Science Library Pad

Web 2.0 from a publisher perspective, using 2Collab as an example

One of the big challenges for all of us developing Web 2.0 is finding out what the users actually want.  That's part of why libraries and publishers are taking various lab, web development group, developer network and contest approaches.  Another big challenge is trying to build a community around your tools.

Just a quick review of some of the online activities:

There are lots of library labs, and a few publisher initiatives, including Elsevier Labs, Elsevier Scopus Labs (accessible only to Scopus subscribers), Ingenta Labs, and Nature's Web Publishing group (I don't think it has a home page, but you can see some of their work on Nature Launch Pad).  In the sort of library-vendor space OCLC and Talis have developer networks.  I think some of the other library catalogue vendors may have developer spaces, but they are usually closed.

Looking at a few more Elsevier things specifically:

Elsevier has SciTopics, which is also on Twitter.

Elsevier also just announced the winner of their Grand Challenge, the Reflect project (if you follow my FriendFeed, you may see some familiar names in the winning team, like Lars Juhl Jensen and Michael Kuhn).

Which brings us to Elsevier's 2Collab.  I had a chance for an advance preview of 2Collab in late 2007.  It takes a somewhat different tack to other academic bookmarking tools, focusing a lot on group collaboration.  I had a chance to see Camelia Csora present about 2Collab as a research collaboration tool (PDF) at NISO Discovery Tools forum in 2008.

There are lots of challenges with these kinds of tools.  Can we integrate them into user workflows?  Can they understand bibliographic metadata, do lookups on DOIs, read COINS from source and embed COINS into their bookmarking pages?  Can we build standard APIs for these services?

Camelia has moved on to ebooks, and I see in my FriendFeed today that the new Product Manager for 2Collab, Michael Habib, will be presenting about 2Collab as a publisher collaboration tool

http://www.slideshare.net/habibmi/engaging-a-new-generation-of-authors-reviewers-readers-through-web-20

You can read more in his posting Engaging a New Generation of Authors, Editors, and Reviewers - Presentation for Boston Editors' Conference.

One of the big challenges in this area is getting people into the new network in order to collaborate - this is the issue that most of the "scientist social networks" have - there's no one there.  Even using Google Docs to collaborate tends not to scale very well, as you end up having to invite and reinvite groups of people to each new document.  FriendFeed as a collaboration space I think has a lot of advantages, in that it brings an immediate, individual benefit (mindcasting/lifecasting unification of web activity) as well as a critical mass of people, as well as lightweight group and discussion tools.

That's not to say you couldn't use 2Collab along with FriendFeed - and it occurs to me that one immediate step all the publishers (and other service providers) could take would be to work with FriendFeed to add their academic bookmarking services added as top level "import" sites.  Right now, despite a strong scientific user community, FF only has the non-academic sites in its list: 

• delicious
• Diigo
• Furl (which is now gone, bought by Diigo)
• Ma.gnolia
• Mister Wong
• StumbleUpon
• Twine
• はてな

The key point is it can no longer be either/or. It's not my site OR your site, it's all of our sites, interconnected. It's also/and.  I have to be able to go seamlessly from LibX to Zotero to Mendeley to Connotea to EndNote to 2Collab to Papers to FriendFeed and back again.  If Zotero has a great tool, I should be able to call it using an API from LibX.  Data can't be trapped at point of creation, it has to be able to flow around the web to be useful.

journal article recommender

CISTI's André Vellino reports

I have finally finished a first version of the Synthese Recommender for journal articles. It is now up on the CISTI Lab web site, complete with a flash video tour, in lieu of documentation.

I know that André would really appreciate any feedback you have; the whole purpose of CISTI Lab is to give you advance access to technology so that we can engage with users worldwide and adjust our offerings (and our thinking) to match your real needs and workflows.

The recommendations are currently biomed based I think.

Next Generation Discovery - NISO Forum - March 2008

http://www.niso.org/news/events_workshops/discovery08/ Next Generation Discovery: New Tools, Aging Standards - http://www.niso.org/news/events/2008/discovery08/
March 27-28, 2008
Chapel Hill, NC

Discovering scholarly information and data is essential for research and use of the content that the information community is producing and making available. The development of knowledge bases, web systems, repositories, and other sources for this information brings the need for effective discovery -- search-driven discovery and network (or browse) driven discovery -- tools to the forefront. With new tools and systems emerging, however, are standards keeping pace with the next generation of tools?

