RSBI use cases in FuGE by dfhrf555fcg

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									RSBI WGs – Use case encoded in FuGE                                                        July 2006

MGED Reporting Structure for Biological Investigation (RSBI) WGs
                Use cases encoded in FuGE
             (http://www.mged.org/Workgroups/rsbi, http://fuge.sourceforge.net)

Use case structure
The use case here reported follows the RSBI structure of INVESTIGATION, STUDY and ASSAY.
An INVESTIGATION is as a self-contained contained unit of scientific enquiry, with a holistic
hypothesis or objective and a design, defined by the relationships between STUDY(s) and
ASSAY(s). STUDY is the ‘container’ for the description of and steps performed on the subject(s) of
the investigation, with distinct periods or PHASE(s). ASSAY ‘contains’ the omics-based or other
test(s) - and its produced data -performed on the subject(s).

Encoding in FuGE
The text below in italics shows how the information can be encoded using FuGE classes and also
where an extension of the model, or the use of CVs/Ontology resource is needed.
There is no one-to-one mapping between RSBI concepts and FuGE classes. The
INVESTIGATION, however, can be encoded by FuGE.Bio.Investigation package, while the
FuGE InvestigationComponent, described as a single functional genomics component (e.g.
microarray, proteomics), can be used to encode a set of STUDY and ASSAY. Details of the latter
two can be encoded as a series of ProtocolApplication.
The mapping is limited to the information related to INVESTIGATION and STUDY. Encoding
information related to the ASSAY would require the use of ‘extension’ of FuGE into a certain
technological domain (e.g. MAGE v2, will use FuGE to model microarray-based tests).

Acknowledgements
The textual description of the use case is based on a real example provided by Matthew Davey,
University of Sheffield, UK (NERC PG&P, Kunin award). Andy Jones of University of Manchester
has assisted in the mapping and encoding the information in using FuGE.

Use case by the Environmental Genomics WG: Application of omics and
standard technologies to assess plant responses to abiotic stress
INVESTIGATION
NAME and/or ID
Plant responses to abiotic stress at range margins: mechanisms and limits to adaptation. NERC
Data Catalogue number #; authors X, Z, Y, published by XY et al.
These requirements are met in the FuGE.Bio.Investigation package.
Investigation class allows capturing the name and free text description of the entire investigation
(inheriting from Describable). The Investigation is an Identifiable class and allows referencing to
external resources, such as the NERC Data Catalogue and a BibliographicReference. Providers
can be recorded by the ContactRole relationship with Investigation class.

DESCRIPTION
The aim of the investigation is to understand adaptive responses to abiotic environmental
challenges faced by plants and the role that these challenges play in limiting plant distributions.
Response of Arabidopsis thaliana and A. l. petraea to controlled environmental challenges will be
used as a model system.
These requirements are also met in the FuGE.Bio.Investigation package.
Investigation class allows capturing free text description of the entire investigation (inheriting from
Describable). Investigation has an association to Material class and this to OntologyTerm to
encode the name of the plant(s) used. The association to OntologyTerm allows defining the type
of investigation design using an external resource of controlled vocabulary terms (e.g.
perturbational design, geographic distribution design).
RSBI WGs – Use case encoded in FuGE                                                      July 2006


