ISA-Tab

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[edit] How the GSC is participating in the ISA-Tab project

This page was established after the first ISA-TAB workshop at the EBI in Dec 2008 to hold GSC case studies based on this format for data exchange.

The GSC is one of many members of the ISA-Tab group and the ISA-Tab homepage can be found here: http://isatab.sf.net/

[edit] The power of the ISA paradigm

The RSBI working group has proposed an "Investigation Study Assay" paradigm for the modularization of minimum information checklists to accomodate reporting of multi-omic studies. This "ISA" construct is now also recognized by MIBBI. The GSC's MIGS checklist was specifically revised to also reflect the ISA structure to help in its modularization - some fields describe the whole Investigation, some the Study and some the Assay (in this case sequencing by any method including ultra high-throughput methods).

The power of this paradigm is the notion that an Investigation can contain one or more studies and assays, or one study with many assays. This is the future of multi-omic standardization, where for example, one sample subjected to many assays (i.e. a water sample assayed with metagenomics and metatranscriptomics) could be uniformly described.

[edit] ISA-Tab

Following evaluation as a strawman at the 1st RSBI workshop in Dec 2007 at the EBI, this set of updated files was made available. The GSC has an action from this workshop was to further evaluate ISA-tab with respect to coding MIGS/MIMS compliant reports. This will add a genome/metagenomic component to the 'multi-omic' coverage which currently includes working on capuring transcriptomics, proteomics and metabolomic reporting guidelines.

http://www.ebi.ac.uk/~sansone/WODS/RSBI-07 - look for ISA-TAB-package_v0.2.zip

This zip file contains a document explaining what ISA-TAB is and what it is for <ISA-TAB-specifications_v0.1.pdf>.

[edit] Capturing MIGS/MIMS in ISA-Tab

The current MIGS/MIMS specification we are using as reference is here (needs final edits to be 2.0 compliant): http://gensc.sourceforge.net/docs/migsmims/

To evaluate ISA-tab for use in capturing MIGS/MIMS compliant reports, we have developed a case study. In this study 4 metagenomes (DNA) and 4 metatranscriptomes were generated using pyrosequencing in a study with a simple experimental design (1 treatment, controls, and 2 time points).

[edit] Case study 1

Title: The response of bacterial communities to ocean acidification

Data: metagenomics/metatranscriptomic submissions to NCBI Short Read Trace Archive and GEO

Jack Gilbert, Dawn Field, Ian Joint

ISA-Tab: Susanna Sansone, Phillipe Rocca-Serra

[edit] Availability of data

The data has been submitted to public databases:

NCBI Short Read Trace Archive:

GEO:

[edit] Completion of ISA-tab file

Example file 1: A minimum representation of the study design has been completed by Phillipe.

Roadmap for building on this draft file

1. ISA-tab will be revised to make ISA-Tab MAGE-Tab backward compatible and our example will be updated by Phillipe

Done (Feb): ISA-Tab launched website: http://isatab.sf.net/

Done (Feb): ISA-Tab version 2 is MAGE-Tab backwards compatible and is being used to build case studies.

Done: 25/2 this template used the basic ISA-Tab template, with the Bergen data: [[Media:ISA-TAB-v0.2-Without-MIMS-Gilbert-et-al-2008v3.xls| ISA-Tab Bergen data I]

Assay tabs are defined by "Technology Type" and "End point"

1.2 Write up this case study for a paragraph or so contribution to the RSBI workshop report (post workshop activities) in the OMICS special issue based on the 5th GSC Workshop

Done: Contributed GSC genome catalogue description to ISA-Tab meeting report and included this case study on the website/paper. Paper to appear in OMICS in summer.

2. Modify it in a further telecon to make the MIGS/MIMS required fields explicit (for GSC data capture in spreadsheet format) - color code it for ease of understanding; consider writing a short 'how to' doc

• Selected to do "MIMS" portion (MIGS as it applied to metagenomes") with special attention to capture of biogeochemical measurements that define habitat (forte of MIMS): (to be uploaded)

Currently all the additional Bergen fields are in green.

Is this ALL of MIMS? It is certainly MORE than MIMS it appears. We could upload this file as an example.

We need to suggest a #comment field that allows a mapping to the required MIGS/MIMS fields to support a generic spreadsheet option that could be parsed into the Genome Catalgoue. Color these in a different color.

2.1 What is in MIGS/MIMS, that needs to be added?

2.2 Write talks for UHTS Workshop and get feedback

3. Circulate in GSC for further comment (already have individuals requesting a spreadsheet option for inputting data to the Genome Catalogue - this will happen in part with community consultation on the ISA-Tab workshop report

3. Evaluate using this ISA-Tab example as a future template for parsing into the Genome Catalogue (is it worth writing a parser versus manual transfer of data if usage is infrequent, assess potential usage of spreadsheet format, get feedback from specific contributors to build further case studies)

[edit] Further Notes

This case study is proceeding through a set of telecons that identify issues and which are roughly outlined here: ISA-Tab notes

[edit] ISA-Tab SourceForge.net Project Summary

• Project name: isatab (04 July 2009)
• Developers on project: 8 (04 July 2009)
• Activity percentile (last week): 92.86% (04 July 2009)
• Downloadable files: 0 total downloads to date (04 July 2009)
• Mailing lists (public): 1 (04 July 2009)
• Discussion forums (public): 2, containing 2 messages (04 July 2009)
• Tracker: Bugs (14 open/20 total) (04 July 2009)
• Tracker: Support Requests (0 open/0 total) (04 July 2009)
• Tracker: Patches (0 open/0 total) (04 July 2009)
• Tracker: Feature Requests (13 open/15 total) (04 July 2009)