I will be presenting.
I also (after fighting with Yahoo accounts) managed to make an Upcoming event.

Other confirmed presenters include Peter Murray, Karen Hawkins (talking about scitopia.org), and Eric Schnell & Dave Munger (talking about researchblogging.org and the BPR3 initiative).

I'm proposing a tag: nisodiscovery2008

UPDATE 2008-03-10: And a Twitter Hashtag #ndf08

ICSTI video - "Assessing the quality and impact of research: practices and initiatives in scholarly information"

Videos of the presentations from the ICSTI 2007 Public Conference "Assessing the quality and impact of research: practices and initiatives in scholarly information" are now available.

You can see the programme with links to presentations, and the video page is separate, with links to each topic (RealVideo format - click on the camcorder icons on each sub-page, not on the presentation titles), I was in Quality, certification and peer review - Part 1, my presentation was Web tools for peer reviewers...and everyone (RealVideo, 35 minutes).  I encourage you to check out the other topics, I found there were some really informative presentations.

(As I said in my previous posting about my presentation, the title is not great, it's more like "categorizing the problem space of journal article exploration, and what new features or metrics we might use in this new space, as well as what new scholarly objects we might certify by applying peer review".)

My hair is, as usual, sticking out at some odd angle.  Fortunately for you, most of the time the video shows the slide I'm talking about. It's probably not entirely clear from the video, but about 14 minutes in the projector died, so I was left talking beside a blank screen (I could still see the slides on my own monitor) for about 5 minutes until everyone decided they'd had enough of that and we took a break and came back when the projector was fixed.

The next (closed, members-only) ICSTI meeting is coming up next week in Paris.  I don't know whether there is an accompanying public workshop.

UPDATE: The first version of this post ended up with an amusingly unfortunate URL.

WorldWideScience.org

The ICSTI 2007 Nancy public conference finished with a presentation of the

WorldWideScience.org

international federated search science portal.

data-driven science - Lee Dirks - June 22 - ICSTI 2007 Nancy

Lee Dirks - Director, Scholarly Communication - Microsoft
"Open access, data-driven science & the impact on research communication"

* basic research ACTIVITY unchanged
  but output options dramatically changed
  - blogs
  - wikis
  - scholarly journals
  - IRs
  - discipkine repositories
  - podcasts

Current Issues vs. Anticipated Trends

* OA to scientific content, specifically data, will become the norm

* international cross-discipline research facilitated by interoperable standards

* "evolved" methods of peer review will be adopted

* preservation of data will become a requirement

* services develop around scientific content and prevail over pure publishing
  - data analytics, publishing workflow tools, long term storage/access

EDUCAUSE "Horizon Report" 2007 - for higher education IT in USA

* key trends
  - academic review and rewards are increasingly out of sync with new forms of scholarship
  - the notions of collective intelligence and mass amateurization are pushing the boundaries of scholarship
* critical challenges
  - assessment of new forms of work
  - isses of IP and copyright continue to affect how scholarly work is done

OA momentum

... S.2695

Blogging
- example: useful chem
- recording experiments that fail

Wikis for Sharing Lab Protocols
- example: OpenWetWare

Bookmarks
- example: Connotea

IR
- 1400+ repositories worldwide

Influence of IRs

http://www.webometrics.info/top3000.asp

The Promise of Data Sharing

PLoS article - Sharing Detailed Research Data Is Associated with Increased Citation Rate

"this is going to radically change science"

ISSUES
- data integration and interop
- annotation
- provenance & quality
- exporting/publishing in agreed formats
- security

"an aspect of competitive differentiation"

Publications as Live Documents

MS will have some results on this later this year

* helps with reproducibility if you can get to the raw data, simulations etc.

Trend: The Rise of Mass Collaboration

* Novartis released all its raw data on genetics of type 2 diabetes

[missed the end of the presentation]

my presentation at ICSTI 2007 Nancy

My presentation is on Slideshare

http://www.slideshare.net/scilib/web-tools-for-peer-reviewers-and-everyone

you can also download the PowerPoint directly from there.
It's in the Creative Commons.

