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Roderic Page › Likes
A collaborative proposal on research metrics - http://cameronneylon.net/blog...
Jean-Claude Bradley, Bill Hooker, Christina Pikas and 14 other people liked this
When we talk about open research practice, more efficient research communication, wider diversity of publication we always come up against the same problem. What's in it for the jobbing scientist? This is so prevalent that it has been reformulated at "Singh's Law" (by analogy with Godwin's law) that any discussion of research practice will inevitably end when someone brings up career advancement or tenure. The question is what do we actually do about this? n opportunity has arisen for some funding to support a project here. My proposal is to bring a relevant group of stakeholders together; funders, technologists, scientists, adminstrators, media, publishers, and aggregators, to identify needs and then to actually build some things.
- Cameron Neylon
Wonder whether Andrew Treolar might have insight to contribute http://andrew.treloar.net/
- Kubke
AT certainly has experience of the problem and also seems to be collecting a lot of data...
- Cameron Neylon
He was strong about making data sets a primary citable object at the data matters meeting where I met him, to make the 'use' of the data as trackable as any publication
- Kubke
Yep, I think that's a key theme. Need to make sure have Dryad and Datacite involvement with this.
- Cameron Neylon
He suggested giving the 'data' a DOI and tap onto the search/link/tracking that already exists for paper publications as something which could provide an initial viable solution
- Kubke
Essentially this is what the DataCite project are doing. I think Dryad is connected with them as well. I worry about using dois for this because I would rather URLs [ducks in case geoff bilder arrives to pummel me (-; ] but the reality is that the scientific mindset seems to be doi = real so I think it's going to be the way we move forward in practice.
- Cameron Neylon
The redirection mainly. Essentially it breaks a whole set of fun things that you can do with URLs. None of which to be fair are very commonly done. Also in principle they could be enabled through the doi redirect. Essentially its a minor quibble that it doesn't add anything technically and breaks some stuff. But the reasons for dois are fundamentally social not technical.
- Cameron Neylon
from twhirl
I'm a big DOI fan. Just yesterday I ran into a few duplicate papers in the Mendeley library. One reason is that there are several URLs associated with a paper: PubMed, Journal HTML page, Journal PDF, institutional repository URL,... Not to mention that many URLs break over time.
- Martin Fenner
And DOIs would really help to automatically find science blog posts associated with a paper. The Journal of Neuroscience editorial about supplementary information in August has no DOI. Almost impossible to find all blog posts (there are many) that talk about this editorial.
- Martin Fenner
All true but I guess my problem is that fundamentally dois are a special system so that generic web tools (and yes particularly semantic web tools) will break over them and the info won't get incorporated into the wider web. e.g. Martin's problem could be solved by an owl:sameAs which would mean that it would be transparent to other web systems. But with dois someone has to build...
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- Cameron Neylon
None of which changes the reality. DOIs are dominant and are here to stay as far as I can tell so I just need to get over it and move on...
- Cameron Neylon
Just added a comment and we need to do more than offering incentives for "re-use".
- joergkurtwegner
While I am a big fan of finer-grained measures of contribution (e.g. peer review), I am not convinced that the current proposal should be stretched to cover such measures. It seems to me that what is wanted here is a hard-nosed, outcome-focused project designed to answer hard questions about ROI. For that purpose, a close focus on re-use is probably optimal.
- Bill Hooker
Nice proposal. It currently focuses strongly on funder needs. Useful, perhaps necessary, but it means delayed and indirect rewards to the jobbing scientist. Would it make sense to work in a more direct focus on "jobbing scientist needs" too, with possible hacks of automated reuse-metric CVs and reuse-metricful tenure packages?
- Heather Piwowar
Joerg - I commented on your comment back at the proposal. Two things really. My view is that the "measuring re-use" idea covers things like review. A good review needs to be "cited" in some way and that re-use measured and rewarded. I'm not quite sure where you're going with the micropayments thing. A kind of micropayments has been tried by EPSRC in the UK where they pay £50 or...
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- Cameron Neylon
Heather, good point. Although the response I've got suggests that people are interested enough in the possibility of getting credit for a more diverse range of things that thats enough at the moment. But yes, the CV is a very good place to realise some benefits. Need to talk to someone inside VIVO I think to see if there is some low hanging fruit there.
- Cameron Neylon
@Bill , @Cameron - I understand your views and the ROI question is important. As long as we agree that there is some measure, recognition, and reward scheme I agree. So, a re-use needs to be tracked otherwise, we need to prevent ab-use of re-use.
- joergkurtwegner
So if I'm reading you right your core point is that we shouldn't assume that simply by measuring something that the rewards will flow from that. That it is important to consider explicit reward schemes, which might include payment or aggregated micropayment?
- Cameron Neylon
Actually it strikes me that both Joerg and Heather are pointing in the same direction here. Keeping up the issue of direct benefits.
- Cameron Neylon
Cameron, what is your timeline for the proposal and what sort of additional help would be useful at this point? The current draft doesn't have references: do you need any? Other help?
- Heather Piwowar
References (both to literature and to other projects) would be a big help. Contacts with funders would be useful if anyone has them. And proof reading still valuable. I'm currently checking with the funder whether this is heading in the right direction and then I'll start pulling in contributors more. Timeline is really about a week though the quicker the better I suspect.
- Cameron Neylon
Also anyone got a good contact on the inside of VIVO? I know that Mackenzie Smith is on their advisory board but don't have any good contacts on the inside. It would be an obvious source of data.
- Cameron Neylon
Sounds good. I've added (REF) indications where it seems like references might be appropriate, to facilitate crowdsourcing. Cameron, please edit as needed based on the intended document length and number of refs expected by the funding body?
- Heather Piwowar
Yep, still working on those last two questions... ;-)
- Cameron Neylon
what came of this?
- Claudia Koltzenburg
Got the money, running the workshop: http://beyond-impact.org
- Cameron Neylon
Get Full Text: Mendeley now works with your local library via OpenURL - http://www.mendeley.com/blog...
suelibrarian, Roderic Page, Just Joe and 4 other people liked this
where is "local"? ;-)
- Claudia Koltzenburg
Claudia++ so, what happens if I am working at home?
- Egon Willighagen
it says there - you identify your library by searching if it doesn't work by IP - I think this is fabulous!
- Christina Pikas
EZ Proxy support is coming, along with desktop and web importer integration, but for now it's just access via Mendeley to local copies of content you already have access to by IP.
- Mr. Gunn
Nice, and handy not just for libraries. Repsitories such as BHL and BioStor provide OpenURL resolvers, so Mendeley users can now look for content there from the comfort of their Mendeley library (see See http://iphylo.blogspot.com/2011...). Any plans to do the reverse, i.e., enable Mendeley itself to act as an OpenURL resolver? At the moment the API doesn't have enough features to enable me to hack one (at least, not without a lot of grief).
- Roderic Page
Top ten reasons why academics do not contribute to Wikipedia - Draft - http://en.wikiversity.org/wiki...
Claudia Koltzenburg, Matthew Todd, Eric and 25 other people liked this
"1. Wiki edits do not count for tenure. 2. Wiki edits take away time from my research. 3. Wiki edits could actually damage my reputation. 4. I do not know what that would be good for. 5. I do not know how to do that. 6. I do not want others to modify what I wrote. 7. The quality of wiki articles in my field is rather low, and I value my time too highly to help fix that. 8. I do not want to spend my time correcting stuff that had been correct before but was vandalized in between. 9. I am not allowed to post my original research in there. 10. None of my peers does it. 11. None of my peers reads here. 12. I do not want others to see the kind of mistakes I make. 13. Why should I deal with an encyclopedia if I have access to primary sources?" Update: Beta version of a survey on the matter is at http://bit.ly/AcaWP .
