Powered by Libraries: Leveraging Libraries for Semantic Web and Linked Open Data Projects

Leveraging Libraries for
Semantic Infrastructure Projects
and Data Management
Services for Maximum Data
Reuse and Visibility

Jackie Wirz, PhD
VIVO, 2012

Powered by Libraries

Hi there – This is Jackie. Since my slides
are not very text-heavy and wouldn’t
make much sense without some
narrative, I’m annotating them inside
these orange boxes.

Jackie Wirz, PhD, BADASS wannabe
VIVO, 2012

asdf

data
can be
complex Word

powered
by
libraries
The amazing thing about libraries is that they literally exist to help people find
information – and you can’t ask for anything better than that while establishing
semantic projects within a research community! This presentation touches on
some of the reasons why research/linked open data can be complex, and why
your library can help out.

Take something as simple as a tomato…

…there are a million ways to interpret
even this simple fruit (yes it’s a fruit!).

tomaytoe PANTONE
1795 C

tomahto

Solanum
lycopersicum
tdTomato
554ex 581em

$64

http://rachaelherbert.blogspot.com/2010/07/you-say-tomatoe.html

And that’s just a tomato – we’re not
even getting to the rest of the health
foods list.

Image from www.blackhealthzone.com

Data can start as a simple unit…

…that grows into an incredible wealth of knowledge.

Image from Nathan Sawaya, LEGO Artist

There are so many data types out there…

…and people hope to build them into fantastical new
areas of scientific research. This is the goal of linked
open data – connect people, data together.

http://byronalexmarshall.blogspot.com/2010/06/dissecting-
details.html
…but there is a problem with that…
(and it’s not just entropy)

data does not
spontaneously
assemble
This is where semantic linkage helps – by helping form
connections and facilitate discovery, we come closer to
making assembly easier. But it still requires a lot of work.

Oh yeah, did I mention that there are just as many diverse types of data
as there are toys? It is a common assumption that it is all digital, but
data comes in all shapes and sizes. And you know what? Libraries are
adept at storing information in all shapes and sizes! From awkwardly
large tomes to archived bits of lunar landing rovers, from digital bits to
teraflops of sequencing data, libraries are adept at cataloging, storing
and helping people find information.

Plimpton 322 Babylonian clay tablet, dated roughly
1800 BCE. This is the first example of Pythagorean
triples: proving that we’ve been writing down
scientific information for a very, VERY long time.

In 1543, Copernicus and Vesalius authored the first scientific
and medical texts. This forever changed the method of
scientific communication – in order to be widely accepted,
science now had to be printed and have data present (the
concept of Visual Certainty, first verbalized as such by Galileo).

Visual Certainty

First journal: Philosophical Transactions of the Royal Society
1665. Nature first published in 1869, Science in 1880.
Really, not much has changed in the methods by which
scientists share information in over a hundred years!

~30,000 journals

Today, there are more than 30,000 journals currently in print!

1,000,000

M'hamed el Aisati (2010)
Published
Papers

1817 2010

~ 50 Million
Articles
According to some counts, there have been more than
50 million articles published in journals. That’s a lot.

Studies by Tenopir and colleagues have shown that the
average amount of time scientists spend reading a
single journal article has gone down…

50

45

40

35

30
1977 1982 1987 1992 1997 2002

Tenopir and King (2007) TRACE Archive

… but that the total number of articles that a scientists
reads has increased dramatically over the last thirty
years.

300

250

200

150

100
1977 1982 1987 1992 1997 2002

Tenopir and King (2007) TRACE Archive

scientists spend
one month a
year reading
journal articles

that’s just journal
articles…

That doesn’t count
posters, grants,
theses, e-mail, and
data. There’s a lot of
data out there… it’s
enough to make a

http://www.scribd.com/doc/5107/They-didnt-study
person depressed.

http://lasirenagrill.files.wordpress.com/2012/03/iceberg11.jpg and
Shutterstock.com
articles

data

If we spend one month a year reading journal articles, we spend 24/7/365 dealing with data.