The title is not so great.

It's mostly about categorizing the problem space of journal article exploration, and what new features or metrics we might use in this new space, as well as what new scholarly objects we might apply the certification of peer review to. 

All the links from the presentation are available at

http://www.connotea.org/user/scilib/tag/icsti2007akerman

The presentation file as well as video of the presentation should be up on the ICSTI site soon hopefully.
You'll get to watch me deal with the projector failing unrecoverably mid-presentation.

UPDATE 2009-02-17: The video is available.

Science-specific Search - Scirus and beyond - Joris van Rossum - June 14 - IATUL 2007

Joris van Rossum
Scirus, Amsterdam, The Netherlands

Science-specific Search: Bridging the gap in dissemination of and access to information

http://www.scirus.com/

Scirus is the free science search engine
he previously worked as a senior product manager at Scopus
(the pay science search engine http://www.scopus.com/ )

Content [Overview]
* How has content provision changed?
* How has information retrieval changed?
* Future trends

Internet has made journal publishing just one of many options for scientific content communication

why is there still journal publishing?
* stamp of authority
* versioning challenge - journal has version of record
* archiving - publishers ensure the article will always be available online

Increasing amount of content available online
* high amount of published content
- Scopus has 30 million abstracts
- ScienceDirect has 8 million articles
* amount of scholarly web content even higher
- Scirus currently indexes over 400 million scholarly web pages
(feel they need to add another 400 million on top of that in order to be complete at this moment)
* size of general web has exploded
- as of August 2005 Yahoo indexed over 19 billion pages
- Google says it indexes 3x more than that

Different content discovery methods
* browsing
* linking
* alerting
* searching
* user collaboration/sharing (potentially very strong, even replacing searching)

based on analysis from ScienceDirect usage logs

Browsing
* used to keep abreast of latest developmetns in subject area
* 31% of all full text article use on ScienceDirect is a result of journal browsing
* users that start this way download on average 1.9 articles

Linking
* very effective content discovery method
* publishers are collaborating through CrossRef to ensure correct reference linking
* 8% of all full text article use on ScienceDirect comes from reference linking
- Same is expect from 'cited-by' links
* next to reference and cited-by links in official literature there is
- web ref and cite-by
- patent ref and cite-by
- clustering
- author linking

citation paradigm applies beyond the official literature

Alerting
* journal issue [TOC] (RSS)
* top articles
* citation
* search

2-4% of downloads come from alerting

Search is the main driver of journal article use
* exponential growth of PubMed and ScienceDirect searches
- growth rates between 20-110% from 2001-2005
* search has overtaken browsing
[missed rest of slide]

search is important because it yields more than just journal results

* general web search (Google) often 1st choice for scientists (66%) and physicians (55%)

* subject-specific search platforms remain important
- avg. # of full text article downloads per sesson from PubMed is 3, from general search is 1.5

screenshot of Scirus, specialised science features

role of librarians in improving integration:
- search on library homepage, OpenURL (Scirus Library Partners)

*** User Collaboration and Sharing - The Future of Information Sharing ***

Combining browsing, linking, alerting and search in a community and network-driven system

... Scirus will launch a new community service in a couple weeks

Q: researchers aren't always searching for articles - in computer science we are interested in
aggregates e.g. projects and research programs
A: the new service will offer topic-based collected search and resources relevant to a particular area

Q (Jens): journal publishing enduring... authority good - versions ? - archival not true!
A:

archiving ScienceDirect - The Hague - for free - even if Elsevier disappears, info will still be available

why is Elsevier concerned about archiving
- helps provide confidence to move everyone to e-only
- gives authors confidence

ChemRank

Mitch just launched ChemRank, a website where we can comment on and vote thumbs up or down for scientific articles.

via chem-bla-ics

So far what it appears to tell us is that the Blue Obelisk chemoinformatics people like articles about Blue Obelisk and chemoinformatics...

