DATA MANAGEMENT 101Nicole Vasilevsky, Jackie Wirz and Melissa HaendelPMCB New Student Orientation20 September 2013

1 | Data definitions

2 | Dealing with data

3 | How the OHSU Library can help

Nicole Vasilevsky, PhD

Project Manager, Ontology Development Group

Jackie Wirz, PhD

Assistant Professor, Bioinformation Specialist

Melissa Haendel, PhD

Assistant Professor, Lead,Ontology Development Group

1 | Data

definitions

Data does not speak for itself…

YOU speak for YOUR data

But First, you need to manage it

But, even more fundamentally…

datameans manythings…

what does data mean to you?

What are data?

Experimental data

Social data

School related data

Personal data

Do you know what metadata is?a. Philosophy

b. describes data

c. dating site

d. data

2 | dealing with

data

Do you get frustrated with any of the following?

a. Storing data

b. Backing up data

c. Analyzing/manipulating data

d. Finding data produced by other researchers/clinicians

e. Ensuring data are secure

f. Making data accessible to other researchers

g. Controlling access to data

h. Tracking updates to data (ie versioning)

i. Creating metadata (ie describing the data to be more useful at a later

time or by others)

j. Protecting intellectual property rights

k. Ensuring appropriate professional credit/citation is given to data

sets/generated

Why?

Personal organization

Efficiency

Credit where credit is due

Accelerate scientific and clinical discovery

Reproducibility of science and medicine

naming | metadata | tools | standards

How?

naming

File naming

Naming conventions

Project_instrument_location_YYYYMMDDhhmmss_extra.ext

Index/grantconditions

Leading zero!

s/n, variableRetain order

Naming: Directory Structure

PCMB presentation

Library presentation

DMICE presentation

Presentations

PMCB Library DMICE

http://ftp.ihmc.us/

ReadMe

Version Control

Versioning

• Save a copy of every version of a file• Follow a file naming convention

Data101_PMCB_Retreat_09-20-13_v1

Data101_PMCB_Retreat_09-20-13_v2

Data101_PMCB_Retreat_09-20-13_Final

Versioning

Versioning

VersioningVersion Control software:• GIT • SVN

Backups

Which of the following do you do? a. Save copies of data on a disk, USB drive, or

computer hard drive

b. Save copies of data on a local server

c. Save copies of data on a central campus server

d. Save copies of data on a web based or cloud server

e. Store data in a repository or archives

f. Automatically backup files

g. Manually generate backup

h. Restrict access to files

1 on your local workstation 1 local/removable, such as external hard

drive 1 on central server 1 remote, such as on a cloud server*

*Depending on the type of data, as cloud servers are not always secure

Where can you backup your data?

Metadata

What is Metadata?

TitleAuthorCall numberPublisherISBN

- Anne Gilliland

Your metadata should make

your data understandabl

e to others without your involvement

MetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadatametadata

MetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadatametadata

MetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadataMetadatametadata

Are you aware of data standards in your field?

data standards

Data standards are the rules by which data are described and recorded. In order to share, exchange, and understand data, we must standardize the format as well as the meaning.http://www.usgs.gov/datamanagement/plan/datastandards.php

Controlled vocabularies

Structured data helps with searching

Craigslist search: Chaise

Craigslist matches on strings only

Craigslist search: Fainting couch

Structured data helps with searching

PubMed indexes articles with MeSH Terms

Structured data helps with searching

Why are CVs and Ontologies useful?

• Can be used to structure your metadata• Are often used to structure information in

databases

Cell Ontology Linnean Taxonomy

Order

GenusSpecies

PhylumClass

Family

Kingdom

tools

File renaming applications

• Bulk Rename Utility (Windows)• Renamer (Mac)• PSRenamer

Data Management tools and repositories

• Purpose: Software where you can organize, store and/or share data

• Often contain metadata to assist with data entry and create structured data

Tools for data management

Repositories use Unique IDs

• Document Object Identifier (DOI)• Example: DOIs for publications

– doi: 10.1371/journal.pbio.1001339

• Unique resource identifier (URI)• A URI will resolve to a single location on the

web• URIs for people

• Example: • John L Campbell, Research Ecologist, Oregon State University, Corvallis

OR• John L Campbell, Research Ecologist, Center for Research on

Ecosystem Change, Durham, NC

standards

nomenclature

antibodies

Western BlotImmunohistochemstry

ELI

SA

Co-immunoprecipitation

ChIP Flow

cytometryELISPO

T

Radioimmunoassay

FACS analysis of T cells from LNs and tumorsT cells were liberated from LNs by disruption between two frosted glass slides. Cells from LNs and tumors were stained with various combination of the following Abs: FITC-CD4, allophycocyanin-CD25, PE Cy7-CD8, APC-CD62L, PE-CD25, PE Cy7-CD25, and biotinylated-KJ-126 and in some experiments made permeable with fixation/permeablization buffers and stained with PE-FoxP3 (eBioscience). Harvested samples, isotype controls, and single stain controls were run on the FACSCalibur (BD Biosciences).

Ruby and Weinberg (2009) J Immunol. 182(3):1481-9.

Which antibody did they use in the paper?

A Solution: Antibody Registry

antibodyregistry.org

Meet the Urban Lab

Meet the Urban Lab

A+ organization!

The Urban lab antibodies

0%10%20%30%40%50%60%70%80%90%

Of 14 antibodies published in 45 articles, only 38% were identifiable

Per

cent

iden

tifia

ble

http://www.force11.org/node/4463

http://biosharing.org/bsg-000532

http://www.biosharing.org/standards/mibbi

Minimum Information for Biological and Biomedical Investigations

data publication and sharing

Why share data?

• Data sharing mandates

• Further science and and medicine

• Build collaborations• Enable new

discoveries with your data

• Can be required at time of publication

Distribution of 2004–2005 citation counts of 85 trials by data availability.

How?

Beyond the PDF: What can be published (and cited)?

Raw Science

Nanopublications

Self-publishing

Beyond the PDF: What can be published (and cited)?

Raw Science

Nanopublications

Self-publishing

Datasets

Code

Experimental design

Argument or passage Blogging

Microblogging

Comments on existing workAnnotations on existing

work

Single figure publications

How?

Data Journals and Repositories

• FigShare• Dryad• DataVerse (social science)• Institutional repositories

www.impactstory.org

3 | How the OHSU Library can help

1 | Large Lecture: Data Management

101

2 | 10 –15 Small Groups: data

playground• 1 researcher paired with 2 or 3 library staff

• Tailored analysis of data reporting and instruction

Save the date:10/09/134-6pm

1k challenge award recipients

Thank you!

URLs to resources

Go to:

http://libguides.ohsu.edu/data