- Daniel Mietchen
from Bookmarklet
@achimraschka @fischblog here we go with a first draft of the ten reasons that keep experts off of wikis.
- Daniel Mietchen
another possibility: involved in too many other projects already and can't handle another area of focus. Similar to #2, but more about fragmented focus than time constraints.
- Heather Piwowar
Negative perceptions: I don't want to be associated with those nasty "wiki" things...
- Cameron Neylon
another: I already do lots of writing and editing and don't want to do any more.
- Heather Piwowar
another one: "Really !? I can edit an article in wikipedia ?"
- Pierre Lindenbaum
@ Cameron I would consider that as being part of #3 above. Added in all the rest plus some rough categories. Current version: "Lack of incentives 1. Wiki edits do not count for tenure. 2. I do not know what that would be good for. 3. None of my peers does it. 4. None of my peers comes here to read about my research. [edit] Disincentives 1. Wiki edits take away time from my research. 2....
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- Daniel Mietchen
One that might be a variant of #9, but probably counts as its own thing: "I don't want the hassle of dealing with Wikipedia's local culture." More people than have edited Wikipedia articles have heard horror stories about nonsensical edit wars, and don't want to deal with that. Having to argue for the significance of an academic scientist whose page is a stub, while lengthy and lovingly detailed pages exist for fictional characters strikes a lot of people as absurd, bordering on Kafkaesque.
- Chad Orzel
I found that people who are inclined to blog tend to avoid community-driven activities like wikis and vice versa. I guess many people look at wikipedia and simply decide that it's not their style.
- Lars Fischer
Thanks for all these comments. I've added Dan's. Now off to #glamwiki . Will get back to this upon return.
- Daniel Mietchen
And here comes the seemingly inevitable request for deletion: http://en.wikiversity.org/wiki... .
- Daniel Mietchen
I am sure WikiEducator would be happy to host the page
- Kubke
shouldn't it be turned into a web poll ?
- Pierre Lindenbaum
The request for deletion debate ended with "keep" this time. @ Pierre: Yes, and help with setting one up is welcome.
- Daniel Mietchen
@Daniel I'll create the poll on G-Docs in the evening
- Pierre Lindenbaum
@Daniel I just send you an invitation for editing the document.
- Pierre Lindenbaum
Here is the poll : http://goo.gl/5GvXC
- Pierre Lindenbaum
Cool - can you add a "Tick all that apply" notice? Merci!
- Daniel Mietchen
Awesome, why not a 5-point likert scale then? (5 radio buttons) - that would make it so much useful!
- ReaderMeter
I guess we should do some test runs before announcing it far and wide.
- Daniel Mietchen
Folks, bear with us while we reformat the poll
- ReaderMeter
Survey in beta: Reasons why academics do (not) contribute to Wikipedia http://bit.ly/AcaWP . Please provide feedback here.
- Daniel Mietchen
I left most of the "I DO contribute to wikipedia" section blank, because I seldom do contribute there. It didn't return an error, but it wasn't exactly clear what I should do there.
- Bill Hooker
I also left the 'I DO contribute to wikipedia' section blank, although I contribute to other wikis.
- Kubke
Bill Hooker, Kubke -- yes that's what we are expecting.
- ReaderMeter
Done the survey. I answered both sets of questions because I have done some edits but not a whole lot.
- Cameron Neylon
Thanks to all those who filled it in so far. We have made some adjustments. Further beta testers welcome.
- Daniel Mietchen
Done :)
- science3point0
Done
- Pierre Lindenbaum
The survey is live now at http://survey.nitens.org/... . Thanks for filling it in or spreading the word.
- Daniel Mietchen
I heard the #1 yesterday in a conf call: "what is a wiki?"
- Egon Willighagen
Can Mendeley not include the "Wikipedia edit count" in their user profiles? That is easily done and would certainly disarm some'motivational aspects'.
- joergkurtwegner
Not as easily done as you think, Joerg. What would count as an edit? Do you subtract from the count if your edit gets reverted? How often do you check? Do big edits count for more than small edits?
- Mr. Gunn
We fixed a design flaw in the survey, now the "individual motivation" section should be unambiguous.
- ReaderMeter
Looking for ways to convert #XML into #MediaWiki. Any pointers/ suggestions?
Mike Chelen, Chris M, Roderic Page and 3 other people liked this
Direct import via Special:Import does not work for XML from places like http://www.plosone.org/article....
- Daniel Mietchen
try to use XSLT.. . @rdmpage has already worked on the PLOS files (e.g. http://code.google.com/p... ) and, on my side, I wrote a stylesheet pubmed2wiki: http://code.google.com/p...
- Pierre Lindenbaum
I am not sure whether XSLT can handle all of the formatting but your links look promising - will definitely dive in there.
- Daniel Mietchen
Brief test, following up on @rdmpage (for background, see http://iphylo.blogspot.com/2010... ): using http://toolserver.org/~diberr... ( script variant at http://search.cpan.org/~diberr... ) to import http://iphylo.org/~rpage... (which he had converted from...
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- Daniel Mietchen
If you're using Semantic MediaWiki, http://www.mediawiki.org/wiki... and http://www.mediawiki.org/wiki... work pretty well.
- Adam Kraut
As mentionned above, Extension:External Data is probably the best option out there. I'm not sure it even requires Semantic MediaWiki - all it does is to import data from XML, CSV, MySQL or LDAP into Templates.
- Laurent Alquier
Thanks for the hint at these Extensions, Adam and Laurent. I haven't tested them yet, but would they allow to produce something like http://www.science3point0.com/coasped... (or better, i.e. with properly formatted images, equations and so on) on the basis of the XML or HTML of the article http://dx.doi.org/10... ?
- Daniel Mietchen
Also, if HTML2wiki is necessary anyway (as it is if we follow Roderic's path), is it then better to produce a HTML version from the XML, or can we simply take the article's HTML?
- Daniel Mietchen
Another interesting starting point would be the PubMed Central XML - it avoids the hassle of dealing with the XML formats of all the individual publishers. As per http://www.science3point0.com/evomri... , a direct search by license is not yet possible, but given that a search for the term evolution and for review articles entered into PubMed...
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- Daniel Mietchen
Just used Special:ImportXML (provided by Extension:DataTransfer) to import the nxml file from the Mar. Drugs article contained in ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/66/f2/ and got the error message"Expected 'Pages', got 'article'Expected <Page>, got <front>Expected <Page>, got <journal-meta>Expected <Page>, got <journal-id>", along with a note "0 pages will be created from the XML...
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- Daniel Mietchen
Some more info on the XML used by PLoS and PubMed (via Richard Cave): "They are all tagged to parse against the NLM/NIH journal publishing DTD. This is a standard DTD for life-sciences publishers and all articles in PubMed Central have to be published in this DTD. PLoS articles are currently using DTD v2.0 (but we'll be at v2.3 within the next few months). Information about v2.0 is at:...
