Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
Hello together, I am really glad to have found this discussion! I think that having a central repository with a dedicated page for each citable item (and possibly subpages for aspects thereof, like figures or tables) is the way to go. http://openlibrary.org/ are heading in this direction (though only for books), and I have long wished to see some wiki version thereof, preferably with semantic integration. Acawiki is the closest I have seen so far, and if WikiPapers goes beyond that, I would also appreciate the possibility to take a closer look at it. Where can your proposal to the Foundation be found, Brian? Aiming at systems allowing for two-way citation is a good idea, too, and I would like to add that http://article-level-metrics.plos.org/. Some further points that come to mind - I have no idea, though, how far they have already been considered in your round (1) the name of the page: Acawiki currently uses the article title, but this creates problems in cases like http://www.ncbi.nlm.nih.gov/pubmed/14707297 and http://www.ncbi.nlm.nih.gov/pubmed/20171346 . Better would be a system based on universal identifiers like DOI and ISBN, if such exists for the kind of media referenced. (2) Aiming at systems allowing for two-way citation is probably a good idea, as they would allow some meaningful addition to the emerging range article-level metrics that more and more publishers (especially those in the Open Access world) are setting up (cf. http://everyone.plos.org/2009/12/09/article-level-metrics-presentation-to-berkeley-and-ucsf/ ). (3) In principle, wikification does not have to be restricted to sources, and semantic techniques could allow to include authors as well (where identification problems are even worse, though solution attempts are on the way, e.g. http://www.orcid.org/ ), or even institutions. (4) Like with other reference management systems, integration with citation workflows is crucial, e.g. portability to and from BibTeX files (cf. http://feedback.mendeley.com/forums/4941-mendeley-feedback/suggestions/286121-export-in-wiki-format ), or direct links to PDF, HTML or XML files the individual wiki user has access to. Several reference managers are building a very large database of metadata - in part taken from public repositories, in part from PDF indexing and in part from manual editing. There might be room for synergies. Cheers, Daniel -- http://www.google.com/profiles/daniel.mietchen ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
In regards to WikiTextrose, Wikicite, WikiPaper, AcaWiki, Wikicat: I have now written a small blog entry related to structured citations: Two-way citations in MediaWiki http://fnielsen.posterous.com/two-way-citations-in-mediawiki In my wiki I use standard MediaWiki templates to structure the bibliographic information. With Semantic MediaWiki and without a 'wikicat' it is possible to get a deep two-way citation, - though the approach might be not be particularly beautiful. I suppose it will result in a lot of semantic queries and bad server load? /Finn ___ Finn Aarup Nielsen, DTU Informatics, Denmark Lundbeck Foundation Center for Integrated Molecular Brain Imaging http://www.imm.dtu.dk/~fn/ http://nru.dk/staff/fnielsen/ ___ ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
On Fri, Jun 25, 2010 at 10:00 AM, Finn Aarup Nielsen f...@imm.dtu.dk wrote: In regards to WikiTextrose, Wikicite, WikiPaper, AcaWiki, Wikicat: I have now written a small blog entry related to structured citations: Two-way citations in MediaWiki http://fnielsen.posterous.com/two-way-citations-in-mediawiki In my wiki I use standard MediaWiki templates to structure the bibliographic information. With Semantic MediaWiki and without a 'wikicat' it is possible to get a deep two-way citation, - though the approach might be not be particularly beautiful. I suppose it will result in a lot of semantic queries and bad server load? /Finn I use Semantic MediaWiki but the solution is not scalable. A new semantic backend using Lucene needs to be created instead. ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
On Tue, Jun 22, 2010 at 8:19 PM, Samuel Klein meta...@gmail.com wrote:
Hello Brian,
Brian Mingus writes:
I wouldn't go so far as to say nobody is working on these ideas. We
recently submitted a project proposal to the Foundation along the
lines of community documentation of scientific (and other) sources.
You are right to call that out -- and your proofs of concept for
documenting scientific sources are the best I know of, in the world of
open code.
And I believe AcaWiki is working with you now, yes? I thought of your
project more as summary and literature-review, rather than a global
WikiCite... something that might one day delegate its citations,
primarily of scientific topics, to a universal WikiCite. (Correct me
if I am wrong.)