Papers for Mac - article organize and PubMed intregration

Search for papers using PubMed, directly retrieve and archive PDFs, and read and study them all from within Papers

http://mekentosj.com/papers/

Reviewed in ArsTechnica

You have other ways of adding your data in addition to dragging and dropping PDFs.  Endnote, RefMan, BibTex and Connotea libraries can be easily imported. For my sins, I'm an Endnote user (or victim), and it was a moment's work to import my library.  The bibliographic information will show up, but there obviously aren't any PDFs attached.  Simply double-click the paper you want and another tab will open to take you to the relevant html page for that article or it's PubMed page, depending upon whether or not it's available as a PDF.  From here you can download it straight into Papers.  You can also export lists of papers back into Endnote or BibTex.

via Digg

collaboration workflow for researchers

I think this work could be summarized as "research workflow is complex".

Scott Wilson's Workblog has a presentation and paper on Collaboration workflow for researchers.

via http://del.icio.us/destarrow/collaboration-research-workflow

article metrics: Faculty of 1000 biology and medicine

Key articles selected and evaluated by a global faculty of top researchers and clinicians.

Faculty of 1000 Biology and Medicine are authoritative online services in which almost 5,000 leading researchers and clinicians share their expert opinions by highlighting and evaluating the most important articles in biology and medicine.

http://www.facultyof1000.com/

It is a subscription service, but you can get a flavour of it from the page of "Hidden Jewels"

http://www.f1000biology.com/top10/jewels

It includes links to full text or to purchase the article.
Articles receive an "F1000 factor", by analogy to classical Impact Factor, as well as additional ratings, e.g. "Must Read", "Exceptional".

Another example of a "soft" peer review system that is yet quite rigourous (one assumes) and, surprisingly, not free.

via a talk by Francis Ouellette, Open Access at the CIHR? (PowerPoint, or available as a PDF)

soft peer review

Via Library 2.0 - Social Software and New Opportunities for Peer Review, I find a fantastic posting about the many different ways in which formal "hard" peer review can be enhanced by open web technologies:

Academic Productivity blog - Soft peer review? Social software and distributed scientific evaluation

Although I don’t think social software will ever replace hard evaluation processes such as traditional peer review, I suspect that soft evaluation systems(as those made possible by social software) will soon take over in terms of efficiency and scalability.

This is very much the position I took in my submission to the Nature peer review web focus, and which I will be re-emphasizing with a community-interaction angle in my upcoming Allen Press Seminar presentation.  I really like the comprehensive view that Academic Productivity has taken in looking at the many types of peer evaluation that can be provided on the open web, and the call for more APIs exposing more data for all of us to use.

I do think the debate about "open" peer review vs. traditional peer review is a bit of a red herring, and it very much concerns me when people suggest that open review can replace traditional (or in the language of this posting "hard") peer review.  We have already had open peer review for years, it's called preprint feedback, mailing lists, ArXiV, letters to the editor... it's a tremendous addition to, but not replacement for, the rigourous anonymous peer review system needed to provide a publication filter.

Google Scholar as good as the library?

This is the conclusion of a research study to be published in the next issue of Internet and Higher Education. I've emailed the authors to see if they're planning on depositing the paper in their Institutional Repository...  It's only a pre-print right now so I can't give you a complete citation, but if you subscribe to Science Direct you may be able to access the article here.

from The Distant Librarian

UPDATE 2007-02-06: You may have better luck with the DOI link

doi:10.1016/j.iheduc.2006.10.002

http://dx.doi.org/10.1016/j.iheduc.2006.10.002

The study is quite small (N=27) and the number of citations compared is also (N=72).  My summary would be "students can get good (trustworthy, high quality) citations by searching through their library or through Google Scholar, but if they search only Google they often get junk and don't realize it".  The specific metrics they used for quality were authority & reputation, objectivity, academic rigor, and transparency.  While these criteria are relevant for academic work, they may be less so for the general public.

UK PubMedCentral (UKPMC) launches

http://ukpmc.ac.uk/

Previously:
August 14, 2006  British Library partnership to run UKPMC

what's in your ideal scholarly portal?

Laura B. Cohen describes her Ideal 2.0 Scholarly Portal in her interesting (and new to me) blog Library 2.0: An Academic's Perspective.

blog link via Confessions

Amazon Computing Cloud - for academics?