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- Daniel Mietchen
Some more on Data Transfer (via Yaron Koren): it requires XML in its own specific format - in order to get your XML into the wiki, one would first have to convert it, probably using XSLT, into the other format. Though it might be easier to just convert the XML into CSV format, i.e. a simple table of data - Data Transfer handles CSV as well, and that one's easier all around.
- Daniel Mietchen
Do check out http://developer.marklogic.com/news... , especially the bibliography at the end, for a lot of information about wiki interchange formats.
- Chris M
Thanks, Chris - this page is indeed full of interesting links, though I couldn't yet find one that would be directly relevant to our problem. Meanwhile, Konrad Foerstner has started to code a PMC2wiki converter, as per http://github.com/konrad... . It is not functional yet, so suggestions, improvements, fixes etc. are very welcome. He also pointed me to ftp://ftp.ncbi.nih.gov/pub/archive_dtd/tools/ViewNLM-v2.3.zip which may be useful to display PMC's XML as HTML.
- Daniel Mietchen
That looks good -- I hadn't known about the ViewNLM-v2.3 distribution, that it contained an XML to HTML transform stylesheet.
- Chris M
An XML2HTML conversion is outlined at http://www.science3point0.com/coasped... .
- Daniel Mietchen
Dynamic links to private tagged Mendeley collections - http://usefulchem.blogspot.com/2010...
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Yaroslav Nikolaev, Alun Salt, Roderic Page and 5 other people liked this
Now that Mendeley is providing an API, Andrew Lang has written code that significantly leverages the information in our private ONS collection. We can now create public links that return the most updated results for specific tags, including multiple tags (which I don't think you can do on Mendeley).
- Jean-Claude Bradley
Thanks MG - looking forward to the fixes but the current system is still a good start
- Jean-Claude Bradley
Pleased to see that my PHP code to access the Mendeley API has been useful (it provides the OAuth layer underneath the ONS service). I guess we'll see more hacks around the Mendeley API until the API gets updated. Slightly puzzled that the ONS code uses string matching to access fields in the Mendeley response, rather than converting the JSON to a PHP object and querying that.
- Roderic Page
@Roderic. Your code is excellent and helped a lot. I use string parsing because that's the way I know best.
- Andrew Lang
Andrew/JC - would you mind if we posted a link to this on the Mendeley support wiki? http://www.mendeley.com/support...
- Mr. Gunn
MG - that would be great
- Jean-Claude Bradley
OK, didn't want to have people pounding it and slowing it down for you, but if you say it's OK, I will.
- Mr. Gunn
MG I don't think that will be too much of a problem - that service is specific to our collection only - people will have to modify the source code to put in their own authentication info and run themselves to use for their own collections The source code is also available at http://onswebservices.wikispaces.com/mendele...
- Jean-Claude Bradley
RT @scilib: Elsevier reports on researcher interest in improving search (using e.g. SciVerse APIs) http://www.researchinformation.info/feature... /via @research_inform
Alexey, Mr. Gunn, Greg Tyrelle and 5 other people liked this
Wow! Elsevier is seriously starting to get it (probably not surprisingly). PLoS One, F1000, Mendeley et al., brace yourselves: "more than 80 per cent of respondents agreed that in the next several years researchers will use knowledge networks as a reliable source for filtering and viewing information."
- Björn Brembs
I suppose the question now is whether they think they understand social discovery well enough to implement something useful themselves or if they want to provide data services to those who do understand it already.
- Mr. Gunn
I'm hoping they have the understanding and foresight of The Scholarly Kitchen :-)
- Björn Brembs
+1 Bjoern. They should hire Kent Anderson to direct their efforts. :-)
- Bill Hooker
A long list of things I don't like about Mendeley - http://scienceoftheinvisible.b...
Peter Miller, Khader Shameer, Graham Steel and 8 other people liked this
"I feel bad. The nice folks at Mendeley just sent me a T-shirt and I'm going to complain about their product. But I want to like Mendeley, really I do. I want it to take over from CiteULike as my online reference manager because, well I'm not sure really, I just feel it should. But I'm still struggling, every time I go back, I just don't get it. Sure it's pretty, but it's a lots less functional for me than CiteULike, which though rough round the edges, "just works". So I thought I might be able to make some progress by facing my demons. To do that, I made a list of all the things (I could currently think of), that I feel are holding me back so that people can tell me what an idiot I am. Yes, really - don't hold back."
- AJCann
from Bookmarklet
AJCann, what cool features should they add, to make 'your' communities split? You indicate being able to find FOAFs based on shared literature references... anything else? Mendeley aggregating comments from 3rd party sources (PostGenomic, Cb, ..., whatever general bookmarking service), like PLoS does with article metrics?
- Egon Willighagen
Mendeley has had a lot of publicity and that in itself will attract people who I might want to track. The other possibility is that CiteULIke might go away, but that would be simpler, because then Mendeley would be the obvious network. The stats they provide right now are getting close to PLoS article level metrics, but again, detailed stats are a premium feature (or likely to be in...
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- AJCann
A follow up: http://chem-bla-ics.blogspot.com/2010...
- Egon Willighagen
You pick it right at the top. You don't like PDFs. Mendeley is most effective for the usecase which includes keeping a pdf on your computer somewhere and wanting to read it elsewhere. I just don't think it fits your use case that well...
- Cameron Neylon
Martin Fenner says he loves PDFs - but he still prefers Papers to Mendeley.
- AJCann
True. But I can't help feel your objection would be a lot less if the interface put the URL links much more front and centre. I mean, you don't have to use the desktop client at all for what you want as far as I can see?
- Cameron Neylon
I am not using the Mendeley client at all... just the web...
- Egon Willighagen
I have been advised that most of the power currently lies in the desktop client. The web component is where the social (such as it is) lives.
- AJCann
Will there ever be one reference manager that fits all needs, is fun to use, and free or affordable? Not very likely. So I think it's good that we have several alternatives, and that also includes Endnote.
- Martin Fenner
+1 Martin
- Graham Steel
The discussion desktop client vs. Web-based also very much depends on how you write your papers. I very much hope we will at some point have a collaborative web-based solution for paper writing (and Google Docs is definitely not the answer). This will change the reference management market completely.
- Martin Fenner
The power lies in the client if you want to manage and/or annotate pdfs or format references in a document. It would be nice to have that annotation possibility for web based versions of papers I have to admit. That could get very interesting if there was an overlay style thing going on.
- Cameron Neylon
+1 Martin
- Jennifer Melinn
I like and use webapps for most things I do, but for heavy-duty tasks, it's just not there yet. We're going to have to wait for further developments around HTML5 before a web-based service can give similar performance to a desktop app, and we'd should also consider how we can serve everyone as opposed to just those who live where broadband access is easy-to-get. I had hopes for Wave (and I still have hopes for the Wave protocol).
- Mr. Gunn
Seems to me that there are three spaces a reference manager can operate in: 1) desktop (incl. mobile), 2) web, 3) API. Mendeley is trying to cover all three, and it feels like their priority is 1 > 2 > 3 which is understandable. However, if they reordered things 3 > 2 > 1, then things would get a lot more interesting. If the web site and the desktop client were built on the same (open)...
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- Roderic Page
I hear ya, Roderic. We've hired new people and are working as hard as we can to fill out the gaps in those areas. Hopefully the API as it matures will allow people to build stuff that we just don't have time to get to (also like Twitter).
- Mr. Gunn
Google Docs is good for getting the text written, but for the markup and citations you have to use something else.
