This document discusses ISA-TAB, a metadata standard for describing experiments. It describes how the author became interested in ISA-TAB through projects that needed to support heterogeneous biological experiments. ISA-TAB structures experiments into investigations, studies, and assays. It allows rich description of experimental metadata so that data is reproducible and reusable. The document also discusses ISA-TAB-Nano, an extension of ISA-TAB for describing nanomaterial experiments, and areas it could be improved.

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

2. 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/

3. 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

4. ISA-TAB - NAMED NODES AND PROTOCOLS
STUDY DESCRIPTION
Source
Name
Characteristic
s
[organism]
Characteristi
cs
[strain]
Protocol
REF
Sampl
e
Name
Factor
Value
[limiting
nutrient]
Factor
Value
[rate]
Unit
culture1 Saccharomyce
s cerevisiae
FY1679 growth
protocol
C-0.07-
aliquot1
carbon 0.07 l/hour
culture4 Saccharomyce
s cerevisiae
FY1679 growth
protocol
N-0.07-
aliquot1
nitrogen 0.07 l/hour
culture5 Saccharomyce
s 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

5. 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
Hybridi
zation
Assay
Name

6. ISACREATOR CONFIGURATOR
WWW.ISA-TOOLS.ORG
6

7. ISACONFIGURATOR:
SIZE MEASUREMENT / DLS
7

8. DEFINE ONTOLOGY SOURCE
8

9. ISACREATOR: ADD ASSAY
9

10. 10
STUDY FILE
ASSAY FILE
DATA FILE

11. 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/

12. ISA-TAB-NANO EXAMPLE
EMORY_ONT-GLEEACSNANO2013
12https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=40566787&pag
e=0&tab=ALL
Assay files
Material files
Study files
Investigation file
https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano+Curated+Examples

13. 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

14. 14
STUDY FILE
ASSAY FILE
MATERIAL FILE

15. 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

16. 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

17. 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

18. 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