OntologyEntry in MAGE

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OntologyEntry in MAGE

• Chris Stoeckert, Helen Parkinson
• Trish Whetzel, Joe White
• Gilberto Fragoso, Liju Fan, Mervi Heiskanen,
• Angel Pizarro
• Ontology Working Group
• MGED6
• 3 Sept. 2003, Aix-en-Provence, France

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Ontology Workshop

• Relation of the MGED Ontology to MAGE
• Brief review of the MGED Ontology
• Policies for coding the MGED Ontology in MAGE
• Examples
• Discussion

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OntologyEntry in MAGE
BioMaterial Package
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OntologyEntry in MAGE
Description Package
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MGED Ontology v1.1.6

• Finished version of the MGED Ontology
• Available at http//mged.sourceforge.net/ontologie
  s/MGEDontology.php
• Two major branches Core and Extended
• Consists of classes, properties, and individuals
  (instances)
• Classes may have instances or be abstract
• Classes may refer to other ontologies, controlled
  vocabularies

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Finished MGED Ontology

• A stable version of the MGED Ontology that can
  code can be based on.
• The next major version will be developed in
  concert with MAGE v2.
• A few minor changes to be finished up this month
• Additions allowed (like MAGE, as long as it wont
  break code).

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Available at http//mged.sourceforge.net/ontologie
s/MGEDontology.php

• html
• Daml file
• Rdfs file
• NCI DTS Browser

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MGED Ontology is registered as GO Xref and at MOBY

• abbreviation MO
• database The MGED Ontology
• object ontology term
• example MOAction
• generic_url http//mged.sourceforge.net/ontologie
  s/MGEDontology.php
• url_syntax http//mged.sourceforge.net/ontologies
  /MGEDontology.phpterm
• url_example http//mged.sourceforge.net/ontologie
  s/MGEDontology.phpAction

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MO has two major branches Core and Extended
daml file in OILed
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MO consists of classes, properties, and
individuals (instances)
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Classes may have instances or be abstract
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Classes may refer to other ontologies, controlled
vocabularies
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Policies for coding MO in MAGE

• All MO terms are to be database referenced
• When the MAGE category in the OntologyEntry tag
  is a MO class with individuals.
• When the MAGE category in the OntologyEntry tag
  is a MO class without individuals because it is
  an abstract class.
• When the MAGE category in OntologyEntry tag is a
  MO property .
• The MO OntologyEntry class and its subclasses.

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Bhattacharjee et al, Proc Natl Acad Sci USA.
2001 Nov 2098(24)1390-5
Lung
Normal Lung (17)
Lung Cancer (166)
Lung Carcinoid Tumor (20)
Small Cell Lung Carcinoma (6)
Lung Adenocarcinoma (127 primary 12 metastases
)
Squamous Cell Lung Carcinoma (21)
RNA Extraction and Labeling
203 Labeled Extracts
Hybridize on Affymetrix chips
Hierarchical Clustering
M. Heiskanen,G. Fragoso, L. Fan NCI
Classification of Lung Cancer,
Subclassification of Lung Adenocarcinoma
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BioMaterialPackage
Bio Material Provider Thoracic Oncology Tumor
Bank Cell Type Epithelial Cell Sample
ID AD145 Sex Male Organism Status Premortem Spe
cies Human
Developmental Stage Elderly Somatic Cell
Type (Cell Type) Epithelial Cell Age 88
Years Clinical History/ Prior Disease State Lung
Adenocarcinoma ClinicalHistory/ Smoking
History 20 cigarretes per day for 20
years.
Disease State Recurrent Lung Adenocarcinoma
Disease Stage Stage IIIA Disease
Location Lung
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BioMaterial Package
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Intra-strain Hybridizations For Strain 129J High
eosinophils, high airway hyperreactivity
Group A
Ova-pre ctrl (1A)
Ova 24 (2A)
Alum 24 (5A)
Alum 48 (6A)
Ova 48 (3A)
28 Hybs
Ova 72 (4A)
Alum 72 (7A)
Group B
Ova-pre ctrl (1B)
Ova 24 (2B)
Alum 24 (5B)
J. White, TIGR
Ova 48 (3B)
Alum 48 (6B)
Ova 72 (4B)
Alum 72 (7B)
RNA Sample is given in (parentheses)
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Ovalbumin induction of asthma
ExperimentPackage

• ExperimentDesignType
• time_series_design
• compound_treatment_design
• strain_or_line_design
• reference_design
• FactorValueCategory AtomicAction
• Incubate time
• 24 h, 48 hr, 72 hr
• Compound_based_treatment
• Ovalbumin alum ovalbumin
• Alum alum (adjuvent),
• strain_or_line
• JAX_mouse_strains 129J, BTBR, C57BL/6,
  BALB/C

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Experiment Package
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MAGE Core Interfaces
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Discussion

• Questions on current policies?
• Need for additional policies?
• Plans for further MO development

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MAGE issues

• Need for additional OntologyEntry associations
• SeqFeature basis
• strandType
• Provided in MO but cant provide database
  reference in MAGE
• No direct association
• Not describable

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BioSequence Package