Science Library Pad

CNI Fall 2007 presentations, podcast

Lots of interesting material from fall CNI.

An audio interview with Birte Christensen-Dalsgaard, Director of Development at the State and University Library in Aarhus, Denmark about the Summa search system and other academic library topics.

Current Experiments & Future Directions in Scholarly Communication - Timo Hannay, Nature

The eCrystals Federation: Open Data Repositories Supporting Open Science
Liz Lyon, University of Bath
Simon Coles, University of Southampton
Manjula Patel, University of Bath

Summa podcast link via DigitalKoans

Previously:
October 26, 2006  the future of the scientific paper and more on open web science (Timo Hannay)
March 31, 2006  presentations on e-Science and e-Biz workflow, and research data preservation (Dr Liz Lyon)
October 11, 2005  ILI2005 - Tuesday 11th - Living with Google: New roles for libraries (Birte Christensen-Dalsgaard)
September 27, 2005  Info Grid 2005 - Tuesday 27th, 09:00 - Developing e-infrastructure to support new research and learning paradigms (Dr Liz Lyon)

future of academic libraries - presentations

Presentations from "The Future of Academic Libraries - the Road ahead" seminar held earlier this week in Oslo are available, including

The future of academic libraries - the road ahead - seen from Denmark's Electronic Research Library (DEFF)

What are the challenges for the academic libraries in the near future?

• Become user oriented in all respects
    – Become digital
    – Develop user-friendly simple systems (“as well known daily systems”)
    – Push the systems to the users in all ways
    – Forget one stop shopping
    – Accept not all content will be used
    – Deliver extra value (content or service)
    – Implement resource sharing – nobody can do everything nationally or internationally

Which services do the academic libraries’ institutions (and users) expect them to deliver?

• Content acquisition (licensing)
• Integrated search and delivery
• Research registration
• Institutional repositories
• Information literacy support
• Study environments
• Virtual reference desk
• VLE support?
• E-science support?

presentation by Bo Öhrström, Deputy Director, Danish Library Agency and overall responsible for DEFF

The presentation also talks about the need for shared infrastructure

Integrated search as an architecture

• Not only a search engine – but a national architecture
• A university has only 5% of the relevant information resources for a user in its own holdings
• The user wants to search in all relevant quality research information independent of which institution provides them.
• The library needs cooperation with other libraries about
    – larger amount of data
    – more seamless document delivery systems
    – new technology access control systems

Denmark has two integrated library search systems, Summa (open source) and Primo (Ex Libris).

There are also presentations with the perspectives from Talis (UK), Finland, Sweden, and Norway.

Link via BiblioBabl.

Previously:
February 05, 2007  Danish library strategies
September 27, 2005  Info Grid 2005 - Tuesday 27th, 11:40 - Overview of DEFF SOA activities

getting HEP to scholarly infrastructure

As an appropriate follow-on to my previous post thinking about domain-specific sites on the net, Rolf-Dieter Heuer, CERN DG-elect, shows us what a High-Energy Physics (HEP) e-Infrastructure for Scientific Communication may look like:

1. Build a complete HEP information platform
2. Enable text- and data-mining applications
3. Demonstrate and deploy Web2.0 applications
4. Preservation and re-use of research data

www.scoap3.org/files/APE2008-Heuer.pdf

As you might expect from the URL, there is also some discussion of the SCOAP3 initiative.

Although there are of course aspects that are unique to the HEP community, there are also lots of ideas that are generally applicable to domain portals for other areas of science.

Previously:
June 11, 2007  IATUL 2007 - June 11 - Dr. Rüdiger Voss - Open Access - SCOAP3
June 11, 2007  OA and repositories : beyond green and gold - Jens Vigen - June 11 - IATUL 2007

library 2.0 presentation from GTEC 2007

A Google search for library 2.0 books happened to turn up this presentation

Library 2.0 Library Services & Web 2.0 (PPT) - GTEC conference - October 16, 2007

UPDATE 2008-09-17: GTEC has updated their site for 2008, in the process managing to break all the links to the presentations.  However I found the presentation on the TBS Information Management Sessions of GTEC 2007 site.

Library 2.0 - Library Services and Web 2.0 (HTML, PDF & PPT download available)

ENDUPDATE

by Donna Bourne-Tyson of Mount Saint Vincent University (MSVU) in Halifax, NS

A couple things I hadn't known

NRCan libraries in delicious - http://del.icio.us/nrcanlibrary

Dalhousie University implementation of LibGuides - http://libguides.library.dal.ca/

open science and the web for research library 2.0?

Peter Murray-Rust points me to Dr. Liz Lyon's keynote for a November 2007 ARL Directors meeting

Open Science and the Research Library: Roles, Challenges and Opportunities?

I saw her present at InfoGrid 2005 and I've downloaded subsequent ones, this one is more Web 2.0 centric than others I have seen.  She has done a lot of deep thinking about the challenges and opportunities related to dealing with scientific data in our new cyberscience world.

