Metadata For CARMEN

Phillip Lord and Frank Gibson

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

The need for clear metadata

• Most neurosciences data is relative simple in structure

• But often contextually complex

• Sometimes associated with behavioural features

Information Extraction

• How do we get extract the information?

http://en.wikipedia.org/wiki/Image:Brain_090407.jpg

http://en.wikipedia.org/wiki/Image:ATTtelephone-large.jpg

istockphoto.com

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

234Two-hybrid17634282Wong et al50576Co-fractionation17507646Aronova et al49117Affinity_Capture-MS17200106Collins et al48

9064Phenotypic_Enhancement17314980Collins et al4714421Phenotypic_Enhancement16269340Schuldiner et al463416Synthetic_Rescue16729061Ye et al45290Co-fractionation16476776Frazier et al44103Biochemical_Activity16319894Ptacek et al43

4179Affinity_Capture-MS14660704Graumann et al42477Two-hybrid16172405Measday et al41215Synthetic_Lethality16118188Milgrom et al40107Affinity_Capture-MS16429126Gavin et al39

6531Affinity_Capture-MS16554755Krogan et al387076Synthetic_Growth_Defect16487579Pan et al374535Synthetic_Lethality16157669Daniel et al36214Synthetic_Lethality15725626Loeillet et al35124Synthetic_Lethality15525520Pan et al34323Synthetic_Lethality15715908Lesage et al33292Synthetic_Lethality15166135Lesage et al32175Affinity_Capture-Western15657441Ingvarsdottir et al31138Biochemical_Activity14574415Ubersax et al30369Affinity_Capture-Western15879519Millson et al29125Reconstituted_Complex15766533Zhao et al28464Two-hybrid11087867Newman et al27134Two-hybrid15590687Hannich et al26157Protein-peptide15563457Kong et al25113Affinity_Capture-MS15353583Krogan et al24181Affinity_Capture-MS15292183Panse et al23116Affinity_Capture-MS11387327Allen et al22125Affinity_Capture-Western11743162Tong et al21232Two-hybrid11489916Drees et al20182Two-hybrid9207794Fromont-Racine et al19160Two-hybrid10900456Fromont-Racine et al18258Affinity_Capture-MS14729968Baetz et al17102Affinity_Capture-MS12052880Sanders et al16370Affinity_Capture-MS14690608Krogan et al15630Affinity_Capture-MS11884590Ohi et al14150Affinity_Capture-MS12150911Grandi et al13456Affinity_Capture-MS12374754Nissan et al12134Affinity_Capture-MS12556496Lindstrom et al11104Two-hybrid16093310Miller et al10

1941Two-hybrid10688190Uetz et al9823Synthetic_Lethality14764870Tong et al8

3411Synthetic_Lethality11743205Tong et al7275Two-hybrid11283351Ito et al6733Affinity_Capture-MS11805837Ho et al5

3596Affinity_Capture-MS11805826Gavin et al43210Affinity_Capture-MS14690591Hazbun et al3164Affinity_Capture-MS14759368Krogan et al2627Synthetic_Lethality16155567Davierwala et al1

SizeTypePMIDAuthor

How do we represent…

LaboratoryExperiments

In silico Analysis

Derived data

Joseph Whitworth

http://en.wikipedia.org/wiki/Image:Joseph_whitworth.jpg

http://en.wikipedia.org/wiki/Image:Screw_thread_Z%C3%A1vit_M16.jpg

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-Publications/About-standards/Glossary/

View from microarrays

Content Standard – Minimal Information

MAGE -- Structure MO -- Terminology

From the MGED society

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

MINI – electrophysiology

• General Features

• Study Subject

• Recording Location

• Task

• Stimulus

• Recording

• Time Series Data

Recording Location

• Recording Location Structure

• Brain Area

• Slice Thickness

• Slice Orientation

• Cell Type– Cell Type co-ordintates– Location conformation

View from microarrays

Content Standard – Minimal Information

MAGE -- Structure MO -- Terminology

From the MGED society

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.

Robot

Reference set of 5,000 mutant strains

‘Folate’ + - + -‘MMS’ - - + +

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

***

Robot

Screen mutants for sensitivity to damage/nutrition

Part of CISBAN in a nutshell

CISBAN dataflow

Neil Wipat, Newcastle University

Data Entry with SYMBA

http://symba.sourceforge.net/Allyson Lister, Newcastle University

Data Entry with SyMBA

Summary

• We are generating metadata “standards” for neurosciences

• We are following a well-trodden path from bioinformatics

• We adopted FuGE and have built MINI

Future Work

• More neurosciences experimental datatypes.

• Minimal Information about a Service– Describe analysis software as well as lab

experiments.

• Outreach!

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),