4A2B2C-2013

Alejandra González-Beltrán, Ph.D

University of Oxford e-Research Centre, UK

The ISA infrastructure:supporting bio-scientists from experimental

design to data publication

[email protected]

4to. Congreso Argentino de Bioinformática y Biología Computacional (4CAB2C) &4ta. Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SolBio)

29-31 October 2013, Rosario, Argentina

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mailto:[email protected]


h"p://www.nature.com/news/2011/110111/full/469139a.html;


h"p://www.economist.com/node/215285937


h"p://www.economist.com/node/215285937h"p://www.ny*mes.com/2011/07/08/health/research/08genes.html:

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Ioannidis( et( al.,( Repeatability( of( published( microarray(gene(expression(analyses.(Nature'Gene*cs(41(2),(149@55((2009)(doi:10.1038/ng.295((

Data Scientist

Visualization

Analysis

Planning

Data Management

Data CollectionPublication

Use existing data

Perform new experiment

Experimental workflow

Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


metadata

data+


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


metadata

data+

Science Reproducibility



Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


retrospective

metadata


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


metadata


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


metadata


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


prospective

metadata

metadata

metadata

metadata

metadata

metadata

metadata


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


metadata tracking infrastructure

prospective

metadata

metadata

metadata

metadata

metadata

metadata

Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


Data Reusability


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


Data Scientist

Visualization

Analysis

Planning

Data Management


Use existing data


Data Reusability


Traceability

Evidence

Provenance

Assessm

ent

Accountability

Retrieval

Mining Science

Reproducibility

Motivation Data Collection

heterogeneous experimental data

Motivation Publicationformats and database fragmentation

Roadmap

• Importance of data+metadata availability

• Experimental workflow

• Multi-omic experiments, heterogeneous data & formats

•

• The Investigation/Study/Assay (ISA) infrastructure

•

•

•

• Experimental workflow revisited

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Differentcommunities

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report&the&same&core,&&essen.al&informa.on&&

use&the&same&term&to&refer&to&the&same&‘thing’&allow&data&to&flow&from&

one&system&to&another&

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report&the&same&core,&&essen.al&informa.on&&

use&the&same&term&to&refer&to&the&same&‘thing’&allow&data&to&flow&from&

one&system&to&another&

Challenges: lack of interaction & coordination, duplication of effort, fragmentation & uneven coverage... hampers interoperability

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Data CollectionPlanning

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infrastructureThe

generic format for experimental description and data exchange

open source software toolscommunity engagement

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semantics

structure

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semantics

structure

Experimental workflow - graph representation

H. Sapiens

33 Years

H1

H2

H1.sample1

H1.sample2

H2.sample1

Labeling

Labeling

H1.sample1.labeled

H2.sample1.labeled

h1-s1.cel

h1-s2.cel

h2-s1.cel

H. Sapiens

35 Years

Scanning

Scanning

Scanning

...

...

...

Spreadsheets for end-users

vocabulary for the description of the experimental workflow

H. Sapiens

33 Years

H1

H2

H1.sample1

H1.sample2

H2.sample1

Labeling

Labeling

H1.sample1.labeled

H2.sample1.labeled

h1-s1.cel

h1-s2.cel

h2-s1.cel

H. Sapiens

35 Years

Scanning

Scanning

Scanning

...

...

...

H. Sapiens

H. Sapiens

H. Sapiens

H1

H1

H2

35

35

33

Years

Years

Years

H1.sample1

H1.sample2

H2.sample1

Labeling

Labeling

H1.sample1.labeled

H2.sample1.labeled

h1-s1.cel

h1-s2.cel

h2-s1.cel

Scanning

Scanning

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...


Spreadsheets for end-users

vocabulary for the description of the experimental workflow

syntactic interoperabilityacross biological experiments of different types

H. Sapiens

33 Years

H1

H2

H1.sample1

H1.sample2

H2.sample1

Labeling

Labeling

H1.sample1.labeled

H2.sample1.labeled

h1-s1.cel

h1-s2.cel

h2-s1.cel

H. Sapiens

35 Years

Scanning

Scanning

Scanning

...

...

...

H. Sapiens

H. Sapiens

H. Sapiens

H1

H1

H2

35

35

33

Years

Years

Years

H1.sample1

H1.sample2

H2.sample1

Labeling

Labeling

H1.sample1.labeled

H2.sample1.labeled

h1-s1.cel

h1-s2.cel

h2-s1.cel

Scanning

Scanning

Scanning

...


Protocol'Process'

Characteristics[…]!Factor Value[…] (independent variables)!Material Type!Comment[…]!

!Date!(day effect)!

Performer!!(operator effect)!

Parameter!Value![…]!

Derived Data File!

Raw Data File!

Data'File'Node'

! DATA!

! Material!

Material'Node'

Sample'Name' Material'Type''

Hybridiza9on'Assay'Name' Assay'Design'REF' Array'Data'File' Protocol'REF' Derived'Array'Data'File'

'

sample1' genomic'DNA' assay1' A-AFFY-107! assay1.cel' data'normaliza9on' assay1.txt'



Material'transforma9ons...'