- Mr. Gunn
Marius, I think online writing tools shouldn't just be copies of desktop word processors with collaborative features thrown in. So it's not just about adding reference management and a few other small things. A scientific paper is a very structured document and the writing tool should reflect that instead of offering font sizes, line heights and similar formatting options that have no meaning for a scientific manuscript.
- Martin Fenner
Roderic, I would love to see reference management being built around APIs. But everybody would want to become the Twitter or Facebook of this API ecosystem, including Mendeley, Scopus and Web of Science.
- Martin Fenner
I don't think there is a market for an affordable desktop application that understands the structure of a scientific document, runs on Windows, Mac and Linux, does reference management, and has collaborative features. Remember Publicon from Wolfram Research? So I think that this scientific writing tool has to be web-based, and HTML5 should be good and fast enough for it. Lemon8-XML is a good start http://pkp.sfu.ca/lemon8
- Martin Fenner
Martin, what a very, very interesting idea. In my undergrad classes, I use "templates" that guide students through writing scientific papers, and students generally like them, but what they'd really like is if I could have "work boxes" next to each bit where they could enter text, hit a button, and poof! Some kind of draft is created. I tried to do that using forms, but do not have the...
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- Mickey Schafer
Martin, the trick is who will do it well. Web of Science & Scopus will be too bound to their commercial interests to do it well, and have no community. Maybe I'm an outlier but I don't use either of these tools. Google is my friend. Mendeley is well positioned to do something in this area, but they'd need to deal with the open data issue, which so far they've not really addressed.
- Roderic Page
Mickey, take a look at the Microsoft Word Article Authoring Add-in http://blogs.nature.com/mfenner...
- Martin Fenner
Roderic, I completely agree. But will be interesting to watch how the new Elsevier SciVerse platform opens up to third-party applications. And then there is Google (which currently doesn't look that interested in scholarly literature) and Microsoft Academic Search.
- Martin Fenner
Thanks, Martin. I was not aware of the add-in, though I'm not sure that the undergrads need that kind of power -- but using the template function in Word might work...hmm. This may be too much for my brain on a Friday afternoon!
- Mickey Schafer
Just to play devil's advocate a little: I don't think it's a good idea to have a tool impose structure on a ms. My ideal would be much closer to a fast, lightweight text editor that gave good, intuitive control over formatting (then it's easy for me to structure my document for myself) and could interface with a reference manager to handle citations. The idea of using forms or templates to write a paper gives me hives!
- Bill Hooker
Martin, I'm not sure how many 3rd party apps will wind up on Sciverse - my impression is that Elsevier considers it a closed system. I would also argue Google is very intererested in scholarly literature (Google Book Search) but not necessarily in schol. research journals. There are journals in GBS but no extra search fields of identifers for articles. I agree with everything else though.
- Elizabeth Brown
We will see how 3rd party apps around SciVerse, Mendeley, CiteULike, Endnote and Zotero develop (they all have APIs). Twitter claims that 250.000 apps are using the Twitter API.
- Martin Fenner
Mendeley could add some FriendFeed features and easily compete in the science social media space. Wouldn't that be interesting?
Jan Wessnitzer, August Muench, Björn Brembs and 5 other people liked this
And on that note, I wish they offered an RSS feed of my dashboard updates.
- Walter Jessen
Feeds are definitely coming in the web updates. What friendfeed features would you like to see? A more dynamic activity feed where things automatically bubble up to the top? Surfacing of friend-of-a-friend items?
- Mr. Gunn
Perhaps the ability to ask questions such as this and provoke discussion? ;)
- Steve Dennis
Yes, I think that would be nice! I guess with the groups feature coming, that ability will kinda be there, right?
- Mr. Gunn
@MrGunn Yes, a dynamic activity feed would be great. Be sure to communicate to Mendeley that comments on an item should also cause it to bubble to the top. Great to hear feeds are coming - looking forward to the improvements.
- Walter Jessen
Programming Things I Wish I Knew Earlier - http://teddziuba.com/2010...
Peter Miller and Roderic Page liked this
RT @ReaderMeter: The alpha of #ReaderMeter is live! Check it out and spread the word: http://readermeter.org
suelibrarian, Steve Koch, Roderic Page and 2 other people liked this
Cute - but the numbers seem unrealstic. I have higher stats than Stuart Schreiber and Brian Shoichet (and other big wigs)? Unlikely :)
- Rajarshi Guha
yeah :) .. highly biased ... but some of it is due to alternate spelling
- Pedro Beltrao
My own stats are not much lower than those of my mentors :-) My Hr says it's 5 but my no. 5 paper is listed as having 4 bookmarks...
- Björn Brembs
Actually, digging deeper, this is really cool stats! Once the userbase of Mendeley is large enough, this will be excellent!
- Björn Brembs
Are the problems with the service or the underlying data tho? For instance Bjorn is missing several bookmarks that you can find if you search on Bjoern as opposed to Björn
- Cameron Neylon
I'd say the data fundamentally - the current data is likely not representative of general readers (and also there's the issue disambiguation etc)
- Rajarshi Guha
Try having a name like Chris Miller. Pretty much any literature search is useless. Not this service's fault, but it's another app highlighting a fundamental problem. What happened to all the momentum behind unique researcher ids?
- Chris Miller
I've sketched how extending ReadMeter by enabling users to log in to their Mendeley account and claim the papers they've authored may help address the author identity problem. See http://iphylo.blogspot.com/2010...
- Roderic Page
@Chris: It looks like there's not much movement behind ORCID (other than people claiming that Thomson Reuters is abusing it for their own ResearcherID).
- Björn Brembs
I find it amazing that this idea of author ID has been kicked around for so long without a solution. I remember we talked about it at Nodalpoint .. some 10 years ago maybe ?. It might be hard to do but it is potentially so useful that it would be worth having some sort of iterative approach even if there were some problems with the initial implementations. How hard can that be ? there just needs to be a sufficient number of publishers/databases agreeing on the common development.
- Pedro Beltrao
@Pedro: if I may hazard a guess: because our literature is fragmented. If we all had accounts in the one place where we publish our papers, we'd each have had a unique ID since the advent of the internet and nobody would even be asking how or why.
- Björn Brembs
Chris - I think I can beat you in the common name game. :) I think the bigger issue with names is the formatting - full names, initials, married, translated characters, etc. Even if one database had all the info there'd be variants based on journal submission requirements and indexing limitations.
- Elizabeth Brown
Touché, Elizabeth :)
- Chris Miller
I would disagree that there is not much movement behind ORCID. It is just hard to see. But people (including myself) work hard behind the scene on technical and business issues.
- Martin Fenner
from iPhone
Passengers near me & Lance Price on way to #microbiome mtg got earful: anthrax, penises, vaginas, wounds, microbes everywhere
Peter E Midford, Steve Koch, Roderic Page and 4 other people liked this
I really have to question the airline security procedures if, after all that screening, you can still end up with an ear full of penises and anthrax.
- Rutger Vos
New blog post: Elsevier launches SciVerse, integrates ScienceDirect + Scopus + More http://blogs.nature.com/mfenner...
Michael Habib, Lambert Heller, Kubke and 11 other people liked this
My first SciVerse impresssion: one big advertisement... where did they hide the actual functionality??
- Egon Willighagen
I like the promise of 3rd party application and open APIs. With the caveat that this might become one big data silo. For biomedical literature searches I prefer Scopus over PubMed.
