RightField Rich Annotation of Experimental ... - Seek for Science

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Oct 22, 2013 (3 years and 1 month ago)

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RightField

The Semantic Annotation of
Experimental Data using Spreadsheets,

Katy Wolstencroft, Stuart Owen, Matthew Horridge,

Olga Krebs, Wolfgang Mueller Carole Goble

RightField



A tool for embedding ranges of ontology terms
into spreadsheets to allow the users of those
spreadsheets to add semantic annotations from
simple drop
-
down lists

RightField



A tool for embedding ranges of ontology terms
into spreadsheets to allow the users of those
spreadsheets to add semantic annotations from
simple drop
-
down lists

Why?


Makes annotation quicker and more efficient


Standardises annotation


Hides the ontology complexity from the users

Describe

experiments

and
results

of experiments


Minimal Information Models

Guidelines,

Checklists,

vocabularies


Managing Biological Data

Necessary for publication, submission to
public databases and sharing

Describe

experiments

and
results

of experiments

Minimal Information Models

Guidelines,

Checklists,


Managing Biological Data

MIACA

M
inimal
I
nformation
A
bout a
C
ellular
A
ssay

MIAME

M
inimum
I
nformation
A
bout a
M
icroarray
E
xperiment

MIAPE

M
inimum
I
nformation
A
bout a
P
roteomics
E
xperiment

MIARE

M
inimum
I
nformation
A
bout a
R
NAi
E
xperiment

MIASE

M
inimum
I
nformation
A
bout a
S
imulation
E
xperiment




MIBBI >30

Describe

experiments

and
results

of experiments

Ontologies and Vocabularies for
Annotation


Managing Biological Data

Gene Ontology

ChEBI

MGED

SBO


BioPortal >270 biomedical ontologies


Data

MIBBI

Model

Ontologies

Microarray

MIAME
:
Minimum

Information

about

a

Microarray

Experiment


MGED


Proteomics

MIAPE
:

Minimum

Information

about

a

Proteomics

Experiment


PSI
-
MI,

PSI
-
MS,

PSI
-
MOD


Interaction

experiments

MIMIX
:
Minimum

Information

about

a

Molecular

Interaction

Experiment


PSI
-
MI

Protein
-
Protein

Interaction

Systems

Biology

Models

MIRIAM
:
Minimal

Information

Required

In

the

Annotation

of

biochemical

Models


SBO
:

Systems

Biology

Ontology

Systems

Biology

Model

Simulation

MIASE
:
Minimum

Information

About

a

Simulation

Experiment

KISAO
:
Kinetic

Simulation

Algorithm

Ontology

SysMO: Systems Biology of Micro
-
Organisms

SysMO Consortium


Pan
-
European consortium



> 100 research groups


> 320 scientists


Distributed, interdisciplinary
projects


Expected to pool data and
results and disseminate


Microbiologists, molecular
biologists, biochemists,
mathematicians....not many
informaticians

SysMO
-
DB


SysMO
-
SEEK


a platform
for systems biology data
sharing


Web based environment for
sharing in the consortium
and disseminating to the
community


Used in other consortia:


Virtual Liver, EraSysBio+,
UNICELLSYS and more....




SOP

Associating Experiments

Investigation

Study

Assay

Construction

Validation

SOP

SOP

http://isatab.sourceforge.net/

SOP

Data Templates and Vocabularies

Construction

Validation

SOP

SOP

Metabolomics

Metabolomics

Mass

Spec

Transcriptomics

Proteomics

Fluxomics

Fitting in with Laboratory practices



Scientists can continue to do what they have
always done


Embedding semantics into the tools already in
use


Excel, excel, excel.....


Ontology terms for marked
-
up cells in drop
-
down boxes

The End Result

Excel
Workbook

Ontology

“Portion” of ontology
terms

Terms Embedded

into


Excel
Workbook

RightField Client

How it Works

Marked
-
up workbook

Saved in plain Excel

Informaticians/ontologists

End Users

RightField Application

Loading Ontologies

Published

ontologies

Multiple
versions

You can also load local ontologies from file or URL

Loading Ontologies

Excel workbook loaded into

RightField with multiple
worksheets

Class hierarchies of

loaded ontologies

Term lists for
selected cells

Methods for specifying
ontology terms

Selected parent term
from the ontology

Excel workbook with
marked
-
up cells

Marking
-
up Columns or Rows

Ontology terms for marked
-
up cells in drop
-
down boxes

The User View

Ontology Information


Ontologies encapsulated


Scientists can work offline


Ensures same versions of ontologies used for a series
of experiments


No special macros or plugins required, just Excel or
Open Office


Versions and URIs captured in hidden
worksheets


Provenance


Comparisons between sheets


Linking back to the vocabularies

Provenance

Term Label

The human readable term
label

Term IRI

The (unique) term
identifier

Ontology IRI

Ontology Version

The ontology that defines the
term

The version of the ontology

Physical Location

The (web) location of the
ontology

RightField Technologies

OWL API

Loading ontologies and reasoning

Apache POI HSSF libraries

Loading and saving of Excel Spreadsheets

Java

Platform Independent

Ontology Languages

RDFS

-

RDF Schema

OBO

-

Open Biomedical Ontologies

OWL

-

Web Ontology Language

RightField in Use


SysMO


Systems Biology of MicroOrganisms


E
-
Lico
-

a virtual laboratory for interdisciplinary
collaborative research in data mining and data
-
intensive
sciences. Case Studies in kidney research


BioBanking in the Netherlands


Outside Biology


Oil and Gas industry


Egyptology specimen classification


Populate

Store / Reuse

Extract

RDF Graph

Using RightField Spreadsheets

Future Developments



Auto
-
complete


Validation of annotation


Populating ontology content
-

Populous


Populous


Generic tool for populating ontology templates


Supports validation at the point of data entry


Expressive Pattern language for OWL Ontology
generation


Helps biologists with ontology design patterns


http://www.e
-
lico.eu/populous


Simon Jupp, Robert Stevens, University of Manchester

Availability


Open source


http://www.rightfield.org.uk

Acknowledgements

Stuart Owen

Katy Wolstencroft

Carole Goble

Wolfgang Mueller

Olga Krebs

Matthew Horridge