METADATA

Is a data about DATA. Describes HOW, WHEN and BY WHOM a particular set of data was collected.

BUT...
Vaste swathes of BIOLOGICAL DATA:

Are described using non-standard terminology Lack sufficient contextual information Not shared

ISA. Project, format, exploitation.

The building of data commons, depends on the use the metadata categories of: Investigation (project context) Study (a unit of research) Assay (analytical measurement)

Specification documentation: release candidate 1, ISA-TAB 1.0. Philippe Rocca-Serra, Susanna-Assunta Sansone and Marco Brandizi. 24 November 2008.

Why ISA?
1. Reproducibility Being able to reproduce the same experimental outcome in a different lab, on different data, is more powerful that repeating the experiment.

Summary of the efforts to replicate the published analyses.

Reproducibility in scientific research: high-throughput omics. Cesare Furlanello, FBK-MPBA: Predictive Models for Biomedicine and Environment. 21 June 2012.

Why ISA?
2. Open Source 3. Ontology Support: represents knowledge as a set of concepts
within a domain, and the relationships between those concepts.

4. Standardization 5. Lots of ISA Commons Participants: GigaScience, HSCI Blood

Genomics Repository, MetaboLights, NERC, etc.

6. Simple and Clear

STEPS THROUGH...

Work with the ISA Team to learn about the data organisation and ISA features. Analyse OMERO metadata format and ISA-TAB and compare them.

Some of the fields of the Investigation file

INVESTIGATION

STEPS THROUGH...
The fields of the Assay file
Protocol REF

Investigation Identifier Sample Investigation Title Name

Investigate ISA-TAB format and </Instrument/Microscope/@Model> && expand it Description$$ output Investigation Description $$Analysis regarding %%<sample identifier>%% $data collection$ <//Image/InstrumentRef/@ID> metadata. Submission Date Investigation
Discuss the content of the fields with Investigation Public Release Date Assay Name Performer Date

$$Analysis Title$$ Parameter Value[microscope]

teleconferences.with configuration] %%Person <//Image/AcquiredDate> <Image/@Name> Comment [Created Contacts%% INVESTIGATION CONTACTS

theImage File ISA Team using

<Image/Pixels/TiffData/UU ID/@FileName>

Protocol REF 1 Derived Investigation Data Transformation Person Last Name $$Person Last Name$$ Data File $$data analysis$$ %%Pipeline Name%% %%Pipeline Steps%% a_OutputImage.txt Investigation Person First Name $$Person First Name$$ Investigation Person Mid Initials Investigation Person Email Investigation Person Phone Investigation Person Fax Investigation Person Address $$Person Address$$ $$Person Email$$

STEPS THROUGH...

Create templates to be filled both by user and our own software. Collaborate with Interface, Django and PyWPS groups in order to create scripts to implement our work into the whole project.