P Rocca-Serra - The open source ISA metadata tracking framework: from data curation and management at the source, to the linked data universe

The open source ISA metadata tracking framework: from data curation and management at

the source, to the linked data universe

BOSC, Long Beach, July 13-14, 2012

Philippe Rocca-Serra (Ph. D)

ISA Team

twitter : @isatools.org

[email protected]://www.isa-tools.org

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Friday, 13 July 2012

MAIN THEME:It is all about structuring experimental information to make it available to computer and software agents to enable mining.

But let’s proceed gradually…

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Notes in Lab Books(information for humans)

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Spreadsheets and Tables( the compromise)

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Spreadsheets and Tables( the compromise)

Facts as RDF statements(information for machines)

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Observations

• Experiments are expensive, often publicly funded, still many fail to see the light.

• Spreadsheets are the most common vehicle for so-called ‘omics’ (functional genomics) experimental metadata tracking

• technology centric repositories form de facto silos• conversions are required to allow for deposition to public

databases.• submitting to common information across a series of

repositories is inefficient

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Case Study

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Many ontologies, Many Formats, Many Requirements…

Grr…Where are the tools!?!

Credits: h/p://liverpoolsolfed.wordpress.com/resources/image-‐bank/demonstraAon/

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ISA framework overview14


Why ISA format and Tools?

–Supporting data provenance tracking–Node/Edge underlying concept–Tabular as a compromise: a presentation layer inspired by Object

model (FuGE,MAGE-OM)–A Generic representation, applied to:•microarray based experiments (MAGE)• sequencing based experiments (SRA)• flow cytometry based experiments (FuGE-Flow Cyt)•mass spectrometry and NMR spectroscopy experiments


Why ISA format and Tools?

investigation

assay(s) assay(s)

data data

external files in native or other for-

mats

pointers to data file names/location

investigationhigh level concept to link related studies

studythe central unit, containing information on the subject under study, its characteristics and any treatments applied.a study has associated assays

assaytest performed either on material taken from the sub-ject or on the whole initial subject, which produce quali-tative or quantitative meas-urements (data)

H. Sapiens

33 Years

H. Sapiens

H. Sapiens

H. Sapiens

H1

H1

H2

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35

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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

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

MAGE-Tab Pride-xml

SRA-xml

ISA metadata specifications:•workflow and process orientated•compatible with checklist enforcement•compatible with external vocabulary resources•compatible by design with existing schemas

Currently finalizing conversion to RDF to explore the growing Linked Data universe, in collaboration with the W3C HCLSIG, Toxbank Consortium)


ISA syntax and Table definition

• Material Transformations: – Input and Outputs of Protocols are Material Nodes (Source Name, Sample Name, Extract Name, Labeled Extract Name.)

Material Node Material Node

Protocol REF

Parameter Value […]

Characteristics[…]Factor Value[…] (independent variables)Material TypeComment[…]


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Date (day effect)

Performer (operator effect)





Protocol REF




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Date (day effect)






Protocol REF




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Date (day effect)


Data File Node





Protocol REF




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Date (day effect)


Comment[…]

Data File Node





Protocol REF




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Date (day effect)


Comment[…]

Data File Node


ISAconfigurator Tables19


ISAconfigurator Tables20


How do ISA tools access Ontology servers?

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isacreator

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

But these are just some of them...we also have a data entry wizard and an import utility...

The ISAcreator...


Select and Annotate in ISAcreator24


Extending ISAcreatorThe Plugin Archictecture


Plugins in ISAcreator

•Plugins can be developed for 3 different purposes:

In ISAcreator, we use the Apache Felix implementation of the OSGi framework...it’s really good.

Search (adds extra search space for ontology tool)

Custom cell editors (for spreadsheet)

Extra general functionality (which appears in a plugin menu)

•2 Examples of ISA plugins:

• Access to local metadata stores: Novartis Plugin to Ontology Widget

• Annotation of findings: Metabolite Identification Plugin (Metabolights Repository contribution to ISA project).


Plugins...example 1 Novartis Metastore Search

Search function on the Novartis Metastore... integrates search results on the metastore in the Ontology search tool.

So, with the Novartis plugin in your Plugin directory, you’ll be able to search the Novartis metastore directly within ISAcreator, and it will handle all the tasks involved with recording term source, etc.


