Create and recieve scientific data

a centre of expertise in data curation and preservation

Create or Receive Scientific data

Dr. Frank Gibson and Dr. Phillip Lord
Frank.Gibson@newcastle.ac.uk
Phillip.Lord@newcastle.ac.uk

Funded by:
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 2.5 UK:
Scotland License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-
sa/2.5/scotland/ ; or, (b) send a letter to Creative Commons, 543 Howard Street, 5th Floor, San
Francisco, California, 94105, USA.

Digital Curation 101, October 6th-10th, 2008, NeSC, Edinburgh


“In the standard
model, one collects
data, publishes a
paper or papers and
then gradually loses
the original dataset.”

- Geoffrey Bowker

Create or Receive


Create or Receive
Slide by Cameron Neylon http://www.slideshare.net/CameronNeylon

If we have a paper a centre of expertise in data curation and preservation

who cares about the data?

Create or Receive
http://flickr.com/photos/nicmcphee/2756494307/


A paper = a claim (or claims)

The full record that supports that
claim should be available for detailed
examination and critique

Create or Receive
Slide by Cameron Neylon http://www.slideshare.net/CameronNeylon


1000+
Databases

Create or Receive

Biocuration: Databases

Create or Receive

Biocuration: Wiki

Create or Receive


Create or Receive

Funders

http://flickr.com/photos/luismimunoznajar/2093185804/or
Create Receive


Create
or
Receive

Create or Receive

Curation aims

Amenable
Preservable
Ownable
Accessible
Citable

Create or Receive


Significant Properties of Data

Content

Syntax

Semantics

Create or Receive


Content

Create or Receive

Publisher

Type

Title

Creator

Source Identifier

Date

Rights

Create or Receive

Simple Dublin Core a centre of expertise in data curation and preservation

Type
Format
Title
Identifier
Creator
Source
Subject
Language
Description
Relation
Publisher
Coverage
Contributor
Rights
Date

Create or Receive


Content:
Domain Specific

Create or Receive


Syntax

Create or Receive


Choosing a Syntax
• Openness
• -is there an open, publicly available specification for the
format; are its specifications in the public domain; is it
unencrypted?
• Portability
• -is the format independent of hardware, operating system, of
other software; is it independent of particular institutions,
groups, or events; is it in widespread current use; does it
contain little or no built-in functionality?
• Quality
• -is it robust; simple; highly tested; loss-free?

Create or Receive


Semantics

Create or Receive


Semantics can be complex

One semantic = many words
Many words = one semantic

Create or Receive


• Excel data example – do I need it?

Create or Receive
•Zeeberg et al. BMC Bioinformatics 2004 5:80 doi:10.1186/1471-2105-5-80 •Zeeberg et al. BMC Bioinformatics 2004 5:80 doi:10.1186/1471-2105-5-80

What is fly? a centre of expertise in data curation and preservation

•Fly
•Fly

•http://en.wikipedia.org/wiki/Image:Air_india_b747-400_vt-esn_arp.jpg

•http://en.wikipedia.org/wiki/Image:MuscuDomestica.jpg

•Fly
•Fly

•http://en.wikipedia.org/wiki/Image:Green_Highlander_salmon_fly.jpg

•http://en.wikipedia.org/wiki/Image:Fly_poster.jpg

Create or Receive


Ontology
• A controlled vocabulary is an association
between formal names (identifiers) and their
definitions.
• An ontology is a controlled vocabulary
augmented with logical constraints that
describe their interrelationships.

Create or Receive


Ontologies for Life science
• Emergence has occurred for two reasons
• Consistent annotation of data
• To add meaning and understanding that can
be interpreted computationally
• Bio-ontologies registered on the OBO foundry

Create or Receive


Application of
Significant Properties
In
Proteomics

Create or Receive


Minimum Information about a
Proteomics Experiment (MIAPE)
• Sufficiency.
• The MIAPE guidelines should require sufficient information about
a dataset and its experimental context to allow a reader to
understand and critically evaluate the interpretation and
conclusions, and to support their experimental corroboration.

• Practicability.
• Achieving compliance with MIAPE should not be so burdensome
as to prohibit its widespread use.

Create or Receive


Minimum reporting guidelines
• Describe content
• Implementation
independent

• Impacts
• Publication
• Syntax
• Semantics

Create or Receive


Syntax for proteomics
• The content in MIAPE GE needs to be structured to
facilitate
• dissemination
• transfer
• storage
• A community development process to agree on a
syntax
• building upon the FuGE data model
• A pre-existing community developed representation of
scientific experiments
• Interoperable

Create or Receive


FuGE
• Model of common components in science investigations, such
as materials, data, protocols, equipment and software.
• Provides a framework for capturing complete laboratory
workflows, enabling the integration of pre-existing data
formats.

Create or Receive


UML/XML/RDBMS
• UML gives structure (but not syntax)
• Very abstract, very general
• XML provides a concrete syntax
• Meta language is interoperable, checkable, viable and has
basic metadata support (language, character coding and so
on).
• Tends toward the verbose. Not (very) searchable for itself.
• Therefore, transfer and archive format.
• RDBMS
• SQL is (sort of) a standard
• Highly computationally amenable form; v. good for searching
• Conversion from XML is possible, but in a number of ways.
• Hard work – nice to have an off-the-shelf implementation.

Create or Receive

GelMLa centre of expertise in data curation and preservation

Create or Receive


Semantics
for
Gels

Create or Receive

Semantics for science

Create or Receive


Curation of Gel experiments
Public
Laboratory Data entry and transfer repositories

I) GelML data entry tools

GelML

MAIPE
GE II) Direct database submission

III) Automated export of GelInfoML

MAIPE
GI
sepCV

Create or Receive

Discoverability and reuse

•Persistent Identifiers
•Rights management

Create or Receive


Persistent Identifiers
• a name for a resource which will remain the same
regardless of where the resource is located
• In biology typically assigned to data upon publication
• Type of identifier dependent on publication method

• Description and Representation Information provides
more information about persistent identifiers

Create or Receive


Rights management
• Difficult to determine
• Lots of legal issues
• In biology/bioinformatics
tends to be open
access

•Creative commons
Create or Receive

Receiving data for curation

Content
Syntax
Semantics
Create or Receive

Who will receive it? Route map

What are their policies on:
Route map
Content, Syntax, Semantics

Plan your experiment to conform to
Content, Syntax, Semantics

Implement experiment to;
Collect appropriate Content
Structure in appropriate Syntax
Ensure Semantics are preserved

Curate…
Create or Receive


Meta Route Map
• How to build the map if you don’t have one
yet.

Create or Receive


Appraise and Select
• Investigates the evaluation and selection of
data for longterm curation and preservation

Create or Receive


Acknowledgments
• The CARMEN project
• www.carmen.org.uk
• The Proteomics Standards Initiative (PSI)
• http://psidev.info
• Colleagues at Newcastle University
• Phillip Lord, Anil Wipat, Allyson Lister

Create or Receive

Create and recieve scientific data

Recommended

Recommended

More Related Content

Similar to Create and recieve scientific data

Similar to Create and recieve scientific data (16)

Recently uploaded

Recently uploaded (20)

Create and recieve scientific data