OBJECTIVE and DESIGN
In order to achieve this aim the project has the following main objectives:
1) To assess the physiological and molecular (transcriptomic and proteomic) responses of A. lyrata
petraea to controlled environmental challenges (high and low temperature), comparing these to
responses found in the model A. thaliana.
2) To assess the factors limiting population growth rates in A. l. petraea populations across a
latitudinal and elevational transect.
These requirements are met in the FuGE.Bio.Investigation, Protocol and Material packages.
Investigation can have several InvestigationComponent, each one summarizing the use of a
technique within an investigation. Each component has Factor (unique or shared with other
components) with an association to OntologyTerm to encode the category and type of factor
tested in the investigation component, using an external resource of controlled vocabulary terms.
This use case is encoded in 1 Investigation with 2 different Material and 3
InvestigationComponent (transcriptomic, proteomic and biometric - population growth-
component). The latter has an association to OntologyTerm that allow capturing the technology
used by each one using an external resource of controlled vocabulary terms (transcriptomic,
proteomic and biometric – a conventional technology).
1) The requirements of the first objective of this investigation are met by the 1 st and the 2nd
InvestigationComponent (using transcriptomic and proteomic technology).
These have the same Factor and FactorValue (abiotic stress: high-low temperature), encoded
with the association to OntologyTerm. FactorValue has DataPartition a quick route that allows
associating a certain factor to a subset (group) of data (e.g. data from stressed plants vs data from
control plants). InvestigationComponent contains all its relevant ProtocolApplications, that
allow describing the investigation flow from the starting materials to the end data. In this use case
A. lyrata petraea is the starting input Material for the (first) ProtocolApplications in one
InvestigationComponent, while A. thaliana is the input Material for the 2nd component.
2) The requirements of the second objective of this investigation are met by the 3 rd
InvestigationComponent (biometric).
A. lyrata petraea is the only starting input Material for the first ProtocolApplications in this 3rd
component. The Factor and FactorValue (different locations: Ireland, NW Wales etc) different and
not shared with the previous two components. FactorValue has DataPartition that allows
associating a subset of data to a certain experimental factor (facilitating comparison of data
different locations).

STUDY
PHASE 1 – FIELD SAMPLING
The main study area will consist of a SW – NE transect from the scattered A.thaliana and A. l.
petraea populations of Ireland and NW Wales, through the more densely occupied landscape of
Scotland, northern limits in NE Sweden and distributional core in Iceland. Additional samples from
the Italian Alps (the species’ southernmost European outpost), Germany, and arctic Russia will be
collected to provide a more complete picture of the European distribution of A. l. petraea.
Samples taken are individual plants, leaf samples and seed samples. Geographic Positioning
System (GPS) information on these samples will be recorded. Also detailed spatial information
about plants within each site will be recorded to allow for studies between plants centimetres,
metres and kilometres apart.
These requirements are met in the FuGE.Bio.Protocol, Material and Data packages.
A PHASE represents a period of time within a higher structure, such as a STUDY. The latter is
defined by a nested structure with which contains multiple phases. A high level Protocol and a
series of children Protocol allow representing the STUDY and its PHASEs. Each Protocol (high
level or child) can be given a name or an OntologyTerm (inheriting from Describable) (e.g. study,
sampling phase) and a unique identifier (inheriting from Identifiable) and parameters (inheriting
from Parameterizable).
An instance of a sampling PHASE protocol, like in this case, is represented by the
ProtocolApplication. This class allows supplying the important parameters about this PHASE
RSBI WGs – Use case encoded in FuGE                                                        July 2006

(e.g. study area where sample where taken) and values from controlled vocabulary terms via the
association to OntologyTerm. The information on who carried out this PHASE (performer) and
when is represented by the ContactRole class, association to ProtocolApplication.
The output of this PHASE is both Data (GPS and spatial information) and Material (A. lyrata
petraea and A.thaliana samples). This type of Data can be represented in several ways: by
InternalData object or ExternalData (as pointer to external file) and as NameValueType triplets or
from controlled vocabulary terms via the association to OntologyTerm (inheriting from
Identifiable). The output Material (plants’ parts) can be uniquely identified (from Identifiable) and
its type represented by via the association to OntologyTerm.

