Dale A. Begley

The Jackson Laboratory, Bar Harbor, Maine, United States

Are you Dale A. Begley?

Claim your profile

Publications (12)76.48 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: The Mouse Tumor Biology (MTB; http://tumor.informatics.jax.org) database is a unique online compendium of mouse models for human cancer. MTB provides online access to expertly curated information on diverse mouse models for human cancer and interfaces for searching and visualizing data associated with these models. The information in MTB is designed to facilitate the selection of strains for cancer research and is a platform for mining data on tumor development and patterns of metastases. MTB curators acquire data through manual curation of peer-reviewed scientific literature and from direct submissions by researchers. Data in MTB are also obtained from other bioinformatics resources including PathBase, the Gene Expression Omnibus and ArrayExpress. Recent enhancements to MTB improve the association between mouse models and human genes commonly mutated in a variety of cancers as identified in large-scale cancer genomics studies, provide new interfaces for exploring regions of the mouse genome associated with cancer phenotypes and incorporate data and information related to Patient-Derived Xenograft models of human cancers.
    Nucleic Acids Research 10/2014; · 8.81 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In recent years the scientific community has generated an ever-increasing amount of data from a growing number of animal models of human cancers. Much of these data come from genetically engineered mouse models. Identifying appropriate models for skin cancer and related relevant genetic data sets from an expanding pool of widely disseminated data can be a daunting task. The Mouse Tumor Biology Database (MTB) provides an electronic archive, search, and analysis system that can be used to identify dermatological mouse models of cancer, retrieve model-specific data, and analyze these data. In this report we detail MTB's contents and capabilities, together with instructions on how to use MTB to search for skin-related tumor models and associated data.This article is protected by copyright. All rights reserved.
    Experimental Dermatology 07/2014; · 3.58 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Mouse Tumor Biology Database (MTB) is designed to provide an electronic data storage, search, and analysis system for information on mouse models of human cancer. The MTB includes data on tumor frequency and latency, strain, germ line, and somatic genetics, pathologic notations, and photomicrographs. The MTB collects data from the primary literature, other public databases, and direct submissions from the scientific community. The MTB is a community resource that provides integrated access to mouse tumor data from different scientific research areas and facilitates integration of molecular, genetic, and pathologic data. Current status of MTB, search capabilities, data types, and future enhancements are described in this article.
    Veterinary Pathology 01/2011; 49(1):218-23. · 1.93 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The Mouse Genome Informatics (MGI; "http://www.informatics.jax.org":http://www.informatics.jax.org) group is comprised of several collaborating projects including the Mouse Genome Database (MGD) Project, the Gene Expression Database (GXD) Project, the Mouse Tumor Biology (MTB) Database Project, and the Gene Ontology (GO) Project. Literature identification and collection is performed cooperatively amongst the groups. In recent years many institutional libraries have transitioned from a focus largely on print holdings to one of electronic access to journals. This change has necessitated adaptation on the part of the MGI curatorial group. Whereas the majority of journals covered by the group used to be surveyed in paper form, those journals are now surveyed electronically. Approximately 160 journals have been identified as those most relevant to the various database groups. Each curator in the group has the responsibility of scanning several journals for articles relevant to any of the database projects. Articles chosen via this process are marked as to their potential significance for various projects. Each article is catalogued in a Master Bibliography section of the MGI database system and annotated to the database sections for which it has been identified as relevant. A secondary triage process allows curators from each group to scan the chosen articles and mark ones desired for their project if such annotation has been missed on the initial scan. Once articles have been identified for each database project a variety of processes are implemented to further categorize and index data from those articles. For example, the Alleles and Phenotype section of the MGD database indexes each article marked for MGD and in this indexing process they identify each mouse gene and allele examined in the article. The GXD database indexing process has a different focus. In this case articles are indexed with regard to the stage of development used in the study as well as the assay technique used. In each case the indexing gives an overview of the data held in the article and assists in the more extensive curation performed in the following step of the curation process. Indexing also provides each group with valuable information used to prioritize and streamline the overall curation process. The MGI projects are supported by NHGRI grants HG000330, HG00273, and HG003622, NICHD grant HD033745, and NCI grant CA089713.
    Nature Precedings 05/2009;
  • [Show abstract] [Hide abstract]
    ABSTRACT: Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations. Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers. MTB is supported by NCI grant CA089713.
    Nature Precedings 05/2009;