“We are Drowning in
Information but
Starved for
Knowledge”
John Naisbitt

“We are Drowning in
data but
Starved for
Knowledge”
Hello there!
Jackie’s bad paraphrase of John Naisbitt

Landscape of OHSU School of
Basic
Science
School of Nursing
Dentistry

Schools

School of School of
Pharmacy Medicine
Clinical
Science

Research
Centers OHSU Resources

Shared
Research
Other
Resources
Resources

Cores

The Library is Basic
School of
Switzerland. School of
Dentistry
Nursing
Science

Seriously.
Schools

School of School of
Pharmacy Medicine
Clinical

+
Science

Research
Centers OHSU

OHSU Library

Shared
Research
Other
Resources
Resources

Cores

More importantly, School of
Basic

the library works School of Science
Nursing
Dentistry

with every single
department, Schools
research center,
and resource in School of School of

the university.
Pharmacy Medicine
Clinical

+
Science

Research
Centers OHSU

OHSU Library

Shared
Research
Other
Resources
Resources

Cores

Librarians: wear dark
glasses, black cardigans, knit
and own several cats.

LIBRARIAN
STEROTYPE

[ME]

NOT TRUE!!!
Librarians are a diverse
group of professionals
with a variety of
expertise and skills. LIBRARIAN
STEROTYPE

[ME]

In addition to basic science nerds like
myself, the library is filled with
information professionals, ontologists,
data specialists and scholarly
communication specialists. LIBRARIAN
STEROTYPE

[Geeks] [MLIS] [ME]
[ONTOLOGY]
[DATA Curation]
[Scholarly Communication]

Stick figures by xkcd.com

Traditional library
services shouldn’t be
overlooked!

traditional
library
services

Remembers, libraries

Image from Wikipedia: Library of Ashurbanipal The Flood Tablet.jpg
have been cataloging,
sorting and helping
people find
information for
thousands of years!

This is a clay tablet
from the Library of
Ashurbanipal.

The library of today is a mix
of classic information
support with cutting edge
technology.

Libraries employ emerging
technology specialists, ITG and
computer support people and
information architects. Nerdy
computer awesomeness? Check!

http://6.mshcdn.com/wp-content/uploads/2012/02/geek-600.jpg

Don’t discount traditional reference!
Reference librarians are experts at
listening to people and discerning the
real source of the question (and it
isn’t as simple as it sounds – just ask
your librarian about the subtleties of
the reference interview sometime).
These professionals have the skills to
listen and interpret questions from a
wide variety of fields and still be able
to find the exact data that people are
looking for. Their specialty is the
ability to adapt to the extreme
subject specialization of patrons,
discern the root of the question and
identify the information that patrons
need.

http://www.mcphee.com/laf/ And we don’t sush people. Ever.

Libraries employ experts in user experience – if
you build it and it is awkward to use, NOBODY
WILL USE IT! We try to keep Lebron James happy
every time he searches our webpage.

Image: Flickr user Keith Allison

digital collection
& metadata
specialist

Metadata: so important, but it can be so complex!
Luckily, libraries employ metadata specialist that
know when to apply the appropriate metadata
schema. This helps us work with researchers in a
way that makes the most sense for them and us!

Digital Librarians help identify repositories across the
world, increasing the chances of finding grey literature
and data not indexed in MEDLINE, WoS or Scopus!

Map from Repository66.org

Image modified from Roz Chast
Ontology Development Group = Awesomeness!
Melissa and Carlo have talked to you about several of
our projects, and it is of note that the library is their
home.

Data Management Plans are great, but they are a
“stick” mechanism to get researchers to engage in data.
Our data specialist provides assistance with this, but…

Diagram from Dan LaSota, U Alaska

…is also looking at other ways to help with data in the
research community in a more integrated fashion. Data
literacy = very important! This is not the ideal way to
label files (but is horridly close to what my file system
looks like).

research
specialist
OK, most people call this type of position a “scholarly
communications librarian”, but since most researchers
have no idea what scholarly communication mean, I
prefer to refer to this field as research specialist. What
does she do?

bigstockphoto_stack_of_papers_1196666
She helps research analyze their research output
through citation analysis. But there’s more! She works
on promoting Public Access, and provides assistance
with the NIH Public Access Policy. Moreover…

http://ufert.se/wp-content/uploads/2012/08/250px-DataTNG.jpeg
…she understands that research output comes in many
different sizes and shapes, and looks to measure
research impact in other ways.

subject
specialist
That’s me!