PHASE 2 – CONTROLLED ENVIRONMENT
For A.thaliana and A. l. petraea seeds of 2 or more different populations or locations/focal points
within a population are taken from field and grown under controlled conditions in the lab.
A. l. petraea seedlings and transplanted rosettes at periphary and core of their distributions are
grown in controlled environment facility under climatic conditions that characterize the southern
and northern distribution limits of the main field studies. These cabinets treatments will be the basis
for transcript and proteomic responses.
These requirements are also met in the FuGE.Bio.Protocol, Material and Data packages.
Also this second PHASE (child) Protocol can be given a name or an OntologyTerm (inheriting
from Describable) (e.g. controlled phase) and a unique identifier (inheriting from Identifiable) and
parameters (inheriting from Parameterizable).
An instance of a controlled PHASE protocol is represented by the ProtocolApplication. In this
case, however, there are two ProtocolApplication (conducted in parallel). ProtocolApplication
allows supplying the important parameters about this PHASE (e.g. controlled growth conditions)
and values from controlled vocabulary terms via the association to OntologyTerm. The
information on who carried out this PHASE (performer) and when is represented by the
ContactRole class, association to ProtocolApplication.
The input and the output of both ProtocolApplication is Material that can have components (the
self-association on Material), so this can be used to define a whole organism and its parts (e.g.
plant’s seedlings and rosettes). A single ProtocolApplication can act on the whole Material (and
this implies that it acts on its parts as well). However, the different Materials could be modeled with
different ProtocolApplications if this fits the semantics better.

PHASE 3 – TREATMENT
The samples are exposed to temperature stress (low and high temperature). Samples of A.thaliana
and A. l. petraea grown at seasonal mean temperature are used as reference.
These requirements are also met in the FuGE.Bio.Protocol, Material and Data packages.
Also this third PHASE (child) Protocol can be given a name or an OntologyTerm (inheriting from
Describable) (e.g. treatment phase) and a unique identifier (inheriting from Identifiable) and
parameters (inheriting from Parameterizable).
An instance of a treatment PHASE protocol is represented by the ProtocolApplication. In this
case, also, there are two ProtocolApplication conducted in parallel, with different parameters’
values (e.g. stress temperature vs seasonal mean temperature). The information on who carried
out this PHASE (performer) and when is represented by the ContactRole class, association to
ProtocolApplication. The input and the output of both ProtocolApplication is Material.
These ProtocolApplication Parameters are also Factor and FactorValue.

ASSAY
As said above, this mapping is limited to the information related to INVESTIGATION and STUDY.
Encoding information related to the ASSAY would require the use of ‘extension’ of FuGE into a
certain technological domain (e.g. MAGE v2, will use FuGE to model microarray-based tests).

DEMOGRAPHIC
Development of a season-specific life table model of the focal A. l. petraea populations, using data
from the permanent quadrats within each sample site. Each population will be surveyed twice per
RSBI WGs – Use case encoded in FuGE                                                           July 2006

year and the survival, growth, flowering and seed set of each focal plant will be assessed. Analysis
of the resulting life table will allow us to ascertain which life stages are most critical to A. l. petraea
population growth in each site and the extent to which summer or winter stresses impinge on the
population growth rate.
In addition, a programme of within site and cross site translocations will be conducted at a cross-
section of focal sites, ranging across the distribution of the sample.

TRANSCRIPTOMICS
Total RNA from the A.thaliana and A. l. petraea treated and reference samples are prepared and
run on Affymetrix Arabidopsis ATH1 Genome Arrays.
Real-time quantitative PCR (qPCR) on further RNA samples will be used to provide independent
confirmation of expression patterns detected by microarray analysis.

PROTEOMICS
Proteomics study of A. thaliana, A. l. petraea are carried out by using 2D-PAGE for protein
separation coupled with mass spectrometry (MS) for protein identification. ProteomeWorks
proteomics suite will be used (Bio-Rad/Waters), comprising equipment for high-throughput 2D-
PAGE, gel imaging systems (GS-800 calibrated densitometer and FXPro Plus fluor/phosphor
imager, PDQuest software), robotic spot-cutter and digester, MALDI-MS and capLC-QTof-MS/MS
instruments. The proteome is analysed over a time course of plants development.

     **********To be completed with other use cases from other RSBI WGs**********


Use case 2- Nutrigenomics WG: Application of omics and conventional
technologies to assess the interaction between diet and gene activity



Use case 3- Toxicogenomics WG: Application of omics and conventional
technologies to assess the toxicology/carcinogenicity of chemical

								
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