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The laboratory mouse has long been an important tool in the study of the biology and genetics of human cancer. With the advent of genetic engineering techniques, DNA microarray analyses, tissue arrays and other large-scale, high-throughput data generating methods, the amount of data available for mouse models of cancer is growing exponentially. Tools to integrate, locate and visualize these data are crucial to aid researchers in their investigations. The Mouse Tumor Biology database (http://tumor.informatics.jax.org) seeks to address that need.
    Nature Reviews Cancer 07/2008; 8(6):459-65. · 29.54 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Mouse Tumor Biology (MTB) database provides access to data about endogenously arising tumors (both spontaneous and induced) in genetically defined mice (inbred, hybrid, mutant and genetically engineered mice). Data include information on the frequency and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background and literature or contributor citations. Data are curated from the primary literature or submitted directly from researchers. MTB is accessed via the Mouse Genome Informatics web site (http://www.informatics.jax.org). Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature, when available. Recently MTB has been redesigned and its database infrastructure replaced with a robust relational database management system (RDMS). Web interface improvements include a new advanced query form and enhancements to already existing search capabilities. The Tumor Frequency Grid has been revised to enhance interactivity, providing an overview of reported tumor incidence across mouse strains and an entrée into the database. A new pathology data submission tool allows users to submit, edit and release data to the MTB system.
    Nucleic Acids Research 02/2007; 35(Database issue):D638-42. · 8.81 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Gene Expression Database (GXD) is a community resource for gene expression information in the laboratory mouse. By collecting and integrating different types of expression data, GXD provides information about expression profiles in different mouse strains and mutants. Participation in the Gene Ontology (GO) project classifies genes and gene products with regard to molecular functions, biological processes, and cellular components. Integration with other Mouse Genome Informatics (MGI) databases places the gene expression information in the context of mouse genetic, genomic and phenotypic information. The integration of these types of information enables valuable insights into the molecular biology that underlies development and disease. The utility of GXD has been improved by the daily addition of new data and through the implementation of new query and display features. These improvements make it easier for users to interrogate and visualize expression data in the context of their specific needs. GXD is accessible through the MGI website at http://www.informatics.jax.org/ or directly at http://www. informatics.jax.org/menus/expression_menu.shtml.
    Nucleic Acids Research 02/2004; 32(Database issue):D568-71. · 8.81 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD's utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu. shtml.
    Nucleic Acids Research 02/2001; 29(1):98-101. · 8.81 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Data integration is key to knowledge discovery in the age of genomics and represents a major, long-standing challenge for the genome informatics community. Integration of data across heterogeneous genome databases requires the identification of common data entities and mechanisms to ensure referential integrity and persistence of these common entities even as our understanding of their biological properties changes. The Mouse Genome Informatics (MGI) database group employs multiple strategies for achieving data integration and maintaining inter-connectedness with other databases, including: (1) the use of permanent, unique accession IDs for identifying core data entities, (2) the application of nomenclature standards for naming genes and strains of mice, and (3) the development and implementation of controlled vocabularies and ontologies to ensure semantic consistency of biological concepts within and across model organism databases
    Bio-Informatics and Biomedical Engineering, 2000. Proceedings. IEEE International Symposium on; 02/2000
  • [Show abstract] [Hide abstract]
    ABSTRACT: The gene expression database (GXD) is being developed to store and integrate expression information for mouse development. GXD addresses many issues that apply to gene expression databases in general, and its data structures and supporting software tools are generalized in design and thus readily adaptable to other life stages and species. Integration of GXD with the mouse genome database (MGD) and interconnections with other relevant databases will place the gene expression data into the larger biological and analytical context. Here, we describe the design and implementation of GXD and illustrate, in particular, the gene expression annotator, an electronic system for submitting expression data to the database.Copyright 1997 Academic Press Limited Copyright 1997Academic Press Limited
    Seminars in Cell and Developmental Biology 11/1997; 8(5):489-97. · 6.20 Impact Factor
  • Dale A. Begley, Martin Ringwald
    [Show abstract] [Hide abstract]
    ABSTRACT: The scientific community is generating an ever-growing amount of gene expression data of an increasingly diverse and complex nature. This proliferation of scientific results raises questions of how to manage, integrate and analyze these data. Even within an individual laboratory it is becoming difficult to manage the data produced. The Gene Expression Database and the Gene Expression Notebook are publicly available electronic tools developed to address these problems.
    Trends in Genetics.