The already-written software (WikiPapers) is exactly what a WikiCite
would be. It is able to get metadata for practically any citation and
add it to the wiki automatically. If there is only one small nugget in
a proposal that the Foundation needs one would like to think that they
would have the foresight to notice that and do everything they can to
get it. It would be _really_ nice if they would at least read your
proposal and give you some feedback about how you can align your
vision with the Foundation's needs. Quite the opposite has happened -
we haven't gotten any real feedback at all. I'm also not sold on
proposals on the Strategy wiki. How are those different from the
proposals that have been accumulating on Meta? As far as I know not a
single one on either wiki has ever turned into a real project.
I am personally not in the loop on the AcaWiki thing - we are working
with them in some way, kind of. Nobody has installed or asked to
install WikiPapers on a wiki outside of our lab, despite that everyone
thinks it's pretty awesome. It's true that it is GPL, but I have not
released the source code precisely because I want it to be a
centralized repository of citations. I expect that whenever it finds
an institutional home lots of modifications will be made, and perhaps
the Foundation would prefer it to be written in PHP rather than
Python, etc.
WMF has a clear need for this or a similar technology, but will that
be enough to mobilize them?
Brian
And I don't think anyone is working on a
wikitextrose equivalent.
To recap: the fundamental basis of this general idea is a centralized
wiki that contains citation information that other wikis can then
reference using something like a {{cite}} template or a simple link.
The community can document the citation, the author, the book etc..
Users can use this wiki as their personal bibliography as well, as
collections of citations can be exported in arbitrary citation
formats. This general plan would allow community aggregation of
metadata and community documentation of sources along arbitrary
dimensions (quality, trust, reliability, etc.). The hope is that such
a resource would then expand on that wiki and across the projects into
summarizations of collections of sources (lit reviews) that make
navigating entire fields of literature easier and more reliable,
getting you out of the trap of not being aware of the global context
that a particular source sits in.
I like that formulation a lot.
We continue to hope that the Foundation
is willing to work with us to draw up a project proposal that works
for them, and we have also offered some programming time (I have
already put in hundreds of hours).
Which reminds me: we need to fix our project-proposal process.
This sounds like a promising project. Did you ever post a version of
the above to strategy.wikimedia.org? I thought that you were going to
work with AcaWiki in the short term and see what you had in common.
David, the Open Library plugin you mention also sounds excellent for
solving the larger every citable source in the world challenge.
--
Samuel Klein identi.ca:sj w:user:sj
___
Wiki-research-l mailing list
Wiki-research-l@lists.wikimedia.org
https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
___
Wiki-research-l mailing list
Wiki-research-l@lists.wikimedia.org
https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
Thanks Samuel, I think it would be great to have more citation tracking in Wikimedia projects! The projects you mention were new to me, but they're quite related to my own research in argumentation, and coming out of the library community, for me, citation analysis is second nature! http://meta.wikimedia.org/wiki/WikiTextrose http://meta.wikimedia.org/wiki/Wikicite Have you run into AcaWiki? It's conceived of as a Wikipedia for academic research and uses CC-BY and Semantic MediaWiki: http://www.acawiki.org/ AcaWiki focuses more on summarizing articles than on linking their citations together.There is a BibTeX importer -- which could be adapted for use in other MediaWiki installations (one of the desired parts of that project). It's a useful place to gather summaries for generals and other reading-based exams--for instance here's Benjamin Mako Hill's collection: http://acawiki.org/User:Benjamin_Mako_Hill/Generals I used to work with AcaWiki, and would love any feedback on the site (offlist). It was interesting to hear of BibDex! http://www.bibdex.com/ I'll definitely take a closer look. One possibility would be to draw on existing projects which are already documenting sources, particularly in confusing and problematic areas, where good source is not obvious or well-understood. For instance, on English Wikipedia, the WikiProject video games has a guideline on sources, documenting particular websites that are and are not reliable: http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Video_games/Sources WikiProject Japan has documented offline resources recommended for the project: http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Japan/Reference_library These projects are far from alone, as a search will show: http://en.wikipedia.org/w/index.php?title=Special:Searchredirs=1search=sources+wikiproject If you want to get Wikicite and WikiTextrose going again -- or others