I was hired because I understand why this cartoon is
too, too true.

http://aocpmr.org/students/journal-club/
I do a variety of things to keep integrated into the
research community. I participate in journal clubs on
campus…

NCBI

…I am a trainer on NCBI resources…

I attend and give seminars in departmental seminar series.

I also teach several classes (data visualization, research
ethics, publishing ethics, presentation skills, and more!).

Demotivational Poster from Despair.com
And I sit on University committees.
Whether I like it or not!

Researcher Administration

So this is how it works: I liaise with the research
community and the University at large (including

Stick figures by xkcd.com
administration), and help target the efforts of our more
specialized Ontology, Data and Research librarians.
Research Liaison

[ONTOLOGY]
[DATA Curation]
[Research Communication]

From the most excellent xkcd.com

Watch out!

LI BRARY

Modified from the most excellent xkcd.com

Example of Research Output from
SciVal. This is cool, but it makes us
at the library wonder…

what happens
between publications?

let’s use more
than the tip of the
iceberg to
connect scientists
together!

Small Scale: we are integrating into a laboratory,
working with them to use laboratory inventory
software. We’ll attend lab meetings, watch them
create and store data, and get the real skinny on how
they deal with data day-to-day.

http://www.flickr.com/photos/duncanmacinnis/2287565841/sizes/o/in/photostream/

Large Scale: I organized a university-wide research
conference that brought together researchers from all
across OHSU.

Over four days, we had 180 posters, 140 oral
presentations, 4 poster sessions, 3 invited keynote
speakers and a lot of coffee

Being an organization that likes to organize, we created an online
schedule that tracked each presenter, displayed their title and session
along with their rank. Presenters were able to link up their persona in
the online scheduling system to Facebook, and could like sessions and
share their participation with friends.

Basic
School of Science
School of Nursing
Dentistry

Remember the
landscape of Schools
OHSU?
School of School of
Pharmacy Medicine
Clinical
Science

Research

Shared
Research
Other
Resources
Resources

Cores

Basic
School of
We got School of
Dentistry
Nursing
Science

researchers to
participate Schools
from EVERY
part of the School of School of

University! Pharmacy Medicine
Clinical
Science

Research

Shared
Research
Other
Resources
Resources

Cores

More
importantly…

University
Librarian

Content Instruction, Ontology
Historical Col. &
Access Services Management & Research & Development
Archives
Systems Outreach Group

We got all
branches of the
library involved.

University
Librarian

Content Instruction, Ontology
Historical Col. &
Access Services Management & Research & Development
Archives
Systems Outreach Group

As much as it is important to make the research
community aware of the library, it is also important to
keep the entire library involved. This helps generate
enthusiasm and create a sense of accomplishment as we
move forward with our work with the research
community.

Oh yeah, baby!

semantic
projects

Melissa, Carlo and Chris have
done an amazing job at this
conference describing how we
are involved with semantic
projects. I won’t go into much
about it here, but I want to
point out that our good
relationships with the
research community make it
easier to initiate, collaborate
and develop projects with the
research community. We
aren’t “crazy folk from the
library” – we’re people that
have helped them with
information, and can be a
valuable part of the research
enterprise.

The challenges of data can be met by the professionals in the
library! Libraries have been helping define and deal with large
volumes of diverse information – extending this to the specific area
of data is a natural extension of our professional work. The answer
could be as close as your local library!

Oh wow, where did the time go? This annotation captures
only a tiny bit of my verbal onslaught, and there is so much
more I’d like to tell you all – please feel free to contact me at
any time. If there is one thing you take away from this
presentation, let it be this:

…libraries
can help you
with that.

wirzj@ohsu.edu

Seriously, contact me at any time. I’d love to hear from you!

Jackie Wirz, PhD
wirzj@ohsu.edu
503.494.3443
Skype: jacqueline.wirz

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