Along related lines Bernard Dumouchel (former CISTI DG) wrote a short comment which asserted that supporting open science was a key possible future role for the academic library, it was for the September 2006 ARL Task Force on Library Support for E-Science ARL/NSF Workshop on New Collaborative Relationships: The Role of Academic Libraries in the Digital Data Universe, the paper is

New Collaborative Relationships: The Role of Academic Libraries in the Digital Data Universe - CISTI submission (PDF)

Unfortunately ARL moved all the files from this event, breaking all the previous links to presentations and reports that I had made.  Data stewardship irony, no?

This is the new site they made, it has working links

http://www.arl.org/pp/access/nsfworkshop.shtml

Previously:
March 31, 2006  presentations on e-Science and e-Biz workflow, and research data preservation
February 15, 2006  roles and challenges for the academic library in e-Science
September 27, 2005  Info Grid 2005 - Tuesday 27th, 09:00 - Developing e-infrastructure to support new research and learning paradigms

Designing Cyberinfrastructure 2007

I am a bit late to this content, but there was a conference "Designing Cyberinfrastructure" in January

http://cyberinfrastructure.us/
or http://www.si.umich.edu/cyber-infrastructure/

with the papers published in a special issue of First Monday in June

http://www.firstmonday.org/issues/issue12_6/

It's more grid, policy and patent focused than about specific IT architecture(s).

Some papers and presentations of interest:

• The Open Science Grid (paper), Building Large-Scale Cyberinfrastructure Through Collaboration (PowerPoint presentation) - Paul Avery
• Cyberinfrastructure and Innovation Policy - Brian Kahin
• Cyberinfrastructure, Institutions, and Sustainability - Chris Mackie
• Implementing Openness: An International Institutional Perspective - Sacha Wunsch–Vincent, Taylor Reynolds, and Andrew Wyckoff

I hope that these sorts of discussions will continue, but also as I indicated, start to encompass the idea of IT architectures for (in Christine Borgman's term) "scholarly infrastructure", that will bring in many more services and capabilities than just the compute and storage focus of the grid initiatives.

Previously:
November 12, 2007  Enterprise Services Architectures - Chris Mackie - DLF Fall Forum 2007
September 30, 2007  Blog for OECD Participative Web goes live (Sacha Wunsch–Vincent played a key role in enabling this)

Enterprise Services Architectures - Chris Mackie - DLF Fall Forum 2007

I was privileged to have been paired with Chris Mackie of the Andrew W. Mellon Foundation on the DLF programme, and fortunately I think our talks were quite complementary.  Chris talked about Enterprise Services Architectures (ESA), presenting a very clear-eyed view of the sustainability challenges of IT infrastructure for higher education, and how ESA and some specific Middleware ESA (MESA) projects are addressing those challenges.  His presentation (PDF) is now available from the DLF site.

presentations from DLF Fall Forum 2007

Some of the presentations are posted on

http://www.diglib.org/forums/fall2007/2007fallprogram.htm

If you want to locate them, just search for [PRESENTATION]

my presentation on SOA for libraries at DLF Fall Forum 2007

Overall I think it went very well, the room was packed (to my considerable surprise) and I got good questions from the audience - for once actually too many questions for my allotted time, so I unfortunately stole 10 minutes from Chris Mackie, whose presentation followed mine.

The slides are up on Slideshare, they were done in Apple Keynote, in case you're wondering.

http://www.slideshare.net/scilib/serviceoriented-architecture-for-libraries/

All of the links and background info for the presentation are available at

http://www.connotea.org/user/scilib/tag/dlf2007akerman

The following is not the actual narrative, but it gives you enough to follow the (mostly conceptual) slides:

I started with a great quote via Katherine Kott of DLF Aquifer, from the previous night's session on collaboration, stating that we need "vision translated into operational success".

Service-Oriented Architecture addresses problems in technology planning,
design and implementation.
First, we must understand what some of these problems are.
Fundamentally, technology implements the desires of the organisation.

Too often we focus on our immediate desires ("What do you want") rather
than long-term planning.
This has meant we get what we asked for (e.g. incremental catalogue
interface changes) rather than what is best for the organisation
(transformed catalogue)

In order to better align our implementations with our goals, CISTI uses
an SOA derived from our Enterprise Architecture.  In our EA methodology,
we start with business needs (Who are you?), and only then proceed to
identifying the gaps to be filled.  But you must look beyond the current
state (Why are you here?  Where are you going?)

So what are the transformational challenges we face?

In a way, we are in a fantastic world for the traditional goal of a
library - ubiquitous, zero-cost, perfect copies of information.  No more
scribes devoting their lives to copying a few books.  But this has
tremendous implications in terms of preservation, versioning, citation
etc.

Also, there are major changes in moving from a physical world where we
engineer bridges, to a virtual world where we "engineer" software.
Software doesn't have most of the constraints that apply in the physical
world, and we have to be careful with analogies to physical objects.  It
would make very little sense (except perhaps to a US Senator) to build
half a bridge, or a bridge that goes nowhere.  But in the software
world, building components, even if they are only part of an overall
goal, can be extremely useful.  And software is not location constrained
- it can be accessed from any location - there should be no "software to
nowhere".  The network is everywhere, and we need to understand how that
transforms our systems design.