Plugins Example 2 - Metabolite Identification plugin

5 Credits: Kenneth Haug: Metabolights


Potential Issues and known hurdles

• The problem of conflicting versions–especially high when working with big consortia–distributed, decentralized groups of users

• Lack of version control and history

• Absence of collaborative features

–Looking for new solutions while retaining the features !•OntoMaton: Bringing Google Doc, NCBO Bioportal and ISA-TAB together !

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OntoMaton: Searching


OntoMaton: Tagging


OntoMaton• Public release: http://goo.gl/2OKFV

• Can be used in any Google Spreadsheet document

• Application:

• Annotating data records

• Supporting ontology development (see OBI Quick Term Templates)


http://goo.gl/2OKFV

http://goo.gl/2OKFV

ISA2RDF work in progress

• Use case on W3C HCLS scientific discourse list–deciding on the granularity of representation–building on previous experience–Evaluating alternative representations.

• Participitation to the Biohackathon 2011–http://blogs.openaccesscentral.com/blogs/bmcblog/entry/

biohackathon_2011_number_1–Discussing best practices• PURL uri and identifiers.org as identifiers

• Openphacts guidelines (http://www.nanopub.org/guidelines/OpenPHACTS_Nanopublication_Guidlines_v1.8.1.pdf)

•

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http://blogs.openaccesscentral.com/blogs/bmcblog/entry/biohackathon_2011_number_1




http://www.nanopub.org/guidelines/OpenPHACTS_Nanopublication_Guidlines_v1.8.1.pdf





Preparing for Linked Open Data

✴ ISA2RDF (Toxbank collaboration) contribution to an ecosystem of software tools supporting the ISA syntax

✴ reliance to internet resolvable identifiers

✴ W3C bio/life science Note on Gene Expression RDF - (PMID: 22449719)

✴ TODO:

✴ Specify comparator groups + analysis methods and resulting measurements and statistical measures






✴ TODO:







✴ TODO:



ISA2RDF: work in progress

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jeliazkova.nina [toxbank project]


ISA2RDF: work in progress

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jeliazkova.nina [toxbank project]


ISA2OWL

• OWLAPI

• ISA Parser (in memory BII object store objects)

• Mapping ISA syntax into target Ontological Space

• Decoupling Mapping from Conversion Engine

• avoid to be tied to a semantic framework


ISA2OWL: mapping in the BFO space as starting point


ISA2OWL: mapping in the BFO space as starting point


ISA2OWL: mapping issues

• Stability over time

• Keeping track of resource versions

• Gaps in coverage

• Use of local extensions

• Direct requests/contributions


ISA2OWL: development

• include graph metadata (graph provenance to aid indexing)

• extend semantic validation of ISA archive

• augment annotation by suggesting additions

• facilitate curation work

• create new mappings to other frameworks(OPML model, SIO,)


Publication...

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; Nataliya Sklyar ; Chris Taylor ; Kimberly Begley; Dawn Field; Stephen Harris; Winston Hide; Oliver Hofmann; Steffen Neumann; Peter Sterk; Weida Tong; Susanna-Assunta SansoneBioinformaAcs 2010 26: 2354-‐2356

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Groups and individuals participating in:MIBBI http://mibbi.org ISA-‐Tab format http://isatab.sf.netOBO Foundry http://obofoundry.orgOBI: http://obi-ontology.org/page/Main_Page

ISA Infrastructure Team:Alejandra Gonzalez-‐Beltran (Oxford)Eamonn Maguire (Oxford)Philippe Rocca-‐Serra (Oxford)

Acknowledgements

collaborators at:Cambridge University

EuNuGOHarvard School for Public Health

FDAs NCTRLeibniz Plant Institute

NERCs NEBCSIDR, INIST

Metabolights, EMBL-‐EBI

Funders:EU Carcinogenomics Project

UK BBSRC

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http://isatab.sf.net

http://isatab.sf.net

http://obofoundry.org

http://obofoundry.org

http://obi-ontology.org/page/Main_Page

http://obi-ontology.org/page/Main_Page

Groups and individuals participating in:Winston Hide: HSPHOliver Hoffman: HSPHShannan Ho Sui : HSPHBrad Chapman: HSPHChristoph Steinbeck: MetabolightsKenneth Haug: MetabolightsPaula de Matos: MetabolightsMagali Roux: INISTFlorian Mazur: INISTAlain Zasadzinki: INISTMarie Christine Jacquemot: INISTNina Jeliazkova: ToxBank

And many more who have to forgive us!

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Questions:

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Technology

P Rocca-Serra - The open source ISA metadata tracking framework: from data curation and management at the source, to the linked data universe