- Martin Fenner
@Neil, I think Rafael Sidi is definately going in the right direction, and so does Anita de Waard... they need some further guidance, I guess... I have not had enough time to talk with either of the two, despite interest from all parties...
- Egon Willighagen
@Martin, yes, the Open API part sounds promising indeed... from the GUI side, there is a huge gap between the Google Search web form simplicity, and what SciVerse now offers... big HCI problem for Elsevier here, I think.
- Egon Willighagen
@Egon, I agree, the SciVerse interface is not an improvement over Scopus/ScienceDirect. But I usually have low expectations...
- Martin Fenner
Ok, this looks like it's only information so far and nowhere to play around with it and test any of the functionality? I can't get past the infomercials, at least...
- Björn Brembs
@Björn - agreed.
- Graham Steel
As before, you need an institutional subscription to use SciVerse/Scopus/ScienceDirect. The functionality is there since this morning.
- Martin Fenner
It will be interesting to see if an institution this size CAN embrace open data, even with advocates like Rafael.
- Mr. Gunn
this development is interesting in that Elsevier is branding other databases with the SciVal logo and promoting interfaces to their bibliographic data outside the library and scientists. This is the first commerical academic publisher to do this.
- Elizabeth Brown
The functionality is at http://www.hub.sciverse.com/action... if you have access. I'm disappointed in the blurk-yellow they chose for its theme, but at least they haven't inflicted that on ScienceDirect or Scopus. #shallow
- Deborah Fitchett
CtrlV-CtrlX-Ctrl-Z.jpg (JPEG Image, 500x500 pixels) - http://www.likecool.com/Gear...
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Antoine Vekris, Steve Moss, Endre Sebestyen and 6 other people liked this
Mendeley is going to be open source - http://blindscientist.genedrift.org/2010...
Sathishk, Roderic Page, len hat and 7 other people liked this
That would be an interesting and welcome move... client and server side?
- Egon Willighagen
omigod! Is pn a sleeper mole ... for mendeley?
- Bosco Ho
This is something that I so want to be true, like the iPad Mini, more money for research, or Bill Gates turning out to be one of the good guys. Oh, wait...
- AJCann
What is the evidence for this claim? Also, this is another blog post that would be easier to read if there were a standard html markup for sarcasm.
- Matt Leifer
connotea code is open source... obviously not a magic bullet for making things better
- Benjamin Good
@Benjamin: indeed, Open Source != Good Project
- Egon Willighagen
Mendeley, Scopus, Talis – will you be making your data Open? - http://wwmm.ch.cam.ac.uk/blogs...
Martin Fenner, Jason Priem, Nic Weber and 4 other people liked this
This is the $64 question. There is also the question of what does "open" mean? Does it mean a dump of all the data (à la GenBank), or does it mean API access?
- Roderic Page
Mendeley’s side - http://blindscientist.genedrift.org/2010...
joergkurtwegner, Roderic Page, Abhishek Tiwari and 5 other people liked this
PARENTAL ADVISORY: Explicit Rant
- marcin
... or a response to censorship attempt.
- pn
I don't understand the phrase "they publish for free, but you have to wait" in connection with OA or PLoS -- in fact the context is not quite clear from that paragraph -- can you expand on that a bit?
- Bill Hooker
I agree, not clear at all. What I meant was that those who cannot pay for the publication (ie no grant money) will eventually get published, but will have to wait.
- pn
To which it should be added: Although it may not be relevant for a particular specialty, the fact--FACT--is that a smaller percentage of OA journals have author-side fees than do subscription journals. Most OA journals do not charge author-side fees at all.
- Walt Crawford
What? Say that again. US$1350 for PLoS ONE, £1125/US$1745/€1375 for BMC Bioinfo, Bioinformatics Open Oxford Regular charge - £1275 / $2250 / €1900, etc, etc
- pn
Paulo, there are at least six different studies showing that the majority of OA journals do NOT charge author-side fees. They may not be the ones you know, but they are in the majority. See http://www.sennoma.net/main... and http://www.sennoma.net/main...
- Bill Hooker
In addition, there is one study (http://www.alpsp.org/ngen_pu...) which found that the majority of TA journals DO charge author-side fees, in the form of page and colour charges, in addition to their subscription fees. I had a look at some of these fees (http://www.sennoma.net/main...,...
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- Bill Hooker
There is an important caveat to my last comment: on the liblicense mailing list, one of the members took issue with my estimate of the average author-side fee charged by TA journals, saying that in 40 years as a publisher he'd hardly seen any such charges. He claimed that Elsevier never levies such charges, nor do a couple of other big publishers. I readily admit that my estimate is...
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- Bill Hooker
Yep, my ignorance then. But this matter was more related to the third-world, "poor" researcher, than to the "first world" pampered one. Here in NA, everyone has a grant or the institution has moneys asido to pay for those things. These are part of the game, but you still has a second-class of researchers that maybe lagging behind (and that's unavoidable). At the same time, I think there must be some kind of "advantage" for people to adopt OA, and a guy from Mendeley might not be the best example.
- pn
That (third-world researchers' access to publication) is a topic of much discussion at PLoS ONE, where the fee waiver is designed to help redress the imbalance. Ditto for BioMed Central. I've never heard of a waiver request from a third-world researcher being turned down, but I did hear of a US grad student being turned down (I forget which journal it was). I don't know of any TA journal that waives its page and colour charges (but I bet plenty of them do).
- Bill Hooker
@Paulo, I have another question, if you're not already sick of me in this thread. Can you point to some specifics about the censorship/thugs/threats? I, too, find Mendeley hype a bit overwhelming, but that's a much less serious issue. I'd like to know more about the censorship stuff.
- Bill Hooker
I asked for a waiver from BMC Bioinformatics as an unfunded grad student, and they knocked off $440 USD. Unfort that still left an unmanageable $1,360. Several people suggested I should "ask twice" and they would knock it down lower, but this sure isn't clear to people who aren't in the know! details: http://researchremix.wordpress.com/2009...
- Heather Piwowar
@Bill, I think the stat that most journals don't charge OA fees is a useful one to highlight that many OA journals are free, but a frustrating one to encounter because it doesn't reflect reality about OA journals where (I bet) most authors want to publish. For example, I wonder what the percent is for OA journals that are indexed in PubMed. I bet much lower.
- Heather Piwowar
Heather: This gets very tricky. "Most authors" who aren't in biomed/medical areas (and, you know, there *are* other areas of research) probably don't much give a damn about PubMed indexing. The "OA means unsupportable author fees" cudgel is used too consistently by anti-OA people to let it pass. Then there's the elephant in the room: *Should* author-side fees be as high as they are in, for example, BMC and PLoS journals?
- Walt Crawford
Hmm. For someone who gave up writing about OA in Cites & Insights, I sure am writing a lot about OA lately (including, notably, an ALA Editions Special Report to come out next year).
- Walt Crawford
Walt, sure, of course. I just gave an example I am familiar with. My point is that it can be frustrating for an author to hear that most journals don't charge OA fees, and then go look for a journal to publish in that doesn't charge OA fees, and find few to none that are appropriate for their paper.
- Heather Piwowar
@Heather, as per my examples above, the TA journals where (one could bet) most authors want to publish probably charge *higher* author-side fees than the high-profile OA journals. It would be interesting to stratify by IF/similar, but one of the things I hope OA will do is to kill this idea of journal prestige stone dead. If it shows up in PubMed or GScholar, there's no difference in visibility between PLoS Biology and J. Obscure Res.