So how do we apply the notions of architecture that we understand from
the physical world, and that have for centuries and continue today to
enable us to build very complex structures with many components (heat,
lighting, electrictiy, plumbing, etc.)

Well, we can use the idea of modeling.  Just as we make models of
physical objects, we can make models of business processes.  But we must
ensure that we don't get stuck in our models or frameworks, and do move
to implementation at some point.

CISTI has found that its methodology, which is focused on getting to the
implementation framework, and beyond that to design and development, has
been invaluable for turning business ideas into implemented software.
We are fortunate in that we are a library with substantial in-house
technology resources, including a dedicated architecture team (the only
library EA team in the world??)

SIDEBAR: I met the Head of eArchitecture for the British Library at my presentation, so now I think I should say "one of the very few library EA teams in the world".  END SIDEBAR

This structure may be different for
academic organisations, with faculty groups that have departmental IT,
central IT, and academic consortia.

Within this larger mehtodological framework, SOA is an approach to
identifying "servicifiable" functions in the organisation, and building
larger service offerings from various combinations of services.

In the architecture analysis phase, CISTI models all of our
technology-related activities, at a high-level this model describes all
the technology-supported activities, with functions such as "provide
library service" that then decompose down into many many lower-level
models.

Recently we have been specifically modeling a Trusted Digital
Repository, using the OAIS model and converting and adapting it.

This EA modeling work then leads to the derivation of SOA services
[depending on audience profile I may talk a lot on this slide about the
details of SOA, or not].

CISTI has used and is using SOA successfully as the foundation of
various projects - this is not just theory.

SOA is also not an agility-killer bureaucracy - services actually
provide pieces that can be used for small experiments, while
simultaneously moving the organisation in its stated general direction.

Ideally, we should all be collaborating on SOA, rather than building SOA
silos.  I have blogged a lot about this, but with little response.  Are
the individual framework groups only talking amongst themselves?  How
can we use their efforts most effectively?

SOA is certainly being explored in many areas of the library space,
including various digital library initiatives and modeling efforts (some
of which will be presented in other forum sessions).

SOA also offers the possibility of improving the catalogue by breaking
it into component services, and enabling the sort of simple layers
(widgets, mashups, javascripty stuff) by providing sustainable,
well-architected underlying service capabilities.

For academic libraries in particular, SOA offers a compelling
opportunity to connect with existing and future scientific activities,
as many Cyberinfrastructure projects have SOA at their cores.  Can we
use modelling at even the highest level (the entire scientific
communication cycle) to guide our service implementations?

Ultimately to build sustainable, non-siloed, modern information systems
to support scholars and citizens worldwide, we need to build many
bridges (this one happens to be built of lego components, in case you're
worried that giant ducks have invaded the US).  Between libraries and
scientists, between technology and business, between funders and
software developers, between computer science and library science...

We need to move beyond frameworks, using solid governance to ensure that
SOA plans become running SOA code, while avoiding getting stuck in giant
projects that don't deliver.  As well, even if you don't have the scale
or the capacity to build your own SOA, you can still participate as a
service consumer.

I'm not crazy in this (at least I hope not), as evidence for which I
present some starting points about SOA in the academic and library
sectors.

Questions...

The End

SIDEBAR 2: In case you're wondering, there's a slight science fiction theme running through the presentation, inspired by the "federation" part of the organisation name.  The Four Questions are from Babylon 5, the goodish aliens, the Vorlons, ask "Who Are You?" and represent the forces of order, the evilish aliens, the Shadows, ask "What Do You Want?" and represent the forces of chaos.  "There Are Many Copies" is from the opening sequence in the new Battlestar Galactica, using the great Creative Commons images I found worked out as a nice way of avoiding using a screencapture (plus using a screencap might have been a bit distracting as it shows a scene from BG where the many copies of Sharon Valerii/Number Eight are not so much wearing any clothes).  I had a better closing quote but I couldn't remember it, so I used a tag line from Buckaroo Banzai Across the 8th Dimension, to close out the "where are you going" questions theme.  END SIDEBAR 2

SIDEBAR 3: I was actually amazed to be able to locate the "bridge to nowhere" Google Earth image.  I had seen the unfinished highway bridge out of the airplane window as the plane was coming in to land in Philadelphia and by the time I thought to GPS-mark it or take a photo it was already past.  Incredibly, doing an image search on

"bridge to nowhere" Pennsylvania

brought it up as the first hit - Google Search, Google Earth and the Internet continue to amaze me. END SIDEBAR 3

SIDEBAR 4: I bought my carbon offsets from MyClimate.org

flight from: Ottawa, ON [Macdonald-Cartier International Airport], Canada, YOW
flight to: Philadelphia, PA [Philadelphia International Airport], USA, PHL
flight via: Toronto, ON [Lester B. Pearson International Airport], Canada, YYZ
return, economy
flight distance: 1'845 km
flight passengers: 1

CO2 Emissions: 0,511 t

Total costs for compensation of your flight: SFr. 20.00

According to Google

20 Swiss francs = 16.3543582 Canadian dollars

SOA and escience info via EDUCAUSE

Ran across a couple items on Service-Oriented Architecture provided by EDUCAUSE:

"Service-Oriented Architecture—What Is It, and How Do We Get One?" by Jim Phelps and Brian Busby in EDUCAUSE Quarterly, Vol. 30, No. 3, 2007

And from the Seminars on Academic Computing (SAC) 2007 (August 3-8, 2007)

Session on Service-Oriented Architecture
Charles F. Leonhardt (Georgetown University), Piet Niederhausen (Georgetown University), and Jens Haeusser (The University of British Columbia) - three PowerPoint presentations plus a podcast

The Institutional Challenges of Cyberinfrastructure and E-Research
Clifford A. Lynch - podcast

There is also an EDUCAUSE tag view you can follow:

http://connect.educause.edu/term_view/Service-oriented%2BArchitecture

Previously:
January 30, 2007  report on [EDUCAUSE] Library Future Roles webcast

Birkin Diana on lightweight SOA

A nice presentation on lightweight SOA (PDF).

global research data library - GRL2020 and PV 2007 presentations online

Global Research Library 2020 - GRL 2020 - http://www.lib.washington.edu/grl2020/presentations.html

PV 2007 - Ensuring the Long-Term Preservation and Value Adding to Scientific and Technical Data - Proceedings

Some presentations of interest:

• Dealing with data down under (PPT)
  Cathrine Harboe-Ree, University Librarian, Monash University
• The Coming Revolution in Scholarly Communication – and Research Libraries (PPT, 10MB)
  Tony Hey, Corporate Vice President of Technical Computing and External Research, Microsoft
• A Service-Based Architectural Approach to Enhanced Data Access (PDF, PPT)
  Lyndon R. Oleson - U.S. Geological Survey (USGS), USA
• Long term digital preservation of scientific and scholarly information: the perspective of the European Commission (PDF, PPT)
  Carlos Oliveira - EC, Luxemburg

tutorial on SOA and Web Services from ICEC06

Several NRC researchers presented a Tutorial on Service Oriented Architecture: (Semantic) Web Services, Business Process Modeling, Software Engineering last year at ICEC2006, The Eighth International Conference on Electronic Commerce.

Slides:

Introduction

Web Services

Formal Methods for Web Services Process Modelling

Semantic Web Services

Wrap-up: Semantic Service Computing (SSC) project in NRC

Medicine 2.0

I must say I'm amazed at the number and quality of weekly presentations in the SciFoo Lives On sessions in Second Life.  This week Jean-Claude and Bertalan (Berci) Meskó moderated "Medicine and Web 2.0".  I won't post the full transcript, but I did learn of some interesting links.

One thing is I don't know if all the in-world presentations are also available externally as PowerPoint/SlideShare/PDF/whatever.

* List of medical blogs in English
http://medblog.nl/2007/08/15/sneak-preview-ranking-english-written-medblogs/

* HONcode standard for trustworthy health and medical web sites
http://www.hon.ch/HONcode/Conduct.html

* Healthcare Blogger Code of Ethics
http://medbloggercode.com/

Above two are perhaps interesting additions to the Peer Review Logo discussion.

* Ann Myers Medical Center - Sprott Shaw College - Hospital Island
http://slurl.com/secondlife/Hospital/132/119/49

* Berci's Medicine 2.0 presentation and extensive link list
http://scienceroll.com/medicine-20/

* BioWizard medical article ranking tool (articles from PubMed)
http://www.biowizard.com/

* TiroMed social network for physicians and med students ("your portal to the medisphere")
http://www.tiromed.com/

I have added these all to Connotea with tag "medicine 2.0"

UPDATE: Jean-Claude has posted the transcript and other notes.  ENDUPDATE

UPDATE 2007-08-28: Berci has also posted his experience in SciFoo lives on in Second Life: Web 2.0 and Medicine.  ENDUPDATE

Next week will be Tuesday Sept 4th (since Monday is a holiday) with topic "definitions of open science".

Previously:
August 20, 2007  open science and the impact factory

open science and the impact factory

Jean-Claude Bradley instigated a session in Second Life - SciFoo Lives On: Open Science.

Next week will be something like "Medicine 2.0".

You can see in the transcript that one part of SciFoo that definitely lived on was a discussion around Open Science and webliometrics, both definitions and how to handle impact.  It seems to me that we get tangled in endless debates about definitions.  I have proposed that the nodalpoint Open Science wiki page be used to come to a consensus definition, but in the meantime:

open science

opening your scientific activities up to public examination, making work available without it having gone through formal peer review

peer review

The process of a group of scientific peers assessing the quality of a submitted piece of scientific work, currently most commonly associated with gatekeeping into a scientific publication, wherein it may also involve aspects of improving both the scientific thinking used in the paper and the expression thereof.  There is no relationship between peer review and closed or open access.

open access

making a publication available without subscription fee, but possibly with usage limitations

free access

unfortunate term due to existing definition of open access, adding element of unrestricted usage and reuse (e.g. text mining)

impact factor

An imperfect measure of the scientific "importance" of an entire journal.  Misused to measure the quality of individual scientific output

(Marked up using HTML definition lists, which you have probably never heard of, which incidentally is why the Semantic Web will fail.)

