Department Blog

Health Sciences Libraries

NIH issues finalized policy on genomic data sharing

September 7th, 2014 by Amy Studer

Image of Genomic Data Sharing Policy logo

On August 26, 2014, the National Institutes of Health has issued a final NIH Genomic Data Sharing (GDS) policy “to promote data sharing as a way to speed the translation of data into knowledge, products and procedures that improve health while protecting the privacy of research participants.”(NIH, August 27, 2014)

According to a post in The Chronicle of Higher Education, “The data-sharing policy, which will take effect with grants awarded in January, will give agency-financed researchers six months to load any genomic data they collect—from human or nonhuman subjects—into a government-established database or a recognized alternative.” (Basken, August 28, 2014)

References and Additional Information:

Basken, P. (August 28, 2014).  NIH Tells Genomic Researchers: ‘You Must Share Data.’  The Chronicle of Higher Education.  Accessed September 7, 2014, from http://chronicle.com/article/NIH-Tells-Genomic-Researchers-/148509/

National Institutes of Health Genomic Data Sharing Governance Committee. (2014). Data use under the NIH GWAS Data Sharing Policy and future directions. Nature Genetics, 46(9), 934-938. doi: 10.1038/ng.3062.  Retrieved September 7, 2014, from http://www.nature.com/ng/journal/v46/n9/full/ng.3062.html

U.S. National Institutes of Health. (2014).  Genomic data sharing.  Accessed September 7, 2014, from http://gds.nih.gov/index.html

U.S. National Institutes of Health.  (August 27, 2014).  NIH Genomic Data Sharing Policy (NOT-OD-14-124).  Accessed September 7, 2014, from http://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-124.html

U.S. National Institutes of Health. (August 27, 2014). NIH issues finalized policy on genomic data sharing.  NIH News & Events Blog.  Accessed September 7, 2014, from http://www.nih.gov/news/health/aug2014/od-27.htm

 

Data: Cooperation and Collaboration Efforts

December 21st, 2012 by Mary Wood

One particular slide from Furlough’s talk is especially noteworthy. 

Research Libraries and “Big Data” 

(made available from Penn State ScholarSphere, much like UC eScholarship

Mike Furlough
Penn State University Libraries
CENDI/NFAIS Workshop
December 11, 2012 Washington, DC 

 

DataONE, Data Conservancy and Data to Insight Center funded by NSF DataNet 

. 

MetaArchive dark preservation archive and GeoMAPP preservation of local/state government spatial data  funded by Library of Congress’ NDIIPP program 

. 

  

National Digital Stewardship Alliance, which includes members from academia, industry, and government, convened to work on Content Standards and Practices Infrastructure Innovation Outreach 

. 

DataCite develop mechanisms to assign persistent, unique identifiers to datasets so that they can be cited 

. 

Digital Preservation Network >75 universities contributed to fund an investigation of a national preservation network 

. 

 Chronopolis at SanDiego, HathiTrust, the Data Conservancy all have slightly different approaches to data storage and transfer 

DuraSpace.org, Digital Public Library of America DPLA, Committee on Institutional Cooperation CIC, Mercury, and Academic Preservation Trust 

On
this
screen
you
see
several
examples
of
the
kind
of
collaboration
I’m
talking
about.
DataOne,
Data
Concervancy
and
Data
to
Insight
Center
have
all
been
funded
by
NSF
through
DataNet.
MetaArchive,
a
dark
preservation
archive
making
use
of
peer-­‐to-­‐
peer
technology,
and
GeoMAPP,
focsed
on
the
preservation
of
local/state
government
spatial
data
were
both
funded
by
Library
of
Congress’s
NDIIPP
program.
There
are
new
ones
emerging
all
the
time.
The
Library
of
Congress’s
NDIIPP
program
has
given
rise
to
the
National
Digital
Stewardship
Alliance,
which
includes
members
from
academia,
industry,
and
government,
convened
to
work
on
Content
|
Standards
and
Practices
|
Infrastructure
|
Innovation
|
Outreach.
DataCite
is
an
organization
founded
by
several
European
national
libraries
and
including
some
North
American
libraries
to
work
with
the
publishing
industry
to
develop
the
mechanisms
to
assign
persistent,
unique
identifiers
to
datasets
so
that
they
can
be
cited.
The
Digital
Preservation
Network
is
the
newest
and
perhaps
the
most
ambitious.
Over
75
universities
have
contributed
at
least
$20k
to
fund
an
investigation
of
a
NATIONAL
preservation
network.
Two
strategies
of
DPN
worth
noting
are:
Preservation
in
enhanced
not
just
through
replication/storage,
but
by
replicating/storing
in
a
diversity
of
repository
infrastructures.
Chronopolis
at
San
Diego,
Hathi
Trust,
the
Data
Conservancy
all
have
slightly
different
approaches
to
data
storage
and
transfer.
Relying

Dealing with Data

June 1st, 2012 by Mary Wood

PLoS Biology May 2012

.

