isa-tab and isa-tab-nano overview

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NINA JELIAZKOVA IdeaConsult Ltd. Sofia, Bulgaria www.ideaconsult.net

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Page 1: ISA-TAB and ISA-TAB-Nano overview

NINA JELIAZKOVA IdeaConsult Ltd. Sofia, Bulgaria www.ideaconsult.net

Page 2: ISA-TAB and ISA-TAB-Nano overview

Why I got interested in ISA-TAB

• FP7 ToxBank project (2011-2015)

http://toxbank.net/ • Database support for http://www.seurat-1.eu/ (highly heterogeneous biological experiments )

• ISA-TAB identified and accepted as a solution

I D E A C O N S U L T L T D . 2

ISA-TAB http://www.isa-tools.org/

Page 3: ISA-TAB and ISA-TAB-Nano overview

The open source ISA metadata tracking tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies. Built around the

‘Investigation’ (the project context), ‘Study’ (a unit of research) ‘Assay’ (analytical measurement) general-purpose Tabular format, the ISA tools helps you to provide rich description of the experimental

metadata (i.e. sample characteristics, technology

and measurement types, sample-to-data relationships)

so that the resulting data and discoveries are reproducible and reusable.

I D E A C O N S U L T L T D . 3

HTTP://WWW.ISA-TOOLS.ORG

Page 4: ISA-TAB and ISA-TAB-Nano overview

ISA-TAB - NAMED NODES AND PROTOCOLS STUDY DESCRIPTION

Source Name

Characteristics [organism]

Characteristics [strain]

Protocol REF

Sample Name

Factor Value

[limiting nutrient]

Factor Value [rate]

Unit

culture1 Saccharomyces cerevisiae

FY1679 growth protocol

C-0.07-aliquot1

carbon 0.07 l/hour

culture4 Saccharomyces cerevisiae

FY1679 growth protocol

N-0.07-aliquot1

nitrogen 0.07

l/hour

culture5 Saccharomyces cerevisiae

FY1679 growth protocol

N-0.1-aliquot1

nitrogen 0.1 l/hour

Source name Sample Name Protocol

REF

Characteristics [organism]

Processed by

Characteristics [strain]

Factor Value [limiting nutrient]

Factor Value [rate] Unit Protocol Parameter

Page 5: ISA-TAB and ISA-TAB-Nano overview

ISA-TAB - NAMED NODES AND PROTOCOLS ASSAY DESCRIPTION (BII-S-1 EXAMPLE)

Sample name

Extract Name

Protocol REF

Processed by

Protocol REF

Processed by Labeled Extract Name Protocol

REF

Processed by Hybridization Assay Name

Page 6: ISA-TAB and ISA-TAB-Nano overview

ISACREATOR CONFIGURATOR WWW.ISA-TOOLS.ORG

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Page 7: ISA-TAB and ISA-TAB-Nano overview

ISACONFIGURATOR: SIZE MEASUREMENT / DLS

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Page 8: ISA-TAB and ISA-TAB-Nano overview

DEFINE ONTOLOGY SOURCE

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Page 9: ISA-TAB and ISA-TAB-Nano overview

ISACREATOR: ADD ASSAY

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Page 10: ISA-TAB and ISA-TAB-Nano overview

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STUDY FILE

ASSAY FILE

DATA FILE

Page 11: ISA-TAB and ISA-TAB-Nano overview

ISA-TAB-NANO

• ISA-TAB-Nano site https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano • ISA-TAB-Nano templates to create ISA-TAB-Nano files • Template glossary for definitions • Example files • Publications • BMC Biotechnology 2013, 13:2

http://www.biomedcentral.com/1472-6750/13/2/abstract • Commentary Nature Nanotechnology 2013, 8, 73-74

http://www.nature.com/nnano/journal/v8/n2/full/nnano.2013.12.html • NanoParticle ontology

http://purl.bioontology.org/ontology/NPO • EC FP7 eNanoMapper project considers using

ISA-TAB-Nano http://enanomapper.net/

Page 12: ISA-TAB and ISA-TAB-Nano overview

ISA-TAB-NANO EXAMPLE EMORY_ONT-GLEEACSNANO2013

12 https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=40566787&page=0&tab=ALL

Assay files

Material files

Study files

Investigation file

https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano+Curated+Examples

Page 13: ISA-TAB and ISA-TAB-Nano overview

I_EMORY_ONT-GLEEACSNANO2013.TXT (INVESTIGATION)