Yes, there are many types of peer review in different disciplines, and yes, things are often considered published and citable without having gone through peer review, such as conference papers and presentations which often go through a sort of editorial board selection instead.

I know these definitions are far from perfect, but good lord, can we get to good enough and go beyond this debate?

What I keep hearing is, how can we impact factorize open science.  Well, the answer is, you can't.  Let's stop trying to find some magic algorithm whereby a machine tells us what quality science is.  What's completely mad to me about this is that we already have processes to assess science quality.  Every time you review a new student, every time you look at a grant proposal, heck, even on the infamous tenure committees and research assessments, a group of humans looks at a portfolio of existing or proposed work, and decides whether it is good enough.

So if I may modestly propose, let's continue to do that, and no one other than journal publishers should ever look at impact factor numbers again.  Arise, qualitative assessment, begone quantitive nonsense.

There is still a place for technology, but it's not in providing some bogus seemly-quantitative quality measure.  It's in enabling us all to present our scientific portfolios online, or to use Euan's words, our "professional lifestreams".  And there is a real problem to be solved.  It starts with students and their scholarly output stuck in closed university systems.  Students move around.  Scientists move around.  Their work history should move with them, not be lost in some scholarly dark web, or frozen as some web page at their previous institution that they no longer can access.

The European e-Portfolio is one effort to address this for students.
Electronic Theses and Dissertations is another piece.
The next step is to have those integrate into some, shall we say, flow or... flux (sekrit inside Nature joke) of the rest of their scholarly activity when they graduate.  Bookmarks created, databases curated, papers reviewed, etc. etc.

That's the technology piece.

The other piece, however, cannot be solved with technology.

Find better ways for humans to review scholarly portfolios and make decisions based on them.  That's going to address this problem of evaluation far better than anything else.

SIDEBAR

And of course you can do some side bits with technology of course once you have all this info circulating around, like ranking relevance to help people find the best, most relevant work in the flood of science that is sloshing around.  Usage factor, other metrics, these may all help in recommending things to read.

END SIDEBAR

References

Richard Monastersky, "The Number That's Devouring Science", Chronicle of Higher Education, Volume 52, Issue 8, Page A12 (2005)

The PLoS Medicine Editors, "The Impact Factor Game", PLoS Med 3(6): e291 doi:10.1371/journal.pmed.0030291 (2006)

Peter A. Lawrence, "The Mismeasurement of Science". Current Biology, 17 (15), r583. doi:10.1016/j.cub.2007.06.014 (2007)

Bruno Granier, "Impact of research assessment on scientific publication in Earth Sciences" (PDF), a presentation at ICSTI June 2007 Public Conference on Assessing the quality and impact of research: practices and initiatives in scholarly information

Richard Akerman, "Web tools for peer reviewers...and everyone" (PDF), a presentation at ICSTI June 2007 Public Conference on Assessing the quality and impact of research: practices and initiatives in scholarly information

Corie Lok, "Scifoo: day 1; open science" (2007)

Alex Palazzo, "Scifoo - Day 2 - Science Communication" (2007)

Alex Palazzo, "Scifoo - Day 3 (well that was yesterday, but I just didn't have the time ...)" (2007)

Previously:
June 2007  Science Library Pad: ICSTI 2007 category

Phil Bradley on library web 2.0

Phil Bradley presented Practical uses for Web 2.0 in a library environment at Umbrella 2007 and then blogged Web 2.0 questions.

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.

Library SOA for catalogues, escience and more - Richard Akerman - June 12 - IATUL 2007

I have posted my presentation to SlideShare

http://www.slideshare.net/scilib/library-serviceoriented-architecture-to-enhance-access-to-science

and you can also download the PowerPoint from there (thanks to Amazon S3 storage via SlideShare).

All of the bookmarks in the presentation along with some supplementary links are available at

http://www.connotea.org/user/scilib/tag/iatul2007akerman

I was pleased with the response to my presentation.  There was interest from people in many different roles and organisations, and I am becoming increasingly convinced that at least for national library scale IT projects, SOA is gaining increasing traction.

I will use this posting as a starting point for discussions and any further ideas I may think to add.

UPDATE 2007-09-06: My paper is available in E-LIS.

biomed lit mining - Dr. Lars Juhl Jensen - June 12 - IATUL 2007

Dr. Lars Juhl Jensen
EMBL-Heidelberg, Heidelberg, Germany

Biomedical literature mining (and why we really need Open Access)

UPDATE: Presentation (PowerPoint) now online.  ENDUPDATE

MEDLINE
17 million citations

too much to read -> literature mining (get a computer to read them)

but to do that, you need access to the papers

discipline: info retrieval - finding the papers
ad hoc retrieval

MEDLINE - abstracts only
but would like to run on full text

next discipline: entity recognition

need synonyms / mapping lists - manual
plus orthographic variation

ihop
http://www.ihop-net.org/UniPub/iHOP/

discipline: information extraction

formalizing the facts - turning text into databases

Jensen et al Nature Reviews Genetics 2006

new discoveries - text mining

http://arrowsmith.psych.uic.edu/arrowsmith_uic/

mining temporal trends

timeline of buzzwords

integration of text and data

http://string.embl.de/

genotype to phenotype

Korbel et al PLoS Biology 2005 heatmap

UPDATE: I'm almost certain he's referencing

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, et al. (2005) Systematic Association of Genes to Phenotypes by Genome and Literature Mining. PLoS Biol 3(5): e134 doi:10.1371/journal.pbio.0030134