- Bill Hooker
And, relating to Walt's comment about elephants and OA author side charges, that kind of consideration is exactly what will create market pressures to bring prices down and demonstrate real value for the costs that remain.
- Cameron Neylon
@Bill, I hear you about journal prestige which is why I suggested "indexed by PubMed" as a filter to look through for one domain, because it does offer objective value to authors in biomedicine. anyway. I do hope the "can't afford to publish OA" idea will die a well-deserved death + three cheers for PLoS waivers.
- Heather Piwowar
@Walt, Cam: Ted and Carl Bergstrom were the first I know of to point out that the best way to find out what a journal should charge is via an efficient market -- which we can only have when journals are economic substitutes as in 100% OA, not complements as in the subscription model.
- Bill Hooker
@Heather: interesting questions, just how do the sets "indexed in PubMed" and "OA" overlap? How many in the intersection, what % of the whole OA set does that comprise, do they charge author-side fees, etc?
- Bill Hooker
I'd love to see some of this data, as well. Another common point raised to dismiss OA is that they're not widely read vanity presses, so Pubmed inclusion goes a little ways to addressing this.
- Mr. Gunn
Bill: You will get no disagreement from me. And finer-grained comparisons could be useful, given folks with the time, resources and energy.
- Walt Crawford
Is there a best-practice XML schema (in use or in development) for cleanly citing specimens, biological collections, etc mentioned in a research paper, to facilitate machine readability? Looking for best-practice recommendation for authors.
Daniel Mietchen, Claudia Koltzenburg, Bill Anderson and Roderic Page liked this
Probably nothing new to you here, but it's all I got: http://www.bgbm.org/tdwg..., http://rs.tdwg.org/dwc..., http://www.codata.org/taskgro...
- Bill Hooker
There's been some work on this (e.g., TaxonPub), albeit pretty preliminary. An example is http://dx.doi.org/10..., which has a XML version that uses BioCol LSIDs for biological collections. See http://dx.doi.org/10... for some more details. Note that these developments focus more on marking up the content of a paper, rather than providing metadata about that paper.
- Roderic Page
Fuge can represent structures for specimens, but its quite generic. Alot of the representation of specimens and cell lines are usually incorporated within larger models. If you are just wanting an ID against some specimen, you may consider using ontologies, such as the cell type ontology, or OBI which deals with the notion of specimens.
- Frank
No TaxPub schema that I'm aware of, but not sure why you'd need this. The NLM journal article tag suite (of which TaxPub is an extension) is defined by a DTD (there's a schema, but they actively maintain the DTD).
- Roderic Page
@researchremix Can you clarify what you mean by "recommendation for authors"? Authors in taxonomy/systematics mostly use MS Word, so citing specimens/collections will, at best, be a URL (and we've precious few of those). Nobody writes papers in XML, so machine-readability is more an issue for publishers (in the same way that publishers add DOIs and PubMed ids to the list of literature...
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- Roderic Page
For species, I found the one at Zookeys quite neat - example: http://pensoftonline.net/zookeys... (hover over species name, or right-click on it).
- Daniel Mietchen
@rdmpage Agreed, and "recommendation for authors" may have been premature. Working on a best-practices article, and we want to highlight ways to make these contributions more traceable. I think the idea is to allow authors to communicate this information cleanly to publishers, then encourage publishers to reveal it in a systematic way. In the mean time, authors could include the XML as supplementary information as a not-terribly-useful but heart-in-the-right-place first step.
- Heather Piwowar
PLoS Reader archive search is finally in the queue for Apple review. Next up is hypertext reading a la @rdmpage: http://vimeo.com/12643047
Roderic Page liked this
Can people suggest some bloggers who blog predominantly about online science to go into an S3.0 aggregator?
Steve Koch, Sandeep Gautam, Michael Nielsen and 6 other people liked this
clarify "online science" please
- Christina Pikas
clarify "science 3.0" please
- Chris Miller
Chris - it's the name of Mark's site, that's all.
- Michael Nielsen
Premoninantly? I'd start at the blogs and blogrolls of people like Cameron Neylon, Dorothea Salo, Jean-Claude Bradley, Peter Murray-Rust, John Wilbanks, Foldit, Christina Pikas, Sarah Kendrew, Terry Tao, the open dinosaur project, Bora Zivkovic, and Galaxy Zoo, and spider out from there. Its seems to me to be really hard to make some decisions: should you put mathematicians like Terry Tao (and, by now, dozens of others) who are actively _doing_ science online on your list?
- Michael Nielsen
Christina, I'd like to aggregate the blogs of those whose posts would be interesting for those who talk about these subjects at science3point0.com. Chris, we were science 2.0 but we had to change it http://ff.im/nTPXj Michael, thats brilliant, thanks so much. I'll start with that and see how it looks, if it doesnt get too much we may start branching out into more specific topics, the likes of Terry Tao etc. Thanks again Michael, can I assume that you wouldnt mind being included?
- science3point0
Yes, of course, that's fine.
- Michael Nielsen
ah, okay. Sorry for the snark.
- Chris Miller
@ChrisMiller, fine with me :-) @mark@science3point0 maybe we should rather start using "S3.0" as this community's brand name? it would still mean "science3.0", but look more like a brand? or not?
- Claudia Koltzenburg
+1 @Michael "should you put mathematicians like Terry Tao (and, by now, dozens of others) who are actively _doing_ science online on your list?" - yepp, and I think the whole paradigm of "aboutness" (like in "about online science") might change
- Claudia Koltzenburg
I think there is value in an aggregator that focuses on the issues and studies around the proceses of doing science online. Also agree that seeing some real uptake in specific places is really encouraging.
- Cameron Neylon
I was wondering if you want 1) people who do science online 2) people who discuss doing science online 3) people online who discuss how science is done (I might fall into this category as much as 2) 4) some combination? Heather Piwowar's blog is an obvious choice - it probably hits all of these categories
- Christina Pikas
Obviously some form of categorisation is the way forward. I was thinking of starting with a general aggregator of all categories and then devloping it into the subsets you have suggested. It all gets a bit Venn Diagram like very quickly though.
- science3point0
I agree with others - I would identify the scope and purpose carefully before assembling a list like this. I would especially try to avoid overlap with the new scienceblogging.org site. Also there should be a link for this in the OAD wiki.
- Elizabeth Brown
I've made a start, feedback always welcome - Made with the blessing of the scienceblogging.org team http://bit.ly/bcwbXH - Theirs has waaaay more content!
- science3point0
Bio/Biomed prefers first-person. Alas, LIS doesn't. Do I use 3rd-prsn for info science or be change I want to see? Research is done by ppl.
Roderic Page liked this
Good to know. My (limited) experience is based on sharp criticism from iSchool folks on my use of first-person in thesis and now an ASIS&T poster.
- Heather Piwowar
Be the change. 3rd person leads to circumlocution and waffle. :-)
- Bill Hooker
Meh, change it up. Use of third person can lead to elevated risk of passive voice in writing, which is its own brand of annoying.
- John
Alex thinks you should be deliberately anachronistic.
- Alex
I've both used 1st person and seen it, even in so-called scholarly LIS papers. There are a few journals that stay as far away from readable English as is editorially possible, not to name **cough J plus an abbreviation Heather used cough** names, but it's certainly not standard malpractice.