are proposed as Brian mentions -- I'd like to be involved. ...recently submitted a project proposal to the Foundation along the lines of community documentation of scientific (and other) sources. So, let me know how I can contribute. :) -Jodi On 22 Jun 2010, at 00:38, Samuel Klein wrote: The idea is to have a wiki-project with an entry for every cited source, author, and publication -- including critical secondary sources that exist only to comment on sources/authors/publications. Aggregate information about the reliability of these sources, where they are used, how they are discussed and linked together. http://meta.wikimedia.org/wiki/WikiTextrose http://meta.wikimedia.org/wiki/Wikicite The wikitextrose proposal aims to gather data about these types of sources, and links between them. The wikicite proposal aims to organize citable statements on other wiki projects so that one can trace the origins of the idea expressed back to sources. SJ On Mon, Jun 21, 2010 at 5:51 AM, Jodi Schneider jodi.schnei...@deri.org wrote: Samuel, This is great! What's the idea for a WikiCite project? -Jodi On 20 Jun 2010, at 22:44, Samuel Klein wrote: Some motivation for a proper WikiCite project. --sj === Begin forwarded message == How citation distortions create unfounded authority: analysis of a citation network http://www.bmj.com/cgi/content/full/339/jul20_3/b2680 Abstract: Objective -To understand belief in a specific scientific claim by studying the pattern of citations among papers stating it. Design - A complete citation network was constructed from all PubMed indexed English literature papers addressing the belief that \u03b2 amyloid, a protein accumulated in the brain in Alzheimer\u2019s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis. Social network theory and graph theory were used to analyse this network. Main outcome measures - Citation bias, amplification, and invention, and their effects on determining authority. Results: The network contained 242 papers and 675 citations addressing the belief, with 220 553 citation paths supporting it. Unfounded authority was established by citation bias against papers that refuted or weakened the belief; amplification, the marked expansion of the belief system by papers presenting no data addressing it; and forms of invention such as the conversion of hypothesis into fact through citation alone. Extension of this network into text within grants funded by the National Institutes of Health and obtained through the Freedom of Information Act showed the same phenomena present and sometimes used to justify requests for funding. Conclusion: Citation is both an impartial scholarly method and a powerful form of social communication. Through distortions in its social use that include bias, amplification, and invention, citation can be used to generate information cascades resulting in unfounded authority of claims.
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
The idea is to have a wiki-project with an entry for every cited source, author, and publication -- including critical secondary sources that exist only to comment on sources/authors/publications. Aggregate information about the reliability of these sources, where they are used, how they are discussed and linked together. http://meta.wikimedia.org/wiki/WikiTextrose http://meta.wikimedia.org/wiki/Wikicite The wikitextrose proposal aims to gather data about these types of sources, and links between them. The wikicite proposal aims to organize citable statements on other wiki projects so that one can trace the origins of the idea expressed back to sources. SJ On Mon, Jun 21, 2010 at 5:51 AM, Jodi Schneider jodi.schnei...@deri.org wrote: Samuel, This is great! What's the idea for a WikiCite project? -Jodi On 20 Jun 2010, at 22:44, Samuel Klein wrote: Some motivation for a proper WikiCite project. --sj === Begin forwarded message == How citation distortions create unfounded authority: analysis of a citation network http://www.bmj.com/cgi/content/full/339/jul20_3/b2680 Abstract: Objective -To understand belief in a specific scientific claim by studying the pattern of citations among papers stating it. Design - A complete citation network was constructed from all PubMed indexed English literature papers addressing the belief that \u03b2 amyloid, a protein accumulated in the brain in Alzheimer\u2019s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis. Social network theory and graph theory were used to analyse this network. Main outcome measures - Citation bias, amplification, and invention, and their effects on determining authority. Results: The network contained 242 papers and 675 citations addressing the belief, with 220 553 citation paths supporting it. Unfounded authority was established by citation bias against papers that refuted or weakened the belief; amplification, the marked expansion of the belief system by papers presenting no data addressing it; and forms of invention such as the conversion of hypothesis into fact through citation alone. Extension of this network into text within grants funded by the National Institutes of Health and obtained through the Freedom of Information Act showed the same phenomena present and sometimes used to justify requests for funding. Conclusion: Citation is both an impartial scholarly method and a powerful form of social communication. Through distortions in its social use that include bias, amplification, and invention, citation can be used to generate information cascades resulting in unfounded authority of claims. Construction and analysis of a claim specific citation network may clarify the nature of a published belief system and expose distorted methods of social citation. -- Samuel Klein identi.ca:sj w:user:sj -- Samuel Klein identi.ca:sj w:user:sj ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l -- Samuel Klein identi.ca:sj w:user:sj ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
