camod – cancer models database

caMOD – Cancer Models Database

http://cancermodels.nci.nih.gov

Cancer models that recapitulate many aspects of the • genesis• progression • clinical course of human cancers

are valuable resources to cancer researchers engaged in a variety of basic, translational, clinical, and epidemiological investigations.

Preface

• Comparison to Humans: • Small• Large number of offspring• Short generation interval• Genetic manipulation (e.g. ES cell technologies)• Genetic makeup somewhat similar to humans

Why use Animal Models?

The Ideal Animal Model

• Faithfully reflect a human disease• Etiology• Pathology• Genetics

• Cancers only in the tissue of interest• 100% incidence• 0% incidence in untreated or unmodified animals• Short latency

• Submission—Data extracted from literature by curators or submitted by scientists.

• Search– Customizes searches or predefined searches.

• System Function Administration— User management and review of models.

Cancer Models Database(http://cancermodels.nci.nih.gov)

The cancer models database (caMOD) is a web-based resource that provides information about animal models for human cancer to the public research community

• 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)

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

• July 2007• caMOD 2.1 achieves Silver compatibility

• December 2008• caMOD 2.5 released (grid service)

• September 2009• caMOD 2.5 achieves Silver compatibility

• June 2010• caMOD 2.6.1 released

History

• 6,009 models• 5,922 Mouse models• 40 Dog models• 12 Rat models• 10 Rabbit models• 8 Zebrafish models• 6 Hamster models• 5 Horse models• 4 Cat models• 1 Goat model• 1 Sheep model

Status(as of August 31, 2010)

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 or other sources)

• Transplantation

• Model Availability (from various sources)

Submission

Submission steps

• 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 Transplantation 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.

Navigating the submission pages

Most parts contain multiple pages Multiple entries per category are possible

• 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

Example

• Duplication function• Deletion of records

Features enabling the user to control data

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)

Different Search Types

• Listing of search results• Columns are configurable and

sortable

Search Results List

Search Result Detail Pages

Admin

Review Process

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

• Screener- initial check of record

• Editor- scientific reviewer with specific area of expertise

Admin – Review of Records

Controlled Vocabularies

• All but the Zebrafish

vocabularies are stored in the

NCI Thesaurus.

• Murine Tissue Types

• Mouse Diagnoses

• Rat Anatomy

• Rat Diagnoses

• Human Anatomy

• Zebrafish Anatomy

• Zebrafish Developmental

Stages

• Staining Methods

• The EVSTree shown is a

separate application used for

rendering vocabularies.

Vocabulary Usage

EVS Tree – an Application for rendering Vocabularies

Integration with other Data Sources and Applications

• caMOD has been designed, architected and constructed to facilitate interoperability with other systems, following caBIG guidelines.

• Information Providers to caMOD:• caBIO to retrieve gene info and clinical trials info through remote API • EVS to provide concept codes and preferred descriptions for concepts through

caBIO EVS API• PubMED• Jackson Laboratory Resources• Rat Genome Database• ZFIN –Zebrafish Model Database• NCI’s Developmental Therapeutics Program• caArray to store microarray data• caIMAGE server to store images• Other sites that store microarray or image data

Interoperability

• caMOD has been designed, architected and constructed to facilitate interoperability with other systems, following caBIG guidelines.

• Information Consumers: caMOD provides information to other systems• CMAP• Websites such as eMice references specific models in caMOD• caELMIR• caNanoLab (future)• CAPR (future)• TP53 database at IARC in France (http://www-p53.iarc.fr/)

Interoperability

UML Model

• 65 Domain objects with over 300 attributes categorized under• caMOD::AnimalModel• caMOD::CancerModel• caMOD::InVivoModel

(Xenograft)• caMOD::YeastModel

• EVSTree utilizes LexEVS 5.x• caBIO 4.x is used to retrieve

additional information about genes and clinical trials

Common Data Elements

• CDEs for caMOD 2.5 have been loaded into caDSR

Vision

To create a cancer preclinical study information resource that will provide structured, searchable access to information about preclinical study protocols and outcomes, linked to detailed information about the animal models used, to related human clinical trials information, and to other molecular, pathology, and compound resources.

• Integration of preclinical and clinical data• Linking preclinical trials information to model data• Linking to clinical trials information / other clinical information• Connect to preclinical and clinical information in other applications

• Enable comparison across model systems (animal model, cell line, yeast, xenograft, human)

• Curation• Curated information from the literature• Add MGI data to MTB data• Integrate with Cancer Gene Index project

Goals

• What models have been used in preclinical studies?

• Which drugs / treatments have been administered?

• What was the outcome of the experiment?Has the same drug been used in (human) clinical trials?

• What was the outcome of the clinical trial?

Support research questions such as:

• See us at our poster• Contact Application Support

• Contact a member of the caMOD Team • Juli Klemm• Maki Duncan• Sima Pandya (Tech Lead) pandyas@mail.nih.gov• Ulli Wagner ulrike@mail.nih.gov• Maureen Colbert (Curator) colbertma@mail.nih.gov

Questions?

Thank you

Thank you for your interest in caMOD!

http://cancermodels.nci.nih.gov