- Walt Crawford
Be the change! And ASIST sure as heck needs some. FTR I <3 them but boy do they need to grow/change.
- Mar₭ Liŋdŋer
from iPod
thanks for feedback, background, and backbone, everybody. very useful.
- Heather Piwowar
given a doi or pmid or url or reference, how do I determine whether a paper is open access?
Dan Hagon, Jodi Schneider, Piotr Byzia and 10 other people liked this
from pubmed, you can do it by ANDing "pubmed pmc open access"[Filter] so for example if you have two pmids, one in BMC Bioinformatics (OA) and one in Bioinformatics (not OA) then this will return the OA one: (20565810 20595460[uid]) AND "pubmed pmc open access"[Filter]
- Heather Piwowar
I also have some python code to return a list of 0/1 depending on the filter results, if you plan to do this often. It uses the eutils library and my custom pypub library, available at github, but woefully underdocumented so ask if you need help getting it going :) http://github.com/hpiwowar
- Heather Piwowar
is the question to idenitfy a paper as OA solely from the reference? I don't know of any schemes that do this.
- Elizabeth Brown
That's what I was thinking. The Pubmed filter tip is a good one for doing this the other way around though. Just from the reference or the number it doesn't seem like there's a good way to tell. There would need to be a comprehensive resource listing open access sources, wouldn't there? This also makes me think about collecting, particularly guitars, where if you study enough you can...
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- Jennifer Melinn
I agree, and would add it would be helpful to have a similar identifer or scheme to identify peer-reviewed sources too. That way the argument that OA journals aren't peer-reviewed could be refuted very easily in a quantifiable way. It's true there's the DOAJ available so it could be done.
- Elizabeth Brown
Given that publishers themselves are hazy as to what "open access" means this will be messy. It would be great if publishers embedded appropriate metadata in the article (HTML or PDF) with an explicit license, but this may take a while to happen. I had a quick look at the meta tags in HTML on various journal sites. OUP adds a Google Scholar-style tag <meta name="citation_access"...
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- Roderic Page
I agree Roderick that embedding content is the way to accomplish this - either with metadata or codes in the DOI, URL or html. Unfortunately publishers are behind in this way of thinking, possibly because originally full-text access happened at the publisher site, while the indexing occurred at the licensed A&I source. These two channels are collapsing and the original question is evidence of this disconnect.
- Elizabeth Brown
Many publishers now seem to "get" the idea of embedding metadata in their web pages (see http://www.monperrus.net/martin...), so they could provide this additional functionality pretty easily. Of course, they'd need to talk to the companies that provide their web infrastructure, which means they'd need to see a reason to do this.
- Roderic Page
BibApp does a fairly good job of providing Open Access information, using the Sherpa/Romeo database. For this BibApp maintains a separate journals database, something that almost no reference manager does.
- Martin Fenner
By "Open Access", you presumably mean "Libre Open Access"? (I think everyone except Stevan Harnad does these days.) On eUtils look up its PMCID, then get do an eFetch on the PMCID and extract the license from /article/front/article-meta/permissions/copyright-statement in the XML? http://eutils.ncbi.nlm.nih.gov/entrez...
- Joe Dunckley
I agree embedding metadata is common among publishers but embedding additional info in a DOI or other identifer/pointer for an article is not high on their priority list. I think the concept that by looking at the basic bibliographic information and/or a link to the content provides context on the publishing model, if it's peer reviewed, externally funded, etc. - is a very new idea. Our students ask for this type of info in their searches and it's not standardized or available in some literature indexes.
- Elizabeth Brown
PLoS "gets it" - open access CC content and RSS makes it possible to create new free Apps http://brow.tumblr.com/post...
Jim Croft, Roderic Page, Mr. Gunn and 2 other people liked this
Yes, but that's not the point. The point is the apps to date recreate paper in digital form, which is a wasted opportunity. It's ironic that a radically new publishing approach has spawned very conservative apps. Is turning pages on PDFs all we aspire to in an app?
- Roderic Page
from iPhone
I don't think it's all we should aspire to. But neither is it a waste to do it well. "Don't Make Me Think" is the title of a well known book on usability and I think that's a great description of this app. You want to read PLoS journals? Here. This app lets you read and gets out of your way. I hope other apps for using content in other ways do come about - from your post it sounds like you have a lot of great ideas. But I think reading is still going to be a popular use of journal text.
- Jenny Reiswig
Given that the whole point of "apps" is to get people to pay for website content, I'd really like to see something more than shovelware. Use the unique aspects of the platform - such as contacts or location or the fact that people will have it with them more places than a laptop, not just the touchscreen. What PLoS "gets" is that OA content allows new forms of re-use. I'd argue that...
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- Mr. Gunn
I have to agree with Rod on this. Replicating a paper medium on screen is at once kitsch, frustrating and irritating. Yes, indeed the application should 'not make me think', but this applies only to the UI. The user should not have to think about what buttons or gizmos do what and ideally they should be the same as the native operating environment - and not only should they work the...
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- Jim Croft
Idea: I'd like to see what Tom and Rod can produce by working on this together. As Tom noted, the app was his baby, not an assignment from PLoS, and I'd love to see what the people in the community can do when they combine their skills and talents and ideas together....
- Bora Zivkovic
@mrgunn the point of apps isn't "to get people to pay for website content" -- if this were true there'd be no free apps, and no apps that didn't use the web. But I agree we need more than shovelware. The Papers app for iPhone/ iPad is one step in this direction (search, annotation, wireless sync with Mac), although still fundamentally a PDF viewer. @BoraZ PLoS could be proactive and create a challenge event to get more people interested in exploring what can be done.
- Roderic Page
@BoraZ, you may get your wish. Tom and I are exchanging emails about handling XML as well as PDFs, and I've put the code for my crude demo online at http://code.google.com/p... (MIT license).
- Roderic Page
Excellent news, Roderic :)
- Graham Steel
Lovely! Excellent! So much more fun when things happen bottom-up, by people in the community wanting to do stuff, than if PLoS starts ordering people around, top-down, telling them what to do. Better stuff is birthed that way.
- Bora Zivkovic
SenchaTouch is pretty impressive on the iPhone / iPad - going to try Android & Palm now... http://www.sencha.com/product...
Roderic Page liked this
Check out the new, free, PLoS iPad app - http://everyone.plos.org/2010...
Kubke, Roderic Page, Bora Zivkovic and 6 other people liked this
The PLoS iPad app is a nice PDF reader. A search function would be very nice.
- Martin Fenner
As per the blurb, Tom Brow is working on that, which is nice.
- Graham Steel
Indeed - this is basically a PDF reader pulling from our RSS feeds. 'Proper' search would be nice, but Tom developed it right in the middle of us releasing our new Search functionality. Now that is done, there are opportunities for stable screenscapes, as well as our future development of an API.
- Peter Binfield
I very much like reading papers on the iPad. But I worry that every publisher starts his own iPad app, creating a silo.
- Martin Fenner
Well, only 2 publishers have even bothered so far...
- Peter Binfield
Quite.
- Graham Steel
Oh yes, and ours is free (!)
- Peter Binfield
Martin, I agree and am very interested in building a DOAJ-wide equivalent. The main obstacles are differing data interfaces (RSS, XML API, HTML only), differing licenses (only some are CC), and differing page layouts (reader needs to crop headers and footers to preserve screen space). Also, it's not clear who would fund such an app, and charging users for it could be perceived as contrary to the spirit of open access.