Dealing with Data: A Case Study on Information and Data Management Literacy
Haendel MA, Vasilevsky NA, Wirz JA (2012)
PLoS Biol 10(5): e1001339. doi:10.1371/journal.pbio.1001339
Article highlighted by the editors of PLoS Biology this week

..References include:

…..NIH Data Sharing Policy
…..Data.gov
…..Science Special Issue: Dealing with Data 2011, 331(6018):639-806

.

CDL UC3 Manage your Data
…..Data management plans and DMPTool

.

.

Data Management Plans: Tips, Tricks and Tools

January 6th, 2012 by Mary Wood

Presenters: Carly Strasser and Perry Willett

Audience: Scientists, librarians, staff and researchers

Wednesday Jan 11 @ 2 pm
and

Thursday Jan 19 @ 10 am (same webinar presented)
.

Summary:   Although scientists learn about methods for collecting data, there is less emphasis on managing the resulting data effectively.
This is an increasingly important skill set, especially since funding agencies like NSF have begun to require data management plans.
In this webinar, we will cover best practices for scientific data management and review how to use the new DMPTool, a free online wizard from CDL for creating Data Management Plans.
There will be time allotted for discussion of data management and the DMPTool at the close of the webinar.

Preregistation required

Webinar will be recorded and available later.

Previous UC3 webinars available here.

Data Management for Scientists – DCXL @ UCD

November 1st, 2011 by Mary Wood

Excel : data storage, management, organization, and analysis

All UC Davis scientific researchers are invited to presentations to be held Thursday 11/3
by Dr. Carly Strasser, Project Manager for DCXL (Digital Curation for Excel), UC Curation Center (UC3), California Digital Library

Both morning and afternoon presentation times are scheduled for a talk and optional hands-on session.
All sessions will be held at the same location in Shields Library.

Dr. Strasser is an expert on data, identifying potential problems, and streamlining workflow.   She is also knowledgeable about data management plans (now required for all NSF proposals), data archives available for your use, and best practices for data management.

.

Shields Library, Library Instruction Lab (LIL), Room 165
first floor, southeast corner

.
“Data management for scientists: how to reduce your workload, reuse your ideas, recycle your data”

It is rare that scientists are formally taught about good data management practices.  Instead we develop our own systems for filing documents, arranging data sheets, handling versions, and documenting analyses that are often unique and unintelligible to others.  In this talk, Dr. Strasser will focus on the common mistakes that scientists make, and how to avoid them. She will cover best practices for data management, which will facilitate data sharing, reuse, and archiving in the future.

10-11am and repeated at 3-4pm
Thursday, November 3, 2011

.

.
Hands-on Session: UCD scientists discussing/viewing their data/spreadsheets

Devoted time to ask questions about your data, show Dr. Strasser your spreadsheet(s), and get feedback from others about your organization strategy. Chat with her about your data sharing, reuse, and archiving practices, and how you use Excel. Share tips and tricks with other Davis scientists.  Attendees are invited to bring their own laptops or, if data is available via Web-accessible spreadsheets, 25 workstations for attendees are available with Internet access.

11am-noon and repeated at 4-5pm
Thursday, November 3, 2011

DCXL – Data Curation Excel

September 15th, 2011 by Mary Wood

DCXL Webinar

UC3 Webinar Thu Sep 22 2pm – 3pm
.

Speaker:  Carly Strasser, UC3

Abstract:
CDL has recently launched a new project dubbed Digital Curation for Excel (DCXL), funded by the Gordon and Betty Moore Foundation and Microsoft Research. The goal of the DCXL project is to facilitate data management, sharing, and archiving for earth, environmental, and ecological scientists. The main result from the project will be an open source add-in for Microsoft Excel that will assist scientists in preparing their Excel data for sharing. Initial ideas include generating metadata, incorporating links to scientific data repositories and their requirements, and using controlled domain-specific vocabularies. The project is in its early stages, so the time is ripe for input from the UC libraries community, the digital archiving and preservation community, and the scientific community. This webinar will cover the project’s goals, timeline, and plan, and leave plenty of time for input and questions from webinar participants.

  • Title:Digital Curation for Excel (DCXL)
    Speaker: Carly Strasser (CDL)
    Slides | Webinar

The UC3 Summer Webinar Series is a forum for timely topics of interest to the UC community. We will highlight projects, services, and developments in areas of digital preservation, web archiving and data curation. We hope to raise awareness of these issues, and the resources and services available to the UC community. Our webinars will feature librarians, scientists, and technologists.

UC3 Webinar Archives

Merritt: Depositing content

July 25th, 2011 by Mary Wood

Merritt: depositing content and providing access

UC3 Webinar Thursday July 28 2:00 – 3:00pm

Abstract: A demonstration of how to deposit content into Merritt, and ways of providing access to digital content in Merritt.

