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Cancer Models Database(caMOD)

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History

January 2000– Prototype is presented during the Mouse Models of Human Cancers (MMHCC)

Steering Committee Meeting– MMHCC adopts the Cancer Models Database (caMOD) as one of their initiatives

July 2000– NCICB assumes responsibility for caMOD

Spring 2001– caMOD 1.0 released (2-tier application)

2001 – 2005– Based on user feedback the application is constantly updated and improved.

December 2005– caMOD 2.0 released (n-tier application, based on caBIG compliance guidelines)

May 2006– caMOD 2.1 released (keyword search highlighting, configurable search results,

saving queries, autocompetion of search fields)

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Cancer Models Database v2.1

• Submission--Data in caMOD are extracted from the public scientific literature by curators and verified by the scientists who generated or worked with the models, or they are directly submitted by scientists.

• Search--Users can retrieve information about the making of models, their genetic descriptions, histopathology, derived cell lines, associated images, carcinogenic interventions, microarray data, and therapeutic trials in which the models were used. caMOD provides links to PubMed for associated publications and other resources such as mouse repositories, detailed information about altered gene, pathway affected, and information about human clinical trials that utilize the same compounds as the pre-clinical trials in the animal models.

• System Function Administration--The Admin function provides services for user registration, review of submitted models and database management.

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The model is the unit of data collection

Model Characteristics (e.g. name, phenotype)

Genetic Description (transgene, targeted modification, genomic segment, induced mutation, spontaneous mutation)

Carcinogenic Interventions (e.g. chemicals, radiation, hormone)

Transient Interference (morpholino oligonucleotides, siRNA experiments)

Publications

Histopathology (e.g. diagnosis, macroscopic and microscopic description)

Cell Lines (generated from the model)

Therapeutic Approaches (e.g. compound, experiment, result)

Images (e.g. image description, staining – stored on image server [caIMAGE])

Microarray Data (link to caArray)

Xenograft / Transplant

Model Availability (from various sources)

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Submission

The submitter provides an overview on why and how the model was generated on the Model Characteristics page.

The parts Genetic Description, Carcinogenic Interventions and Xenograft offer the opportunity to describe in more detail how the model was generated.

Other parts describe the results of experiments performed or observations made on this particular strain.

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Navigating the submission pages

Most parts contain multiple pages Multiple entries per category are possible

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Example

double transgenic animal crossed with a knock-out animal, treated with UV-light

Genetic Description Enter Transgene Transgene 1

Genetic Description Enter Transgene Transgene 2

Genetic Description Enter Targeted Modification Knock-out Gene

Carcinogenic Interventions Enter Radiation UV-light

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Features enabling the user to control data

Duplication function

Deletion of records

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Search

Simple Search

Advanced Search

Table of Contents (predefined searches)

Drug Screening Search (comparison of drug screening experiments in yeast models, xenograft models, genetically engineered models and humans)

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Search Results

Listing of search results

Columns are configurable and sortable

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Search Result Detail Pages

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Review Process

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Admin – Review of Records

Coordinator- can name screeners and editors- assigns records and comments to screener and editor

Screenerinitial check of record

Editorscientific reviewer with specific area of expertise

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Comments

Can be used to add data to existing records

Can be used for scientific discussions

Will be screened before they go online

Commentator will be identified by name and email address (user account is required to make comments)

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Interoperability

caMOD has been designed, architected and constructed to facilitate interoperability with several systems, following guidelines from caBIG model driven architecture.

Information Providers to caMOD:– caBIO to retrieve gene info and clinical trials info– PubMED– Jackson Laboratory Resources– NCI’s Developmental Therapeutics Program– caArray to store microarray data– caIMAGE server to store images

Information Consumers: caMOD provides information to other systems– CMAP– BioGopher– Websites such as eMice references specific models in caMOD– caELMIR (future)

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Architecture

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caMOD Grid Node

The caMOD Grid Data Service node is generated using the caGrid Toolkit.

The Data Type Definitions extracted from the caDSR registered caMOD model are used to build an XML schema or XSD that is used to define the input and output data types of the Grid services.

The XSD is registered in the Global Model Exchange (GME) and used to describe the contract of the grid service and to validate the XML serialization of the API Domain Objects during data requests.

Applications communicate with the caMOD Grid Data Service node following the caGrid services protocol.

The caMOD API domain objects are serialized/deserialized by the caMOD Grid Data Service to and from XML adhering to the XML Schema (XSD) that is registered in the Global Model Exchange (GME)

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UML Model

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UML Model

76 Domain objects categorized under– caMOD::AnimalModel– caMOD::CancerModel– caMOD::InVivoModel (Xenograft)– caMOD::YeastModel

Application specific classes under– caMOD::Comments & Logging– caMOD::Admin– caMOD::Preferences

EVSTree utilizes caBIO 3.1 API

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Vocabulary Usage

NCI Thesaurus for murine organ and diagnosis terms

NCI Thesaurus for human anatomical terms

NCI Thesaurus for staining methods

NCI Thesaurus for mouse and rat strains

EVSTree – Reusable component for rendering EVS concepts

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Common Data Elements

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Becoming even more integrated

Connecting to the Jackson Mouse Tumor Biology Database and Mouse Genome Informatics resources

Inclusion of additional controlled vocabularies provided by EVS (working with the EVS team to add needed vocabularies to the system e.g. vocabulary for proliferative diseases found in rats)

Questions?23