ENDUPDATE

where are we now?

the tools are there... we need the text

Q: how are researchers using tools?
A: unfortunately many of them aren't aware the tools exist

Q: copyright obstacles - collections of abstracts copyrighted (protection of database) - is this a problem?
full text - could authors prepare a second abstract for literature mining specifically?
A: extraction of facts... isn't really copyright violation
rather than having second abstract, just deposit semantic information and data directly into a database

Q: how does this relate to Biomart?
http://www.biomart.org/
A: they are trying to glue together different data sources

library service discovery and delivery

I get the sense that Daniel Chudnov and I are talking about similar problems from different angles.
I'm talking about how to get from ideas to more standard (network) services for libraries to expose and consume, he's talking about how to ensure that all available services get jammed everywhere in a user's environment.

One Big Library - NASIG 2007 talk: A New Approach to Service Discovery and Resource Delivery

paper on library SOA and the BIBSYS system

Moving towards a service-oriented architecture (abstract) / Erlend Gutteberg (BIBSYS, Trondheim)

from European Library Automation Group - ELAG 2007: Library 2.0 - Papers and Speakers

BIBSYS "supplies library and information systems to over 100 libraries and institutions of higher education in Norway".

my presentation on Internet community for Allen Press Emerging Trends

Here's my presentation "The Internet - A Scholarly Community?" from the 2007 Allen Press Emerging Trends seminar:

Download AllenPress.ppt (converted to PowerPoint)

Original Keynote format available upon request.

I have also posted it to Slideshare.net

There are supplementary bookmarks available at

http://www.connotea.org/user/scilib/tag/ap2007akerman

I thought the presentation went well.  A lot of the content is in me talking, so I don't know how much you'll get from just the slides.

Sidebar 1: Using K790 as Bluetooth Remote

I tried using my K790 phone as a remote control but that was not a big success for a couple reasons:
1) It kept going to sleep, so instead of just clicking to the next slide, I first had to hit a safe button to wake it up, then click to the next slide
2) Although Bluetooth should have good range (10 metres), I wasn't able to control from either end of the stage and at at least one point, I lost the connection altogether and had to re-establish it

So: not recommended unless you're going through your slides quickly (or know how to disable sleep mode) and you're fairly close to the podium.

Sidebar 2: Carbon Offset for Travel

I'm doing double carbon offset, on the theory that at least one of them might do some good:

Green My Flight Summary
Itinerary:
OTTAWA - YOW to WASHINGTON - IAD: 725.0 km

Total Distance: 1449.9 km
Total Emissions: 197.0 kg
Program Cost: $7.00

MyClimate

flight from: Ottawa, ON [Macdonald-Cartier International Airport], Canada, YOW
flight to: Washington, DC [Washington Dulles International Airport], USA, IAD
return, economy
flight distance: 1'448 km
flight passengers: 1
CO2 Emissions: 0,34 t
Total costs for compensation of your flight: SFr. 13.71
+ SFr. 5 "handling charge"
+ credit card foreign exchange fees

(Google says 18.71 Swiss francs = about 17.50 Canadian dollars)

thoughts and notes on Allen Press Emerging Trends Seminar

I enjoyed the Allen Press seminar, I really value the opportunity to meet with people working on ways to support scholarly activity using technology, and to see presentations of some of their work.

The strongest theme I heard from the technology side was a plea for increased semantic markup of journals, to build the "web of data".

I find it interesting that the more I progress in my career, the more I find most challenges are about people/"humanities" issues and finances - I often wonder whether some courses in human behaviour and economics should be mandatory for all technologists.

In this vein, some other themes I heard were more about psychology and sociology:
- can we find ways to recognize and reward scientific contributions outside of the published paper?
- if you're not providing an explicit reward, can you find ways to tap into activities that researchers already are doing (e.g. helping them to capture and annote citations, as Zotero does)
- is it possible to construct systems that discourage negative behavior (e.g. to prevent "flamewars" of vitriolic discussion)

As I suggested in my talk, I think we need to leverage knowledge from existing systems, like the "ignore list", moderation, FAQs, and other conventions of USENET discussion groups.

My presentation will be online within the next few days, it's been ready for months, but I still need to make sure all of the supporting Connotea bookmarks are available.  The presentations are also supposed to be up on the Allen Press site within a few days.

UPDATE 2007-04-15: My presentation is now online.  ENDUPDATE

By some sort of technogeek harmonic convergence, I ended up at the speakers' dinner the night before sitting with Konrad Förstner (homepage, blog) and Josh Greenberg.  Not only did we have a lively discussion, it worked out well because the three of us were all speaking in the same section of the programme, at the start of the day.

