1st (RSBI) ISA-Tab Workshop – Scope and Outcome

Tackle today's need for exchange of multi-omics experiments• Evaluate the ISA-TAB straw-man (incomplete) proposal

- It builds on this existing paradigm of the MAGE-TAB- It shares the same motivation for the use of spreadsheet (versus the ‘complex, but expressive’ MAGE-ML)

• Current use cases- Submission (import) and download (export) tabular format

- Note: not human created but assisted by a ‘tool’ (e.g. forms)

- Also, as exchange format while the suites of FuGE-ML based modules are under development - At that stage, ISA-TAB can finding utility as a user-friendly presentation layer for the XML-based formats (via an XSL transformation)

Work plan on how to move forward• The ISA-TAB may not fulfil everybody needs

- Hard to make one measure to fit all

• What need to be modified or changed, how to test it, etc.- To be finalized with interested parties

Semicolon-separated fields into a tabular format (e.g. Person Role) – Phil J

• Formatting issues

• Problem when sources are two different CVs/Ontology

Section dividers – Michael M

• Is an empty line the best way? Roles to be defined (e.g. Protocol)

• Or should each section be in different tabs, e.g. for sorting*?

CVs/Ontology and keywords/comment (free text) – Weida T, Philippe RS

• Which fields need CVs/ontology vs free text (e.g. Factor must be a CV)

• For CVs/Ont: what about having ‘term’, ‘id’ and ‘reference’? Chris T

Ensure that id (how?) columns are the only one carried across tabs – Allyson L

• E.g. in both Study and Assay tab Characteristic[MaterialType] is repeated

Technical Challenges – To Be Solved (1)

Need for [qualifiers] to be CV/Ontology – Philippe RS• Allowing free text is problematic?

Restricting FactorValue – Michael M• Is there ever case where FactorValue is neither Characteristics or Parameter?

There may be a problem with how ISA-TAB currently deals with protocols and protocol parameters (inherited from MAGE-TAB)

• Parameters and characteristics have the same weight • Either we capture all parameters/characteristics in the protocol section, or

we have it only in the study/assay sections

What if the contact is not a person? – Chris T• Example: Person X is quitting, so wants to fill in a job title or role instead• Do we need to worry about this, or is it simply not worth modelling?

Technical Challenges - To Be Solved (2)

Reference system between ISA-TAB’s Study and (SDTM) SEND and CDISC – Michael M

• Also reference between ISA-TAB’s Studies – when e.g. samples are ‘reused’

Referencing out to other Protocol Formats – Weida T• In the Reference tab it would be nice to reference other formats of studies that

aren't applicable to us directly • Examples of references would include SDTM, SEND, and CDISC

Possibility of renaming “Sample Name” to “Specimen Name” – Jen F• Alternatively, could use Char[MaterialType] = specimen• Work for an CV/ontology (to be discussed in OBI)

Normalization Method: should it be required? – Stefan W Normalized data isn’t worth much without knowing the normalization procedure Put in normalization as a data in – data out protocol?

Technical Challenges - To Be Solved (3)

When a field is critical to one system but not to another - Weida T• Fully optional, marked as MI-compliant (choice is up to each system) and

absolutely mandatory (for EBI systems)• The latter are the ‘linking names’ to successfully understand/parse it

Current (and suggested) use cases - Phil J• Submission (import) exchange (in the absence of all the FuGE-based modules)• Download (export)• Sorting* possibly

Some (referenced) fields are redundant - Stefan W

• In Study, however, it is when there are multiple study you need to know who did which one

High level classification for Assay – Weida T, Phil J

• Pairing of ‘endpoint’ (gene expression) and ‘technology type’ (DNA microarray)

Questions with (possible) Answers

IDs – Michael M

• For each ISA-TAB submission human generated files (internally unique if), software generated (globally unique ids, e.g. LSID)

Improve I/S/A definitions - Michael M

Move ‘Ontology Source Ref’ up in then Reference file - Michael M

General comments about the separation of a study into multiple studies

• It is left to the submitter, for their convenience

• Need to be made clear, also the use of Investigation to ‘group’ related Studies

Questions with (possible) Answers

1st ISA-Tab Workshop – Outcome and What Next (1)

What have we achieved these two days?• Initial ‘evaluation’ of the the ISA-TAB straw-man proposal• Listed technical issues that need to be addressed• Started creating a new example…

-We should have enough info now to develop a sound plan

When can we meet next and what the goal would be?• Around May?• Finalize the draft specification + example (to be published)

What do we need to do before then?• Create examples in the various domains (using published experiments)• Identify leading persons, responsibilities timelines et

Dissemination plans and documentations• Create webpage, list etc (google) – Philippe• Refine document (iterative) – Philippe, Weida, Susanna

Technical challenges• Allyson/Nataliya

1st ISA-Tab Workshop – What next (2) Biological domains

• Dawn: genomics/metagenomics• Norman: environmental• Jennifer/Philippe: toxicology• Jennifer: clinical• Stefan: cell assay

- Identify the papers + create Studies in your domains and –with the help of the leaders below- work on creating Assays

Technological domains• Dawn: sequencing • Phil: proteomics• Nigel: metabolomics• Tim: transcriptomics/PCR• Stefan/Philippe: cell assay (non-omics)• Jennifer: histopathology

- Define the required column headers + Assist biological domain leaders above and work to define fields in the your Assay tabs

1st ISA-Tab Workshop – What next (2)

Implementation (ideas-plan)• Phil/Marco

- Excel (some versions are GLP) and open office, etc.- Initial design of BioMAP-Harvest/ISA-tab-Harvest (based on PrideHarvest)

Conversion to FuGE and reverse (XSL transformation) (ideas-plan)• Allyson/Philippe/Marco

Timelines/deliverables (end of each month):• JAN: Examples/papers identified (from biological groups); webpage up • FEB: Define columns headers in each technology domains defined • MAR: Technical challenges addressed; Study tabs filled• APR: Assay tabs filled; check/review examples• (Iterative): refine the document• (mid?) MAY: Meeting

- Spec, examples ready, ideas on implementations and FuGE conversions