! Material!

! DATA!

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A growing ecosystem of over 30 public and internal resources using the ISA metadata tracking framework (ISA-Tab and/or format) to facilitate standards-compliant collection, curation, management and reuse of investigations in an increasingly diverse set of life science domains, including:

• stem cell discovery• system biology• transcriptomics• toxicogenomics• also by communities working to build a library of cellular

signatures

• environmental health• environmental genomics• metabolomics• metagenomics• nanotechnology• proteomics

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Implementa)on+at+Harvard+

ISA

h1p://discovery.hsci.harvard.edu/+

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Implementa)on+at+the++European+Bioinforma)cs+Ins)tute+

h5p://www.ebi.ac.uk/m

etabolights+

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Create template(s) to fit the type of experiments to be described!!

Create!templates(detailing!the!steps!to!be!reported!for!different!inves4ga4ons,!complying(to(community(standards,!e.g.!configuring!the!value(s)!allowed!for!each!field!to!be!!•  text!(with/without!regular!expression!tes4ng),!•  ontology!terms,!•  numbers!etc.&!

We#now#have#GSC#compliant#configura7ons#for#submission#to#ENA.#

&&&

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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…!

Developed to be a user friendly way to enter standards-compliant metadata: it has lots of features...

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Data Collection

+Design Wizard Planning

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OntoMaton:(a(Bioportal(powered(Ontology(widget(for(Google(Spreadsheets(Maguire(et(al,((2013(Bioinforma?cs(

Data Collection

•  Ontology(search(and(automated(tagging(((relying(on((NCBO(Bioportal(services)(on(Google(Spreadsheets(•  Collabora=ve(annota=on;(support(for(distributed(users(•  Version(control(&(history(

Data Management Data Management

Data Management Data Management

Shifting towards a new system

Analysis Analysis

The interesting bit...doing something with our data and metadata...

Analysis of ISA Tab data in the R language. Brings together the context and data to enable more meaningful analysis.

Also suggests packages to use for analysis based on the data types in the ISA Tab file.

Analysis of ISA-Tab data in the Galaxy Environment.

Creates Galaxy Library objects from ISA-Tab files.

Analysis of ISA-Tab data in the GenomeSpace Environment.

Load and edit files stored on distributed servers.

Created by Brad Chapman at the Harvard School for Public Health

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Run Assays4

SAMPLE1

SAMPLE2

SAMPLE3

SAMPLE4

SAMPLE5

SAMPLE6

SAMPLE7

SAMPLE8

SAMPLE9

SAMPLE10

SAMPLE11

SAMPLE 1

SAMPLE 2

SAMPLE 3

SAMPLE 4

SAMPLE 5

SAMPLE 6

SAMPLE 7

SAMPLE 8

SAMPLE 9

SAMPLE 10

SAMPLE 11

FILE 1

FILE 2

FILE 3

FILE 4

FILE 5

FILE 6

FILE 7

FILE 8

FIL

FIL

FIL

Experiment Design Analysis

Arabidopsis thaliana

Treatment groups

70% 90% 100%

Collect Samples1 2 3 5

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Parses ISA-Tab datasets into R objects, allowing to update them and save them after analysis.

Bridges the ISA-Tab metadata to analysis pipelines of specific assay types, by building objects for use in other R packages downstream: currently considering mass spectrometry (xmcs package, xcmsSet) and DNA microarray (Biobase package, ExpressionSet)

Suggests packages in BioConductor that might be relevant for an assay type, according to the BioCViews annotations.

Gonzalez-Beltran et al. The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. In press

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Publicationdata submission

Publication

Publish, along with your research

articles

& specialised community repositories

Share, link and reason over

experiments with linked data

Getting your work out there...

Publication

http://gigasciencejournal.com

http://www.gigasciencejournal.com/content/1/1/3#B19






http://gigadb.org/dataset/100035








• 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

Narrative SectionA brief article-like document like with:•Title•Abstract•Background & Summary•Methods•Technical Validation•Usage Notes •Figures & Tables •References

Structured SectionDetailed descriptions of the experimental procedures used to produce the data•Following community-defined minimum information requirements •for a level of detail sufficient to reproduce the experiments•Using ontologies & controlled-vocabularies•To maximise consistency of the descriptions


Data Descriptors served by Scientific Data

Narrative SectionA brief article-like document like with:•Title•Abstract•Background & Summary•Methods•Technical Validation•Usage Notes •Figures & Tables •References

Structured SectionDetailed descriptions of the experimental procedures used to produce the data•Following community-defined minimum information requirements •for a level of detail sufficient to reproduce the experiments•Using ontologies & controlled-vocabularies•To maximise consistency of the descriptions


Data Descriptors served by Scientific Data

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


























































Data Scientist

Visualization

Analysis

Planning

Data Management


Science Reproducibility

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funders

core isa team

Questions?

You can email [email protected]

View our bloghttp://isatools.wordpress.com

Follow us on Twitter@isatools

View our websitehttp://www.isa-tools.org

View our Git repo & contributehttp://github.com/ISA-tools

Thanks for your attention!











4A2B2C-2013

Education

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