Konrad's presentation is already available: Revolutionizing scientific communication and collaboration (PDF).

I took some raw notes on a few of the presentations.
I don't know how useful they are, but since this work blog started as a place to hold my conference notes and make them searchable, it seems appropriate to continue this tradition.

Donald King

sources used by researchers for their work
- journal article 35%
- discussion with colleagues 20%

the ultimate factor for an information channel is its accessibility

Competition for scientists' time
- additional time is due to communication activity

National Survey

* key attribute: trustworthiness
* followed by timeliness
* followed by quality

trustworthiness of websites (as judged by surveyed researcher) was low

trends in scientists' reading patterns

* reading more
* rely on libraries more

everyone has to continue to learn

trends in how articles are identified: no big change 1977 to 2006

main shift is from A&I to online searching

most readers obtain articles from library collections, not preprint archives

252 artices read per scientist per year (increase from 150 in 1977)
source is about 50/50 library collection and other (131/121)

reasons
* decrease in personal subscriptions
* more reading of articles identified by online bib searches
** electronic collections have broadened access to articles

a lot more articles now identified by automated searches, 63 per scientist now

library collections: about 80% electronic use - this saves readers about 20 hours/year
breadth of reading has increased, read double the journals from 1977

time per article has declined from 48 minutes to 34

Article Age - older articles are judged more valuable and are more likely to come from libraries

(decline in personal paper journal libraries)

Reading of Older Materials may be increasing (with digitization)

* Libraries will continue to be an essential participant in the journal system for the foreseeable future

* Newly proposed system models need to be advance cautiously and with demonstrable successes

Q: Are researchers still browsing in the same way?
A: Mostly from personal paper subscriptions.
Also browsing means keeping up with literature in general.

------------------------

Jaron Lanier
"Avoiding Mob Science"

about Ted Nelson

about history of Internet/networking

people as "pack animals"
social roles

when you allow anonymous comments on blog entries... it can evolve into fighting packs

Internet allows "increased efficiency" of harassment

How to use governance to bring out the best in people?

morality and economics

open source: a lot of talent spent duplicating things that were already available, and diverted into
politics

we can start to observe now what does and doesn't work on the web

- ArXiv (quiet "kook filter")
- edge.org is similar

having a lot of openness is good, but total opennes is a disaster

filtering "can be cheap but it can't be free"

economic challenges - Web 2.0 seems to transmute volunteer labour into money

hard to make "partially open systems"

the iPod is a dongle

"Can we physicalize scholarly publishing in some new way?"

be realistic in adopting Web 2.0, prepare for negative behavior, design to manage it
preserve the value of scholarly publications and the scholarly process

Q: Could a tshirt be a way to physicalize a journal?

(Richard's comment: "I wrote this paper and all I got was this lousy tshirt" :)

-----------------------------------------------

Panel: The Great Promise of Research Data Commons

slide showing decline of availability of (collected/generated) research data over a creator's lifespan

John Wilbanks
"The Research Data Commons"

a commons approach makes research go faster, and makes it easier to use technologies that don't yet exist

seems to be easier for fundamental data vs. individial experiments

example of Bermuda agreement

to make the sharing possible, you need markup and storage

when there are gaps in the data, you block the ability to map the network of knowledge

"we need to treat the literature itself as data, because we need computers to process it for us"

"this has to be about answering questions, not technology"

the commons will help scientists to ask better questions

three things for publishers to do:

- markup
- provenance - e.g. link to other stuff from same author
- trust

sw.neurocommons.org

-----

Steve Bryant
PubChem
"An open information resource linking chemistry and biology"

Entrez
1,500,000 users/day
50,000,000 hits/day

having the data available lets you do many computations with it,
as well as comparisons with other data sets

NIH Roadmap

"GenBank model"
highly automated

18,000,000 chemical structure records

links to contributor web sites and other NCBI databases

about 35,000 people/day

optimize discoverability

(complex example)

exploratory structure-discovery tools

(Richard says: free the humans)

-------

Robert Peet
"Data sharing and exchange: Experiences within the Ecological Society of America"

supplemental data

way to cite and find data

need to change the culture to encourage deposit of supplementary info

vegbank.org

To be published somehow as online proceedings.  "U.S. National Vegetation Classification"
- dynamic standard

www.ecoinformatics.org

metadata, datasets, workflow

Taxonomic database challenge: Standardizing organism and community names

* movement within ESA to require access to data

Set standards
- formats
- archiving and access

* assure quality control (peer review)

Digital repositories and libraries
* archive and provided access
* meet instituational responsibility to granting agencies
* (one I missed)

Publishers
* Embed citation links for standard data elements
* (others)

Q: Open Text Mining ?
A: Creative Commons is trying to jumpstart

------------------------

Peer Review, Dynamic Documents, and the Wisdom of Crowds

Irv Rockwood

Recommends as a good overview "Peer Review in Health Sciences" (PDF), from the BMJ

"it's easy to criticize peer review, but it's harder to come up with a better system"

New possibilities:
- open peer review
- author selects reviews
- post-publication review

ETAI all articles posted for 90 day review
- revise, pass-fail

Biology Direct
- author selects reviewers
- reviews published alongside author's response

PLOS One
- prepub review on technical issues
- open peer review

Is editorial peer review broken, and if so, what should we do about it?