• s_EMORY_ONT-GleeACSNano2013-phys_chem.txt a_EMORY_ONT-GleeACSNano2013-physchem_size_DLS.txt a_EMORY_ONT-GleeACSNano2013-physchem_stability.txt a_EMORY_ONT-GleeACSNano2013-physchem_TEM.txt a_EMORY_ONT-GleeACSNano2013-physchem_drug_content.txt a_EMORY_ONT-GleeACSNano2013-physchem_drug_release.txt a_EMORY_ONT-GleeACSNano2013-physchem_protein_assay.txt a_EMORY_ONT-GleeACSNano2013-physchem_relaxivity.txt

• s_EMORY_ONT-GleeACSNano2013-in_vitro.txt a_EMORY_ONT-GleeACSNano2013-in_vitro_cell_viability.txt a_EMORY_ONT-GleeACSNano2013-in_vitro_targeting.txt a_EMORY_ONT-GleeACSNano2013-in_vitro_stability.txt

• s_EMORY_ONT-GleeACSNano2013-in_vivo.txt a_EMORY_ONT-GleeACSNano2013-in_vivo_health_status.txt a_EMORY_ONT-GleeACSNano2013-in_vivo_histology.txt a_EMORY_ONT-GleeACSNano2013-in_vivo_therapeutic_efficacy01.txt a_EMORY_ONT-GleeACSNano2013-in_vivo_therapeutic_efficacy02.txt

13 … and 6 m_* (Material) files

Page 14: ISA-TAB and ISA-TAB-Nano overview

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STUDY FILE

ASSAY FILE

MATERIAL FILE

Page 15: ISA-TAB and ISA-TAB-Nano overview

Material Source Name Material Name Manufacturer Lot Identifier Material Description Material Synthesis Material Design Rationale Material Intended Application Term Accession Number Term Source REF Material Type Term Accession Number Term Source REF Material Chemical Name Term Accession Number Term Source REF

Characteristics[size] Unit Term Accession Number Term Source REF Material Constituent Material Linkage (removed in 1.2) Material Linkage Type Term Accession Number Term Source REF Material Data File Material Data File Type Term Accession Number Term Source REF Material Data File Description

I D E A C O N S U L T L T D . 15

ISA-TAB-NANO 1.1 MATERIAL TEMPLATE FIELDS

Page 16: ISA-TAB and ISA-TAB-Nano overview

ISA-TAB-NANO 1.2 RELEASE NOTES Modified the ISA-TAB-Nano 1.1 version to address user comments. • Removed the Material Linkage column from the Material File. The

Material Constituent column identifies the materials that are linked if the Material Linkage Type is specified.

• Modified the Material Linkage Type description to indicate that if the linkage type is an entrapment or encapsulation, the Material Type column can specify whether the constituent is entrapped or encapsulated.

• Rephrased Material File instructions as follows: "Materials of different chemical composition or physical characteristics should be described in separate Material files."

• Enhanced the definition of material Characteristics to indicate that nominal particle characteristics (or vendor supplied) should be included in the Material File as characteristics. Experimentally determined characteristics should be included in the Assay File.

I D E A C O N S U L T L T D . 16 https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano+1.2+Release+Notes

Page 17: ISA-TAB and ISA-TAB-Nano overview

DISCUSSION (+/-) What is the best approach describe nano materials in ISA-TAB? Sample identifiers in ISA-TAB are in principle not restricted to biological samples Biological samples characterisation are described in ISA-TAB without any

extension ISA-TAB practice to describing chemical compounds = ontology entry. What if –

no proper ontology entry; or batch identifier / composition (impurities, additivies) are important?

(Ideas) Chemical or material composition can be described without introducing ISA-

TAB extensions Generic types of materials could be defined in an ontology and used for

annotation similar to ChEBI ; or The OpenTox compound service plugin for ISACreator

https://github.com/ToxBank/toxbank-isa-plugin Material samples can follow the usual ISA-TAB rules

I D E A C O N S U L T L T D . 17

Page 18: ISA-TAB and ISA-TAB-Nano overview

CONCLUSIONS ISA-TAB • (+)Very powerful and flexible data model • (describes the experimental graph) • (+)Ontology definition and annotation of all entities • (-)Metadata only; data files not standardized • (+)But we have experience in ToxBank in standardizing data files

(and converting to RDF) https://github.com/ToxBank/isa2rdf • (-)Data preparation time consuming, requires

knowledge of both data modelling and biological assays. Need of tools hiding the complexity.

ISA-TAB-Nano • (+)Extends ISA-TAB • (+/-)Is this the best approach describe NM in ISA-TAB? • (-)Under development • Tools not available, examples under development

I D E A C O N S U L T L T D . 18