much more valuable for both Biostar and the readers of the article. The Datacite hinted by Simon seems perfect. I think that questions like that one should be cited, not just acknowledged. At least, answers provided a technical support like any methodological paper. In other cases, answers provided insightful advice in how to gather and treat data. That's non-trivial! Do not configure authorship but probably deserves a full citation!
That's my opinion.
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Jarretinha
One solution I applied to this specific question is to save an instance of the series question/answers of this thread to PDF. Subsequently this pdf is then saved on Nature Precedings (http://precedings.nature.com/documents/6041/version/1) together with its own DOI: doi:10.1038/npre.2011.6041.1
So I guess if you consider a biostar answer valuable, just save it, get your doi and attribute/acknowledge.
==Edit==
This thread was submitted to an alt-metrics workshop. The slides are here: http://precedings.nature.com/documents/6043/version/1
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Andra Waagmeester
One could reference the publication that describes BioStar. This has been published in PLoS Computational Biology.
I have come across a few questions and answers where people mention ideas that could really lead to new research efforts and publications. In other words you would take the original idea for that work from a BioStar question. Of course based on what is said above and the Creative Commons license you would have to somehow acknowledge that. But I think in such cases it would make more sense to contact the person whose idea you are going to use and discuss what should be done. Depending on the importance of the idea for the publication it could even make sense to offer a co-authorship. In such cases the discussion will likely also lead to a better publication.
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