Hi Samuel, That's really GREAT - we need that a lot for many sensitive topics. Sincerely, Pavlo On Tue, Jun 22, 2010 at 2:38 AM, Samuel Klein meta...@gmail.com wrote: The idea is to have a wiki-project with an entry for every cited source, author, and publication -- including critical secondary sources that exist only to comment on sources/authors/publications. Aggregate information about the reliability of these sources, where they are used, how they are discussed and linked together. http://meta.wikimedia.org/wiki/WikiTextrose http://meta.wikimedia.org/wiki/Wikicite The wikitextrose proposal aims to gather data about these types of sources, and links between them. The wikicite proposal aims to organize citable statements on other wiki projects so that one can trace the origins of the idea expressed back to sources. SJ On Mon, Jun 21, 2010 at 5:51 AM, Jodi Schneider jodi.schnei...@deri.org wrote: Samuel, This is great! What's the idea for a WikiCite project? -Jodi On 20 Jun 2010, at 22:44, Samuel Klein wrote: Some motivation for a proper WikiCite project. --sj === Begin forwarded message == How citation distortions create unfounded authority: analysis of a citation network http://www.bmj.com/cgi/content/full/339/jul20_3/b2680 Abstract: Objective -To understand belief in a specific scientific claim by studying the pattern of citations among papers stating it. Design - A complete citation network was constructed from all PubMed indexed English literature papers addressing the belief that \u03b2 amyloid, a protein accumulated in the brain in Alzheimer\u2019s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis. Social network theory and graph theory were used to analyse this network. Main outcome measures - Citation bias, amplification, and invention, and their effects on determining authority. Results: The network contained 242 papers and 675 citations addressing the belief, with 220 553 citation paths supporting it. Unfounded authority was established by citation bias against papers that refuted or weakened the belief; amplification, the marked expansion of the belief system by papers presenting no data addressing it; and forms of invention such as the conversion of hypothesis into fact through citation alone. Extension of this network into text within grants funded by the National Institutes of Health and obtained through the Freedom of Information Act showed the same phenomena present and sometimes used to justify requests for funding. Conclusion: Citation is both an impartial scholarly method and a powerful form of social communication. Through distortions in its social use that include bias, amplification, and invention, citation can be used to generate information cascades resulting in unfounded authority of claims. Construction and analysis of a claim specific citation network may clarify the nature of a published belief system and expose distorted methods of social citation. -- Samuel Klein identi.ca:sj w:user:sj -- Samuel Klein identi.ca:sj w:user:sj ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l -- Samuel Klein identi.ca:sj w:user:sj ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
Hmmm, WikiData is this http://www.mediawiki.org/wiki/Wikidata + http://meta.wikimedia.org/wiki/Wikidata ? (Google knows some external wikidatas http://www.wiki-data.com/ http://softwareas.com/wikidata-hackathon-wikidata-a-wiki-of-companies-data ...) On Tue, Jun 22, 2010 at 3:11 AM, Samuel Klein meta...@gmail.com wrote: On Mon, Jun 21, 2010 at 7:51 PM, Pavlo Shevelo pavlo.shev...@gmail.com wrote: Hi Samuel, That's really GREAT - we need that a lot for many sensitive topics. Yes. Also for reconciling differences between sources in different languages - which often carry their own quiet biases. The Foundation is now in a position to help support this sort of work with better contacts and brainstorming (than it was 5 years ago when these ideas were first developed), but someone still needs to design and run these projects... I don't think anyone is working on these ideas at the moment. (Erik, David Strauss, Stirling -- any recent thoughts on the matter? WikiData as a concept has been worked on in various ways, but I haven't seen any discussion of this particular implementation.) Sincerely, Pavlo On Tue, Jun 22, 2010 at 2:38 AM, Samuel Klein meta...@gmail.com wrote: ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
On Mon, Jun 21, 2010 at 6:11 PM, Samuel Klein meta...@gmail.com wrote:
On Mon, Jun 21, 2010 at 7:51 PM, Pavlo Shevelo pavlo.shev...@gmail.com
wrote:
Hi Samuel,
That's really GREAT - we need that a lot for many sensitive topics.