- Tom Brow
Hi Tom. Nice to see you on FF.
- Graham Steel
Tom, these are all valid points. I would like an iPad app that allows me to subscribe to journal table of contents RSS feeds, and would pull in the PDF (via the DOI) of those papers I want to read in fulltext. Version 2 of the app would consider using something else than PDF. The Nature iPhone app uses ePub, which allows for some interesting features, mainly linking of references and...
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- Martin Fenner
Duncan, you mean that iSilo handles RSS feeds and retrieves the fulltext papers? Papers for Mac does something similar, but not using RSS (rather a custom PubMed search for recent papers in a particular journal).
- Martin Fenner
@Duncan, sorry for not getting it. Another interesting observation: iPad can't display Cell Press "Article of the Future", because Safari browser doesn't understand Flash (and Apple has no intentions of changing that).
- Martin Fenner
I would pay for a paper reading app and I don't think it is contrary to open access since there are many ways to read if freely online. These sort of projects are exactly the type of thing that publishers *should* making money off. Tools that make it easier to find/read/etc the content.
- Pedro Beltrao
+1 Pedro.
- Bill Hooker
+1 Pedro.
- Martin Fenner
In the style of #eurovision And tonight's results are now in from Scotland - and the vote goes to.....??? +1 Pedro (10 points)
- Graham Steel
Seeking ~working examples of applications running on semantic web technology. Links anyone?
Egon Willighagen, Roderic Page, Andrew Su and 2 other people liked this
Gene Expression Altas http://www.ebi.ac.uk/gxa/
- Frank
Thanks frank. Does this atlas use RDF or OWL anywhere under the hood?
- Benjamin Good
thanks again frank, I was looking for OWL evidence in the gxa API but didn't see it in the doc. Can you get RDF versions of the query results (like the json and xml) ?
- Benjamin Good
Not sure if a doc tagger is what I was after for my purpose, but thanks for the link. I want to focus on things that couldn't really exist without the semweb standards. that is a pretty cool though...
- Benjamin Good
Bioclipse: see some recent screenshots here -> http://annziproject.blogspot.com/2010...
- Egon Willighagen
Nice one Egon (and student). I was very happy to find your endpoint http://rdf.farmbio.uu.se/chembl... alive, responsive, and with a working example that was easy to locate. Hope you can keep it going!
- Benjamin Good
GoPubmed: http://www.gopubmed.org
- Chuck Borromeo
Also, NextBio http://www.nextbio.com
- Chuck Borromeo
Are GoPubmed and nextBio using RDF or OWL in their implementations? I know they are both 'semantic' but I (though I know opinions will differ) won't attach the semantic ~'web' to them unless they are making use of the standards. (we've had semantic technologies for almost as long as we have had computers - i think the semantic web is different...)
- Benjamin Good
Hi Ben, your initial post didn't mention the OWL and RDF requirement :) Both companies are private entities so their information about their knowledge engines is a bit sketchy. However, I think both are scouring the web and converting data into RDF and OWL. They both discuss their ontologies and GoPubmed says they welcome inquiries into including their system in your own application.
- Chuck Borromeo
It did say semantic ~web though ;).
- Benjamin Good
Engage or become irrelevant - http://cameronneylon.net/blog...
Roderic Page, Casey Stark, Mr. Gunn and 16 other people liked this
Friday and Saturday last week I had the privilege of attending the first Sage Congress. Hopefully this will be the first in a series of posts that cover that meeting because there is simply so much to think about and so much to just get on and do. This is not a post about public engagement work by scientists. It is not about going to schools and giving talks. It is not about engaging with the main stream media to present your work to the great unwashed. It is about engaging with the people who will be driving your research agenda within ten years, about how the way researchers connect with society will be changed over the next decade whether they like it or not.
- Cameron Neylon
pq:"“The public” is not some homogeneous group of barbarians at the gate of our ivory towers." No no, of course not. It's a highly heterogeneous group of barbarians, and they long since over-ran the gates of the ivory towers. :-) (Obdisclaimer after that sort of comment: I agree with Cameron, that this is largely a good thing.)
- Bill Hooker
This is a fantastic post.
- Heather
You're right of course Bill. It's just that most academics continue to assume that they're the hired help...
- Cameron Neylon
... when in fact it's we, the researchers, who are exactly that -- the hired help. I've said for years that science should be viewed as a service industry (even if it is really, really slow service).
- Bill Hooker
Yup, slow and surly for the most part. I have to admit it's not always obvious how to go about doing this kind of thing effectively. But step one, find the right community.
- Cameron Neylon
I think I've fixed it - though I'm not sure how, are you still seeing it?
- Cameron Neylon
Ok, think it's fixed now - I've got some plugin incompatibility issues I need to work through obviously...
- Cameron Neylon
Provocative title and I like the thinking
- joergkurtwegner
Great post! I discovered this via Gilles Frydman's Twitter feed (@gfry) in my browsing around the web pages and Twitter feeds of participants at the Health 2.0 Conference this week. At the risk of mentioning kindred spirits you and/or your readers may already be aware of, Douglas Rushkoff gave a talk at SXSW earlier this year on <a...
more...
- Joe McCarthy
I like Gilles post at http://e-patients.net/archive... making a case for the concept of "patient as platform" which is a great soundbite that captures my view well. Sounds like the panel was really interesting certainly.
- Cameron Neylon
RT @mekentosj: To celebrate the Ars Design Award, Papers for iPad will be available for only $9.99 during the WWDC this week! http://mekentosj.com/news...
Roderic Page liked this
I just started using iPhone yesterday. papers for iPhone useful app? I love papers on my mac...
- Heather Piwowar
from BuddyFeed
I like it on the iPad a lot, haven't used it on the iPhone that much...
- Euan
Why I won't bother changing anything in Wikipedia: http://en.wikipedia.org/wiki...
Jim Croft, Peter Miller, Roderic Page and 2 other people liked this
We need a distributed format for managing knowledge, that allows branching versions tailored to particular user groups.
- Mike Chelen
Mike, I was just thinking the same thing! We need to get Wikipedia into something like git so that each person can choose to pull the edits from the branches that he or she likes.
- Lars Juhl Jensen
And I'm not the first to get that idea - take a look at the Levitation Wiki project: http://levit.at/ion...
- Lars Juhl Jensen
There is an ongoing need for distributed wikis. Interwiki links http://en.wikipedia.org/wiki... were one attempt to address these issues, which can include both trust and availability. Some more efforts are mentioned here: http://www.gossamer-threads.com/lists...
- Mike Chelen
It's possible to use Git directly with a wiki that stores content in text-based files, such as DokuWiki. It gets difficult to manage edits though because there are two different revision systems, the internal wiki edit history, and the Git version controls. What is the interface like for Levitation?
- Mike Chelen
Another functioning project is Tiddlywiki http://www.tiddlywiki.com/ which lets the user download a working copy of each site. The changes can be integrated with a server through the ccTiddly plugin http://tiddlywiki.org/wiki...
- Mike Chelen
Please Mr. Jobs: change the way science moves forward: http://lesposen.wordpress.com/2010... #PLoS #openaccess
Roderic Page, Martin Fenner, Frank and 2 other people liked this
Not sure Apple, with their hostile attitude towards openness, would be the company I'd nominate to move science forward. It would be a nice little niche moneymaker for Apple, though.
- Mr. Gunn
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