Overview of the ISA format and software suite
Help researchers to
curate, store, analyse, share and publish their experime...
Focus on the experimental context and compliance to standards

user community

The International Conference on Systems Bio...
Rationale for developing ISA

 Researchers and bioinformaticians in both
academic and commercial arenas, along with
fundi...
Rationale for developing ISA







Capture all salient features of
the experimental workflow
Make annotation explicit...
Rationale for developing ISA

transcriptomics

proteomics

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

allow data to flow from
one system to another

use the same w...
To compare and integrate data we need interoperable standards
epidemiology

plant biology

microbiology

Biologically-deli...
Mapping the landscape of standards, work in progress
See more at:

+ 303

Estimated

Source: MIBBI,
EQUATOR

Source: BioPo...
Dealing with fragmented standards for the experimental context

user community

The International Conference on Systems Bi...
General-purpose, configurable format, designed to
support:
- several omics standards checklists, terminologies
- reference...
1
1

Create template(s) to fit the type of
experiments to be described
Create templates detailing the steps to be
reported f...
1

Or describe, curate your experiment using a
desktop-based tool
Report and edit the description using this tool,
(also c...
1

Describe, curate your experiment with
geographically- distributed collaborators
Report and edit the description of the
...
2
3
4
5
6
Data papers
•
•
•
•
•

New open-access, online-only publication for descriptions of scientifically valuable datasets
Only content type...


A grass-root collaborative that works to facilitate collection, curation and
sharing of experiments using a common, str...


A grass-root collaborative that works to facilitate collection, curation and
sharing of experiments using a common, str...
Community involvement and uptake
1st ISA-Tab
workshop
2nd ISA-Tab
workshop

3rd ISA-Tab
workshop

User workshops/visits - ...
2012

2013

2013

2012

2013

Nanotechnology
Informatics Working Group
ISA - a short overview - Dec 2013
ISA - a short overview - Dec 2013
Upcoming SlideShare
Loading in …5
×

ISA - a short overview - Dec 2013

439 views

Published on

Published in: Technology, Education
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
439
On SlideShare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

ISA - a short overview - Dec 2013

  1. 1. 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
  2. 2. Focus on the experimental context and compliance to standards user community The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  3. 3. 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)
  4. 4. Rationale for developing ISA     Capture all salient features of the experimental workflow Make annotation explicit and discoverable Support data provenance tracking Use community standards
  5. 5. Rationale for developing ISA transcriptomics proteomics genomics
  6. 6. A wealth of community, different norms and standards, e.g.: allow data to flow from one system to another use the same word and refer to the same ‘thing’ report the same core, essential information 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
  7. 7. To compare and integrate data we need interoperable standards epidemiology plant biology microbiology Biologically-delineated views of the world Generic features (‘common core’) - description of source biomaterial - experimental design components MS Arrays Gels Columns Scanning transcriptomics Arrays & Scanning proteomics MS Technologically-delineated views of the world NMR FTIR Columns metabolomics
  8. 8. Mapping the landscape of standards, work in progress See more at: + 303 Estimated Source: MIBBI, EQUATOR Source: BioPortal + 130 + 150 Databases, annotation, curation tools MAGE-Tab GCDML AAO CHEBI SRAxml CML SOFT DICOM FASTA GELML MITAB …. SEDML… OBI VO PATO ENVO XAO MzML DO …. MIAPA MIRIAM MIQAS MIX REMARK MIGEN MOD SBRML …. MIAME TEDDY PRO BTO IDO… …. MIQE MIAPE CIMR MIASE …. CONSORT MISFISHIE…. ….
  9. 9. Dealing with fragmented standards for the experimental context user community The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  10. 10. 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
  11. 11. 1
  12. 12. 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.
  13. 13. 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…
  14. 14. 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.
  15. 15. 2
  16. 16. 3
  17. 17. 4
  18. 18. 5
  19. 19. 6
  20. 20. Data papers
  21. 21. • • • • • 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
  22. 22.  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
  23. 23.  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      environmental health genomics metabolomics metagenomics nanotechnology      proteomics stem cell discovery system biology transcriptomics toxicogenomics
  24. 24. Community involvement and uptake 1st ISA-Tab workshop 2nd ISA-Tab workshop 3rd ISA-Tab workshop User workshops/visits - start Other tools implement ISA-Tab Core developments Straw man ISA-Tab spec ISA software v1 Final ISA-Tab spec 2007 2008 1st public instance: Harvard Stem Cell Growing number of Discovery Engine systems starts to adopt ISA framework Conversions to Pride-XML/SRA-XML/ MAGE-Tab Database instance at EBI 2009 2010 Links to analysis tools starts RDF/OWL format starts 2011 2012 Publications The ISA software suite: supporting standards- ISA chapter in : Open Source compliant curation at the Software in Life Science community level Research OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets. Bioinformatics Woodhead Publishing Bioinformatics 2013
  25. 25. 2012 2013 2013 2012 2013 Nanotechnology Informatics Working Group

×