Declan Butler has an article in Nature (behind the paywall) about researchers using Amazon's compute services

The service is still in a test phase, so few scientists have even heard of it yet, let alone tried it. But it is a movement that experts believe could revolutionize how researchers use computers. In future, they will export computing jobs to industry networks rather than trying to run them in-house, says Alberto Pace, head of Internet services at CERN, the European particle-physics laboratory near Geneva. CERN has built the world's largest scientific computing grid, bringing together 10,000 computers in 31 countries to handle the 1.5 gigabytes of data that its new accelerator, the Large Hadron Collider, will churn out every second once it is switched on next year.

"I see no reason why the Amazon service wouldn't take off," Pace says. "For a lab that wants to go fast and cheaply, this is a huge advantage over buying material and hiring IT staff. You spend a few dollars, you have a computer farm and you get results."

[Dutch computer scientist Rudi] Cilibrasi, a researcher at the National Institute for Mathematics and Computer Science in Amsterdam, was using Amazon's service to test an algorithm aimed at predicting how much someone will like a movie based on their current preferences. He says he is a convert: "It's substantially more reliable, cheaper and easier to use [than academic computing networks]. It opens up powerful computing-on-demand to the masses."

Amazon puts network power online
Nature 444, 528 (30 November 2006) | doi:10.1038/444528a; Published online 29 November 2006

He emphasizes in particular the new capabilities enabled by virtualization.

via Declan's blog

Previously:
August 24, 2006  Amazon EC2: the AmazoGrid

Canadian privacy - RefWorks

CBC Radio is reporting this issue today.

Dozens of Canadian university and college libraries are changing how they arrange for their students and faculty to do online research, in part because of a U.S. law intended to detect possible terrorist activity.

The universities subscribe to RefWorks, a popular American research tool that helps academics with research, as well as with completing citations and bibliographies.

...

"It's an issue of privacy — [that's] what it comes down to," said Karen Lippold, a librarian at Memorial University in St. John's.

Conceivably, the searches of a student or faculty member doing work on a sensitive issue could be flagged and then stored in the U.S.

"The U.S. Patriot Act allows the U.S. government — without any kind of notification — to have access to people's personal information, and so the feeling was that it left people vulnerable. Their research could be looked at by the U.S. government," Lippold said.

As a solution, Memorial and a number of other universities have abandoned U.S.-based servers, and are now using facilities at the University of Toronto.

CBC's servers are having technical difficulties, so I got the story from the Google cache (ironic, yes?)

http://www.google.com/search?q=cache:www.cbc.ca/technology/story/2006/10/31/patriot-act.html

CBC - Patriot Act fears prompt universities to patriate computers - October 31, 2006

UPDATE 2006-11-11: Story in the Globe today - Universities move to hide work from U.S. eyes

chem blog space

The Chemical blogspace site uses the Postgenomic software, but drawing its data from a selection of 19 chemistry blogs, it gives a picture of discussions in the chemblogosphere.

via chem-bla-ics

Tool Kit for Expert Web Search goes wiki

It has the scope of listing the best tools for searching the Web from the perspective of an academic librarian.

http://wikis.ala.org/LITALibrary2.0/index.php/Tool_Kit_for_the_Expert_Web_Searcher

yeah, you read that right, wikis.ala.org

What I'd be interested to know is what percentag of academic searches even make it to Google Scholar, let alone other search engines.  I suspect 90+% of searches even by academics are done using just regular Google.

via LITA Blog - Tool Kit for the Expert Web Searcher now a wiki

academic space: aggademia

A lot of people are trying to figure out what the right combination of features may be to support a scholarly communication space.  Nascent points to some recent discussion, and Alf Eaton, newly arrived at NPG, whips up a prototype.

Last week on Inside Higher Ed there was an article by Scott McLemee describing his wishlist for an 'academic aggregator' that would both a) collate new information from the web of academic publishing into one place and b) allow people to build directories of links on academic topics.

The follow-up discussion on Crooked Timber and elsewhere (Long Sunday, Epiphatic Exhaustion) seemed to agree this would be a useful idea to put into practice and—coincidentally—it was along the same lines as something I'd been playing with already. To see if it's really an idea that could work, I've put a test site online: Aggademia.