Jaron Lanier

- there's a tendency to (try to) use Web 2.0 to replace hard work with superficial easy work

Chris Surridge
PLoS ONE

- peer review slow, inefficient, more papers than ever

asked to do three things
1. separate good from bad
2. select papers for journals
3. give status to a paper
(4. improve the paper)

academic editors decide whether to publish (perhaps using some degree of peer review)

David Baldwin
Eco Society of America (Ithaca, NY)

- humanities has system of "working papers"

Q: different models of peer review for different disciplines?
A: yes

pondering SOA the UK and Aussie way

Service-Oriented Architecture (SOA) is not for the faint of heart, nor for those weak in technology expertise. 
SOA is fundamentally a methodology for systems design, informed by an overall Enterprise Architecture (EA).

If you don't have the scale of organization, or the organizational technical expertise, to sustain an EA and advanced development group, then SOA may not be for you.  You may want to focus more on consuming services and connecting services together.

Or in other words, we just have the latest in a line of IT best practices:

• If you're big enough to have an extensive software development shop, use SOA as your guiding methodology.  If you have a smaller shop, you may use or develop services defined by some other group, in their SOA.
• If you're big enough to have substantial IT infrastructure, use EA to guide the planning for that infrastructure.

Keeping that in mind, the library environment as a whole is clearly of the scale to benefit from an SOA, it's just a matter of how we put it all together.  Who defines the services?  Who will the service providers be?  What will the business model be for service consumers?

All this by way of introducing some recent reports and presentations on SOA, as well as signalling that I will be providing more of my library SOA thoughts in a few upcoming venues.

Firstly the National Library of Australia IT Architecture Project Report (PDF) has gotten some attention for its prominent mention of SOA.  (Thanks to Lorcan for pointing it out to me, DLTJ also mentioned it today.)

Second, via Brian Kelly I see that there were recent JISC conference presentations on EA and SOA.

e-Framework, SOA and EA: Using the e-Framework, Service Orientated and Enterprise architectures to develop more flexible and better aligned ICT infrastructures  Abstract

• Session commentary
• Presentation "The e-Framework, SOA & Enterprise Architecture" - JISC (PowerPoint)
• Presentation "Enterprise Architecture" - Open Group (PowerPoint)

Overall I think both SOA and EA are challenging topics to present simply.  That being said, I think both are typically presented far over to the extreme of complexity.  What was it that the rather inaccurately titled SOA for Dummies said you had to have in your SOA?  ESB, registry, broker, supervisor, BPM, yadda yadda... It's simply not true.  That's what you'll get if you let the kindly vendor hold you by the hand and take you into the twisty SOA maze.  All you actually need for SOA is to make sure you're using some basic software design principles:

autonomous, loosely-coupled and coarse-grained services with well-defined interfaces that support

the flexible reuse of application logic through composition

(The above an extraction from my 2005 presentation "Service-Oriented Architecture Methods to Develop Networked Library Services" which I am uploading to Slideshare... now.)

The same for EA.  Zachman is all well and good, but you need to be a mega-corp to fill in all the Zachman boxes, and even then the methodology doesn't help you much in translating that knowledge into action.  CISTI uses a much simpler and more practical methodology (based on InfoMajic) that focuses on translating business needs into an implementation framework.

There is lots of work and complexity in doing feasible EA and SOA without making it even more complex.

This may be why most of the published outputs available for library SOA are currently at such a very very high framework level.  I have to say, these frameworks don't do much for me.  As a technology person, all I see is some Dewey Decimal system for services, a top-level set of categories.  To actually start doing any service implementation work, you need to go much deeper, with models of how the detailed business functions inter-connect and inter-relate.

I wish I knew how to take the overall library community to that next level.  e-Framework (JISC - DEST - NZ MoE - SURF) is a piece, DLF Services Framework is a piece, Knowledge Exchange (JISC - DEFF - DFG - SURF) http://www.knowledge-exchange.info/ is as well... Maybe it's simply impossible given the scales of organizations involved to go beyond the highest-level conceptions.

All I know is we at CISTI can think of some relatively easy Web Service wins within an overall SOA - copyright / pricing services, query services - there are lots of possibilities.  Until we start getting more service providers and consumers up, we're all sort of stuck.

What do you think?  Is SOA too abstract or unachievable for your organization?  Are the service frameworks too high-level to impact on your development work?  Would you actually consume some library Web Services if more were available (keeping in mind the service interface might be simpler than full SOAP).  Are there services you're already providing that aren't being consumed?  Are the digital library people producing services that aren't being used by the rest of the library?  The Fedora repository already has Web Services, Amazon and Google already do - where do you see libraries fitting in?

Lots of questions... any answers?

I feel that I'm kind of reaching the limits of what I can do in terms of fairly abstract SOA evangelism - and I'm hoping there may be some concrete initiatives around which some services can coalesce...

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