Yes. Also for reconciling differences between sources in different
languages - which often carry their own quiet biases.
The Foundation is now in a position to help support this sort of work
with better contacts and brainstorming (than it was 5 years ago when
these ideas were first developed), but someone still needs to design
and run these projects... I don't think anyone is working on these
ideas at the moment.
(Erik, David Strauss, Stirling -- any recent thoughts on the matter?
WikiData as a concept has been worked on in various ways, but I
haven't seen any discussion of this particular implementation.)
I wouldn't go so far as to say nobody is working on these ideas. We
recently submitted a project proposal to the Foundation along the
lines of community documentation of scientific (and other) sources. In
the implementation we use in our lab all wiki articles that reference
an article are referring to the same citation on the same wiki page
(WatsonCrick53, etc.). The article that contains the citation
information is comprised of an infobox with metadata about the
citation garnered from various web apis and further arbitrary
documentation (we also show a list of other sources that this source
cites, and vice versa, etc..). We continue to hope that the Foundation
is willing to work with us to draw up a project proposal that works
for them, and we have also offered some programming time (I have
already put in hundreds of hours).
To recap: the fundamental basis of this general idea is a centralized
wiki that contains citation information that other wikis can then
reference using something like a {{cite}} template or a simple link.
The community can document the citation, the author, the book etc..
Users can use this wiki as their personal bibliography as well, as
collections of citations can be exported in arbitrary citation
formats. This general plan would allow community aggregation of
metadata and community documentation of sources along arbitrary
dimensions (quality, trust, reliability, etc.). The hope is that such
a resource would then expand on that wiki and across the projects into
summarizations of collections of sources (lit reviews) that make
navigating entire fields of literature easier and more reliable,
getting you out of the trap of not being aware of the global context
that a particular source sits in.
We continue to wait for Foundation feedback, but it has been
challenging to get more than sparse conversations. It doesn't seem as
though they have met to discuss the topic, which is unfortunate.
Brian Mingus
Graduate student
Computational Cognitive Neuroscience Lab
University of Colorado at Boulder
___
Wiki-research-l mailing list
Wiki-research-l@lists.wikimedia.org
https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
Re: [Wiki-research-l] Fwd: modern foundations of scientific consensus
Samuel Klein, 22/06/2010 02:11: The Foundation is now in a position to help support this sort of work with better contacts and brainstorming (than it was 5 years ago when these ideas were first developed), but someone still needs to design and run these projects... I don't think anyone is working on these ideas at the moment. There's also Sunir Shah: http://meatballwiki.org/wiki/BibDex Nemo ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
[Wiki-research-l] Fwd: modern foundations of scientific consensus
Some motivation for a proper WikiCite project. --sj === Begin forwarded message == How citation distortions create unfounded authority: analysis of a citation network http://www.bmj.com/cgi/content/full/339/jul20_3/b2680 Abstract: Objective -To understand belief in a specific scientific claim by studying the pattern of citations among papers stating it. Design - A complete citation network was constructed from all PubMed indexed English literature papers addressing the belief that \u03b2 amyloid, a protein accumulated in the brain in Alzheimer\u2019s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis. Social network theory and graph theory were used to analyse this network. Main outcome measures - Citation bias, amplification, and invention, and their effects on determining authority. Results: The network contained 242 papers and 675 citations addressing the belief, with 220 553 citation paths supporting it. Unfounded authority was established by citation bias against papers that refuted or weakened the belief; amplification, the marked expansion of the belief system by papers presenting no data addressing it; and forms of invention such as the conversion of hypothesis into fact through citation alone. Extension of this network into text within grants funded by the National Institutes of Health and obtained through the Freedom of Information Act showed the same phenomena present and sometimes used to justify requests for funding. Conclusion: Citation is both an impartial scholarly method and a powerful form of social communication. Through distortions in its social use that include bias, amplification, and invention, citation can be used to generate information cascades resulting in unfounded authority of claims. Construction and analysis of a claim specific citation network may clarify the nature of a published belief system and expose distorted methods of social citation. -- Samuel Klein identi.ca:sj w:user:sj -- Samuel Klein identi.ca:sj w:user:sj ___ Wiki-research-l mailing list Wiki-research-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wiki-research-l
