ISA - a short overview - Dec 2013

Overview of the ISA format and software suite

Help researchers to

curate, store, analyse, share and publish their experiments

Susanna-Assunta Sansone, PhD (associate director, PI)

Philippe Rocca-Serra, PhD (technical coordinator)

Alejandra Gonzalez-Beltran, PhD (senior developer)

Eamonn Maguire, DPhil candidate (senior developer)

Pavlos Georgiou, MSc candidate (developer)

and new team member to be recruited

The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone

www.ebi.ac.uk/net-project

user community

Focus on the experimental context and compliance to standards

Rationale for developing ISA

Researchers and bioinformaticians in both

academic and commercial arenas, along with

funding agencies and publishers, embrace

the concept that community-developed

standards are pivotal to structure and enrich

the annotation of

• entities of interest (e.g., genes,

metabolites, phenotypes) and

• experimental steps (e.g., provenance of

study materials, technology and

measurement types)

Rationale for developing ISA

Capture all salient features of

the experimental workflow

Make annotation explicit and

discoverable

Support data provenance

tracking

Use community standards

Rationale for developing ISA

transcriptomics proteomics genomics

A wealth of community, different norms and standards, e.g.:

report the same core,

essential information

use the same word and

refer to the same ‘thing’ allow data to flow from

one system to another

To track provenance of the information and ensure richness of data and experimental

metadata descriptions, to maximize sharing and reusability

Key challenges:

lack of coordination, fragmentation and uneven coverage

Technologically-delineated

views of the world

Biologically-delineated

views of the world

Generic features (‘common core’) - description of source biomaterial

- experimental design components

Arrays

Scanning Arrays & Scanning

Columns

Gels

MS MS

FTIR

NMR

Columns

transcriptomics proteomics

metabolomics

plant biology epidemiology

microbiology

To compare and integrate data we need interoperable standards

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CONSORT

MAGE-Tab

GCDML

SRAxml SOFT

FASTA DICOM

MzML

SBRML

SEDML…

GELML

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Mapping the landscape of standards, work in progress

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Databases, annotation,

curation tools

The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone

www.ebi.ac.uk/net-project

user community

Dealing with fragmented standards for the experimental context

General-purpose, configurable format, designed to

support:

- several omics standards checklists, terminologies

- reference to CDISC SDTM file(s), and

- conversions to (a growing number of) other metadata

formats, used by public repositories

1

1

Create template(s) to fit the type of

experiments to be described

Create templates detailing the steps to be

reported for different investigations, complying

to community standards, e.g. configuring the

value(s) allowed for each field to be

• text (with/without regular expression testing),

• ontology terms,

• numbers etc.

We now have configurations for submission

to EBI repositories, complying to several

community standards.

1

Or describe, curate your experiment using a

desktop-based tool

Report and edit the description using this tool,

(also customized using the templates) with a

spreadsheet like look and feel, packed with

functionalities such as

• ontology search (access via )

• term-tagging features

• import from spreadsheets etc…

1

Describe, curate your experiment with

geographically- distributed collaborators

Report and edit the description of the

investigation using customized Google

Spreadsheets (importing the ‘template’ created

by the ISA configurator) enabled with ontology

search and term-tagging features.

2

3

4

5

6

Data papers

• New open-access, online-only publication for descriptions of scientifically valuable datasets

• Only content type: Data Descriptor, narrative + structured parts

• Initially focused on the life, environmental and biomedical sciences

• Data Descriptor will be complementary to traditional research journals and data repositories

• Designed to foster data sharing and reuse, and ultimately to accelerate scientific discovery

www.nature.com/scientificdata

A grass-root collaborative that works to facilitate collection, curation and

sharing of experiments using a common, structured representation of the

experiments that

• transcends individual biological and technological domains and

• can be ‘configured’ to implement (several of) the community standards

A grass-root collaborative that works to facilitate collection, curation and

sharing of experiments using a common, structured representation of the

experiments that

• transcends individual biological and technological domains and

• can be ‘configured’ to implement (several of) the community standards

proteomics

stem cell discovery

system biology

transcriptomics

toxicogenomics

environmental health

genomics

metabolomics

metagenomics

nanotechnology

Community involvement and uptake

Core developments

2008 2009 2010

1st ISA-Tab

workshop 3rd ISA-Tab

workshop 2nd ISA-Tab

workshop

Final ISA-Tab spec Database instance

at EBI

ISA software v1

2011

1st public instance:

Harvard Stem Cell

Discovery Engine

RDF/OWL format starts

Conversions to

Pride-XML/SRA-XML/

MAGE-Tab

User workshops/visits - start

Growing number of

systems starts to adopt

ISA framework

Publications

2007 2012

Straw man

ISA-Tab spec

Other tools

implement ISA-Tab

Links to

analysis tools

starts

2013

Bioinformatics

The ISA software suite:

supporting standards-

compliant curation at the

community level

Bioinformatics

OntoMaton: a Bioportal

powered ontology widget for

Google Spreadsheets.

Woodhead Publishing

ISA chapter in : Open Source

Software in Life Science

Research

Nanotechnology

Informatics Working Group

2012

2012

2013

2013

2013