Webinar archive:
Slides | Webinar |

The UC3 Summer Webinar Series is a forum for timely topics of interest to the UC community. We will highlight projects, services, and developments in areas of digital preservation, web archiving and data curation. We hope to raise awareness of these issues, and the resources and services available to the UC community. Our webinars will feature librarians, scientists, and technologists.

UC3 Webinar Archives

Data Management Planning Tool: UC3 Webinar

July 8th, 2011 by Mary Wood

The Data Management Planning Tool (DMP Tool):
….
a tool to help researchers meet funding agencies’ data management requirements

Come to the Carlson Health Sciences Library conference room – 2:00pm Thursday July 14 – for the next UC3 webinar.

NSF, Budget, Finance & Award Mgt (BFA)

Speakers:
Patricia Cruse, Director, UC Curation Center, California Digital Library

Abstract:
In January 2011 the National Science Foundation (NSF) announced that a data management plan must accompany all grant submissions. This major requirement by the NSF will undoubtedly be taken up by other funding agencies. In response to the NSF demand, a group of US libraries and research institutions have formed a partnership to build a Data Management Planning Tool (DMP Tool) to assist researchers in creating a data management plan. The UCLA Library, the UCSD libraries, and the UC Curation Center at the CDL are leading this initiative for the UC campuses.

The DMP Tool will be tailored to the requirements of US research funding agencies, as well as to the UC systemwide and campus policies. This tool will be freely available, allowing researchers across the UC to initiate a data management plan quickly and to provide answers to various data management questions relating to their research. The goal is move research data management forward at the national and international levels, ultimately facilitating information exchange at the data level. Join us to gain a better understanding of the DMP Tool, its uses, and availability.

Archive:

Webinar Slides | Webinar |

Data as Publication: UC3 Webinar

June 24th, 2011 by Mary Wood

Data as Publication

Come to the Carlson Health Sciences Library conference room – 2:00pm Thursday June 30 – for the next UC3 webinar.

Speakers:
John Kunze, Associate Director, UC Curation Center, California Digital Library
Catherine Mitchell, Director, Publishing Program, California Digital Library

Abstract:
There is an increasing need to establish a new publishing paradigm to cope with the deluge of data artifacts produced by data-intensive research, many of which are vital to data re-use and verification of published conclusions. Due to the limitations of traditional publishing, most of these artifacts are not usually disseminated, cited, or preserved. At the California Digital Library (CDL), one promising approach to the problem is to wrap these artifacts in the metaphor of a “data paper,” which is a somewhat unfamiliar bundle of scholarly output with a familiar facade: minimally, a set of links to archived artifacts and a cover sheet containing familiar elements such as title, authors, date, abstract, and persistent identifier, just enough to create basic citations, build “overlay journals,” and enable discovery of data by Internet search engines. Additional elements that permit deeper domain-specific discovery and re-use, such as variable names, methods, etc., are planned. A pilot implementation at CDL will bring a number of existing services to bear on the problem, including (a) the Merritt repository for safe, stable storage for datasets; (b) EZID for generating, managing, and resolving persistent identifiers; and (c) eScholarship for publishing data papers and overlay journals.

webinar  archive:
Slides | Webinar |

The UC3 Summer Webinar Series is a forum for timely topics of interest to the UC community. We will highlight projects, services, and developments in areas of digital preservation, web archiving and data curation. We hope to raise awareness of these issues, and the resources and services available to the UC community. Our webinars will feature librarians, scientists, and technologists.

Data Sharing by Scientists: UC3 Webinar

June 10th, 2011 by Mary Wood

Data Sharing by Scientists: Practices and Perceptions

Come to the Carlson Health Sciences Library conference room12:30pm Wednesday June 15 – for the UC3 webinar on NSF’s Data Observation Network for Earth (DataONE)

Speakers:
Carol Tenopir, Professor of Information Sciences, Director of Research, College of Communication and Information, Director of the Center for Information and Communication Studies, University of Tennessee
Mike Frame, Deputy Center Director for the Center for Biological Informatics, U.S. Geological Survey

Abstract:
Guest speakers will discuss results of a survey of scientists and their data sharing practices. A primary goal of NSF’s Data Observation Network for Earth (DataONE) is to ensure preservation and access to multi-scale, multi-discipline, and multi-national science data, particularly in the Earth and Environmental Sciences. As a means to measure project success and to better understand the needs of the community, DataONE has conducted a baseline assessment of the data sharing practices and preferences of domain scientists. The survey was motivated by the understanding that improving access to the sharing of data requires changes in both technology and expectations of the scientific community. This webinar will present the key finding from the assessment including data management practices, barriers to sharing data, and more. The California Digital Library, the National Center for Ecological Analysis and Synthesis UCSB, and the UCSB Library are active participants in the DataONE initiative.

.

webinar archive:

slides, audio recording

The UC3 Summer Webinar Series is a forum for timely topics of interest to the UC community. We will highlight projects, services, and developments in areas of digital preservation, web archiving and data curation. We hope to raise awareness of these issues, and the resources and services available to the UC community. Our webinars will feature librarians, scientists, and technologists.