Metadata For CARMEN

1
Metadata For CARMEN

• Phillip Lord and Frank Gibson

2
Problems

• In the standard model, one collects data,
  publishes a paper or papers and then gradually
  loses the original dataset.
• THE NEW KNOWLEDGE ECONOMY AND SCIENCE AND
  TECHNOLOGY POLICY Geoffrey Bowker, University of
  California, San Diego

3
The need for clear metadata

• Most neurosciences data is relative simple in
  structure
• But often contextually complex
• Sometimes associated with behavioural features

4
Neuroscience spike data

• The raw data is just a waveform
• But what is the experiment for?
• What stimulus is the organism/tissue receiving?
• Even, which channel is which?
• The data sets being produced are (reasonably)
  large (10s of Gb, or 1Tb in three months)

5
Information Extraction

• How do we get extract the information?

http//en.wikipedia.org/wiki/ImageATTtelephone-la
rge.jpg
6
Multi-Author data
Author PMID Type Size
1 Davierwala et al 16155567 Synthetic_Lethality 627
2 Krogan et al 14759368 Affinity_Capture-MS 164
3 Hazbun et al 14690591 Affinity_Capture-MS 3210
4 Gavin et al 11805826 Affinity_Capture-MS 3596
5 Ho et al 11805837 Affinity_Capture-MS 733
6 Ito et al 11283351 Two-hybrid 275

From Katherine James, NCL
7
(No Transcript)
8
How do we represent
In silico Analysis
Derived data
Laboratory Experiments
9
(No Transcript)
10
(No Transcript)
11
Joseph Whitworth
12
Metadata

• Description of results
• Sample
• How it was generated
• Equipment
• Processing steps
• Expensive to capture
• Important to validate result

Lab-book
Lab-book
Lab-book
Lab-book
Lab-book
Lab-book
Lab-book
Lab-book
Lab-book
13
The need for standards!

• established by consensus and approved by a
  recognized body, that provides, rules,
  for the optimum degree of order in a given
  context
• BSI -
• http//www.bsi-global.com/en/Standards-and-Publica
  tions/About-standards/Glossary/

14
View from microarrays

• Content Standard Minimal Information

MO -- Terminology
MAGE -- Structure
From the MGED society
15
Life science communities
Society Domain Website
The Genomics Standards Consortium (GCS) Genomics http//darwin.nox.ac.uk/gsc/
Microarray and Gene Expression Data Society (MGED) Genomics www.mged.org
Proteomics Standards Initiative (PSI) Proteomics http//psidev.info
Metabolomics Standards Initiative (MSI) Metabolomics www.metabolomicssociety.org
Flow Cytometry experiment Community Flow Cytometry www.flowcyt.org
16
(No Transcript)
17
MINI electrophysiology

• General Features
• Study Subject
• Recording Location
• Task
• Stimulus
• Recording
• Time Series Data

18
Recording Location

• Recording Location Structure
• Brain Area
• Slice Thickness
• Slice Orientation
• Cell Type
• Cell Type co-ordintates
• Location conformation

19
(No Transcript)
20
View from microarrays

• Content Standard Minimal Information

MO -- Terminology
MAGE -- Structure
From the MGED society
21
Functional Genomics Experiment
(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.

22
Part of CISBAN in a nutshell
Screen mutants for sensitivity to damage/nutrition



Robot
Robot

• Data curation.
• Functional analysis.
• Interactions with in silico
• programme.

Reference set of 5,000 mutant strains
23
CISBAN dataflow
Neil Wipat, Newcastle University
24
Data Entry with SYMBA
http//symba.sourceforge.net/
Allyson Lister, Newcastle University
25
Data Entry with SyMBA
26
Summary

• We are generating metadata standards for
  neurosciences
• We are following a well-trodden path from
  bioinformatics
• We adopted FuGE and have built MINI

27
Future Work

• More neurosciences experimental datatypes.
• Minimal Information about a Service
• Describe analysis software as well as lab
  experiments.
• Outreach!

28
Acknowledgements

• MINI Frank Gibson, Paul G Overton, Tom V
  Smulders, Simon R Schultz, Stephen J Eglen, Colin
  D Ingram, Stefano Panzeri, Phil Bream, Evelyne
  Sernagor, Mark Cunningham, Christopher Adams,
  Christoph Echtermeyer, Jennifer Simonotto, Marcus
  Kaiser, Daniel C Swan, Martyn Fletcher, Phillip
  Lord
• CISBAN Anil Wipat (PI), Allyson Lister (Research
  Associate),

29
(No Transcript)