LIB 100, Information LiteracyWake Forest University

November 18, 2010

Research information sharing

and

Jeffery Loojeff@jeffloo.com

information synthesis

University of California, Berkeley Wake Forest University

Sharing research information

Letting others• see your research work• use it• build upon it

WE WILL DISCUSS

1. The research practice of sharing research information

2. A model of research sharing known

as Open Access publishing

3. Developing synthesis skills to deal with the increasing volume of shared information

RELEVANCE

Know where to find quality research works at no cost

Information synthesis skills that may be helpful for your future career

Part 1

“Genome Race”

To determine the order of the chemical “letters” that make up our DNA.

Chemical “letters”A, T, G, and C

automated DNA sequencing technology

Benefits of genome sequencing

Medical contributions• detecting genes that lead to

diseases• may lead to “personalized

medicine”• may lead to gene therapy

Human biology contributions• facilitate comparative genomics• identify “model organisms”

The Genome Race

PUBLIC EFFORT PRIVATE COMPANYFirst to identify the sequence of the human genome?

International Human Genome Sequencing Consortium (IHGSC)

The public effort

began in 1990

1. carefully divided the human genome into large fragments

2. the DNA fragments were allotted to an international consortium of laboratories

3. each lab to sequence the fragments

Celera’s approachstarted in 1999whole genome shotgun sequencing

1.human genome randomly broken into small pieces

2.sequenced the little random pieces

3.used computers to find overlaps between the pieces and then link together

Fragment # 1

Fragment # 2

Reconstruction

yellow indicates overlap

Pace of sequencing (overall)

Sharing genome sequence data

Public effortLoaded results into the publicly accessible database, GenBank

Celera Private approachIn process of seeking patent protection on some genes

EntrezGenBank

According to Dr. Craig Venter, Celera used public data

“How can you ‘beat’ the runner who hands you the baton?”

Who won the genome sequencing race?

June 26, 2000

It was a tie!

Dr. Craig Venter Celera Genomics

Dr. Francis CollinsNational Institutes of Health

February 2001, published drafts

April 2003, complete genome identified

Public effort Celera

What happened in the end?

2005Celera Genomics made data available in public database

What does this case highlight?

1. different approaches to scientific research - collaborate or not

2. different ways of sharing research results - publicly share or not

3. information technology has a powerful impact on research approach and sharing

Different approaches

Celera

individual effort

powerful computer systems to facilitate this massive project

Public effort

divided the work internationally

computer systems to coordinate and merge results

Different management of results

Public effort deposited data in a publicly accessible database

Celera was seeking to patent some genes

Part 2.

Open access publishing

Publishing of scholarly works that is:

Digital and online

Free of charge to the reader

Free of most traditional copyright and licensing restrictions

(e.g., permission for users to re-distribute, remix, and reuse the content)

How is it free?

In traditional publishing, readers or libraries pay a fee for access

Free for the reader

Author finds funding to pay for publication

Sample open access publications

PLoS OnePLoS BiologyPLoS Medicine

Find OA articles in the life and health sciences via:

PubMed CentralBioMed Central

Sample open access resources

http://www.doaj.org/

open access databases of research data NCBI EntrezPubChem (small molecule and bioactivity)

Value of open access publishing

1. greater audience / more publicity

2. authors retain ownership and control

3. advance knowledge because publications and ideas are shared

4. meeting obligations to share research workNIH Public Access Policy, http://publicaccess.nih.gov/ Open access policy of the Wellcome Trust

Part 3. Synthesis skillsHow do we cope with increasing volume of shared information?

Howard Gardner’s Five Minds for the Future

Synthesizing is:taking information from disparate sources, understanding and evaluating that information objectively, and putting it together in ways that make sense

Kinds of synthesisNarrativesTaxonomiesComplex concepts Rules and aphorisms Powerful metaphors, images, and themes Embodiments without wordsTheoriesMetatheory

See handout, page 4.

TaxonomiesCategorizing items in terms of salient characteristics

Periodic table of elements

Linnaean classification of plants and animals

Powerful metaphors, images, and themes

Invoking metaphors to bring concepts to life

combining digital works to create a new work

PadMapper = Google Maps + apartment rental listingshttp://www.padmapper.com/

Mashups

visual representations of information, data, or knowledgehttp://www.infographicsshowcase.com/

Information graphics

Embodiments without wordsworks of art that capture a lot of ideas

Picasso's Guernica expresses the horror of the Spanish Civil War

Cultivating synthesis skills

1. Digest new information (i.e., recognize, learn, and understand)

2. Organize it.

3. Apply the new knowledge.See handout, page 4.

Examples

For professionals:Recognize new knowledge or skills.

Learn and apply.

For college students:In assignments, collect different types of information, and then organize them in a helpful manner.

Experiment with visuals, layout, and organization.

Summary Open access publishing is a model for sharing research information

With greater sharing, there will be a larger volume of information

In response, develop synthesis skills for digesting, organizing, and applying new knowledge

Sharing information and collaboration are important research practices

References

Please review the transcript at: http://www.jeffloo.com/stuff/2010/sharing-transcript.pdf