I think there's an interesting challenge - should our academic spaces be author-centric?  article-centric?  topic-centric?  collaboration enablers?  workflow enhancers?  all of the above?

Should we even be building sites, or just pieces (e.g. Web Services) that people can mash up according to their needs?

Word 2007 and the bibliographic processing future

There is an opportunity for the library and scholarly community to work with the various word processor builders to get to some common standards.

The main players that I'm aware of being Word 2007 and OpenOffice.

Jennifer Michelstein of Microsoft has the (mis)fortune of starting her MS blogging career with the posting [Word 2007] Academic features: citation & bibliography tools.

There's some nice stuff, but I have two concerns:

1. The focus is on building your Master List inside of Word.  Yes, you can share lists, but I don't want Word to be the citation master at all

Once a source is created, it lives in two places: your Master List and your Current List. The Master List is the database of all sources ever created. The Current List includes all of the sources that will be used in the current document.

The purpose of the Master List is to save you from re-typing and re-entering information about sources that you commonly use. For example, if you are a Shakespeare scholar and always cite the same five Shakespearean references, you can just select these sources in your Master List and click Copy to add them to your Current List. Now you can cite them throughout your document.

Maybe Connotea is my "master list", or EndNote, or Bookends.  You know, separation of concerns?  Let my bibliographic software be the master of citation management.  Make Word the master of communicating with all major citation repositories, whether local on my machine, or out on the web.

2. They will talk to libraries... somehow.  With a software development kit (SDK) that doesn't exist yet.  Um, how about we get that kit, immediately?

we are building a platform on the Research and Reference pane, to enable connecting to a library database and importing metadata about sources. We’ll publish an SDK so that Microsoft or any 3rd party data provider can build a service that fits nicely into our Bibliography tools. This project is underway, but the functionality isn’t available externally in Beta2. This sounds like a topic better handled in its own post.

darcusblog (Bruce D'Arcus, of the OpenOffice Bibliographic Project) has written extensively (and critically) about the current state of the art in citation management in Word 2007

via Dan on eScience

an actual use of Web Services

Microsoft is using CrossRef Web Services to assist in the indexing of scholarly content for Windows Live Academic Search, a beta of which was launched in April 2006. This new search service is designed to help students, researchers and university faculty conduct research across a spectrum of academic journals. The program is a cooperative effort between Windows Live Search, CrossRef, and several leading publishers. Windows Live Academic Search can be found at http://academic.live.com

CrossRef PR - July 12, 2006

Hey, CrossRef has a blog.

Previously:
December 02, 2005  CrossRef search and Web Services

more on science discussion aggregation

Over the past few columns, I’ve pointed to some opportunities and difficulties created by emerging forms of digital publishing. In particular, the item from last week – the one suggesting that university presses might benefit from working out a modus vivendi with academic bloggers — has generated interest and discussion. The space available online for the discussion of new books is, for all practical purposes, boundless. Meanwhile, the traditional forms of mass media place pay ever less attention to books.

Inside Higher Ed - Aggregate This! - July 12, 2006

via if:book aggregator academica

Previously:
July 17, 2006  rank and discuss articles in PubMed Wizard and elsewhere

rank and discuss articles in PubMed Wizard and elsewhere

It seems to me that the "article exploration" space is getting a lot of interest.

Via Really Simple Sidi I find BioWizard, including

PubMed Wizard
1) Rank and View Rankings of all Journal Publications in the PubMed Database!
2) Post Comments on any Publication (Discuss, Share Ideas, Ask Questions)

Lab Wizard
1) The world’s only Online Network for anyone involved in the Life Sciences
2) Create Personal Profiles and share Research Interests, List your Publications!
3) Easily Make a Lab Homepage, Upload Links, Photos, Events, Contact Info
4) Browse the Network for Collaboration, Colleagues, Make New Friends

Forums and Blogs
1) View and Comment on Blogs by the World’s Premier Scientists
2) The most comprehensive Forums for Life Science on the Internet

PLoS ONE is also apparently going to be in this space.

Previously:
March 29, 2006  uBioRSS - biology-aware RSS feeds
March 09, 2006  physcomments.org - comments on physics papers in arxiv and elsewhere
March 03, 2006  postgenomic - life sciences blog tracker 2.0