Genetic, Biological, and Information Resources

ORIP supports a variety of resources that provide genetic analysis, biological materials such as cultures, reagents, and on-line information about model organisms used in biomedical research. Services available through these resources include genetically engineered model organisms, diagnostic services, cell lines, human tissues, snake venoms, and information systems that can help researchers identify specific model systems, particularly tissues, molecular pathways, and protein interaction networks similar to those known to be associated with human health problems.

Genetic Analysis Resources

A Comprehensive Canine Genetics Resource Including Gene and Variation Annotation
R24 OD018250

Research Emphasis/Objectives

We are developing an in-depth, easily accessible annotation of the dog genome to support disease research. The domestic dog is an important model for a wide variety of human diseases, including cancer, inflammatory disease, cardiovascular diseases and neurological and behavioral traits. We are using RNA-Seq to generate a more complete gene set and ChIP-seq to map histone marks implicating different regulatory states in different tissues. We are integrating this new data with available SNP data sets, published association signals, and other existing genome annotations to generate a resource easily accessible to the research community. The annotation will be served on the CanFam3.1 genome using the UCSC browser through a Track Hub that we build and manage.

Services Provided

Sequencing

Whole genome sequencing to 30x coverage (six dogs)

RNA-seq using a strand-specific Tru-Seq protocol for (1) 6 adult dogs, 30 adult tissues and 11 primary cell lines from each; (2) 5 tissues from 4 different canine embryonic timepoints.

ChIP-seq using five histone marks (H3K4me3, H3K36me3, H3K4me1, H3K27acetyl, H3K27me3) on 11 primary cell lines from six adult dogs.

Contact Information

Vertebrate Genomics Group
Broad Institute
415 Main St 75A-6078-A
Cambridge MA 02140

Principal Investigator

Elinor Karlsson
Phone: 617-714-7703

Resource/Additional Contact

Jeremy Johnson
Phone: (617) 714-7935
Development of Validated Drosophila in vivo RNAi Models of Human Diseases
R24 OD011176

Research Emphasis/Objectives

Remarkable conservation exists between Drosophila and humans at the level of genes and gene functions. There are identifiable fly orthologs for about two-thirds of human disease genes and all of the major signal transduction pathways have been conserved between flies and humans. The availability of RNA interference (RNAi) for gene-specific knockdown of mRNA levels has accelerated the pace at which researchers can undertake the type of molecular genetic analyses that make Drosophila a powerful system for studying biological processes relevant to human health and disease. The objective of this resource project is to produce a large collection of in vivo Drosophila RNAi models of human disease in which loss-of-function of the gene is associated with disease state, the human disease (HuDis)-transgenic RNAi project (TRiP) Resource of Disease Models. Toward this objective, studies aim to: 1) compile a prioritized list of human disease genes using the Online Mendelian Inheritance in Man database and a community nomination process; 2) identify 900 high-confidence fly orthologs of these genes, make two transgenic Drosophila RNAi fly stocks per gene, perform phenotypic characterization, quantitative PCR and rescue to validate the resource; and 3) further characterize the most promising disease models. The HuDis-TRiP fly stocks are likely to serve as disease models by mimicking the human disease state at the cell, tissue and/or organism level. The stocks and validation information are made immediately available to the community via the stock center and various websites.

Services Provided

Animals

The overall goal is to generate RNAi lines targeting Drosophila orthologs of highest- confidence human disease-associated genes. Resource of more than 1600 Drosophila RNAi lines targeting 900 such orthologs are generated and made immediately available to the community through the Bloomington Drosophila Stock Center (BDSC).

Strain Information

The strain information is searchable at various websites, including BDSC; Drosophila RNAi Screening Center (DRSC); Transgenic RNAi Project (TRiP); RNAi Stock Validation & Phenotypes (RSVP); and FlyBase.

Animal Validation

Quantitative PCR and phenotype characterization data for RNAi lines are generated, which can be searched and viewed at the RSVP website.

Contact Information

Harvard Medical School
77 Avenue Louis Pasteur, NRB 337
Boston, MA 02115

Principle Investigator

Norbert Perrimon, Ph.D.
617-432-7672
Fax: 617-432-7688
Gene Library Resource for the Sea Urchin Strongylocentrotus purpuratus
P40 OD010959

Research Emphasis/ObjectivesPhotograph of multiple purple sea urchins grouped together underwater

The Sea Urchin Genome Resource prepares and distributes high-density arrayed filters (macroarrays) containing large genomic and cDNA libraries from the sea urchin (Strongylocentrotus purpuratus) and other echinderm species. The genomic DNA in bacterial artificial chromosomes includes a range of species covering divergence times from 20 million to 540 million years. The resource also grows and ships individual library clones as identified and requested by users. The resource has developed robust protocols for hybridization on the macroarrays and analysis of the results. The majority of this information is posted on the Sea Urchin Genome Project website, EchinoBase.

Services Provided

Animals

Procuring wild specimens from marine life vendors

Biological Materials

Library filters and clones

Training

Use of the QBot for arraying and printing macro-array libraries

Contact Information

The California Institute of Technology
Division of Biology 156-29
1200 East California Boulevard
Pasadena, CA 91125

Principal Investigator

R. Andrew Cameron, Ph.D.
Phone: 626-795-8421
Fax: 626-795-3382
Genomic Sequencing To Establish A Macaque Genotype And Phenotype Research Resource
R24 OD021324

Research Emphasis/Objectives

This research resource will establish the first genomically characterized, pedigreed rhesus macaque research colony. Comprehensive genotype data on more than 1,000 Indian-origin rhesus macaques will support genotype-phenotype analysis of inherited diseases or disorders characterized within the Oregon National Primate Research Center rhesus macaque breeding colony. In addition, the genotype data will enable the identification of study subjects based on specific genetic characteristics.

Services Provided

This resource will produce comprehensive genotype data on more than 1,000 pedigreed rhesus macaques. A database will be developed to facilitate genotype and phenotype data access on the subjects.

Animals

Indian-origin rhesus macaques.

Biological Materials

Genotyping

SNVs will be identified from genome-wide sequence data, and will also be imputed among related individuals, guided by GBS-generated frame work markers.

Contact Information

ONPRC
505 NW 185th Ave
Beaverton, OR 97006

Principal Investigator

Betsy Ferguson, Ph.D.
Phone: 503-533-2403
Fax: 503-690-5384
Large-scale Discovery of Functional Genetic Variation in Rhesus Macaques
R24 OD011173

Research Emphasis/Objectives

This project provides new information to NIH funded investigators who are using rhesus macaques (Macaca mulatta) by discovering novel genetic variation present in the rhesus macaque populations maintained by the national primate research centers. Using whole genome and whole exome sequencing, we have identified >48 million single nucleotide variants in rhesus monkeys, drawing DNA samples from all the rhesus colonies in the NPRC program. This novel information concerning genetic variation in rhesus populations provides researchers with new data about potential genetic factors that may influence their research studies or that they can use to design more sophisticated analyses that consider genetic factors. As part of this work, we identified potentially damaging mutations in several thousand genes, where each damaging mutation provides a potential new macaque model of human genetic variation. We continue to sequence additional rhesus macaques and add new variants to our growing database of functional genetic variation in this species.

Services Provided

Free access to a database of novel genetic variation for rhesus macaques (Macaca mulatta).

Contact Information

Jeffrey Rogers
Human Genome Sequencing Center
Baylor College of Medicine
One Baylor Plaza
Houston, Texas 77030

Principal Investigator

Jeffrey Rogers
Phone: 713-798-7783
Fax: 713-798-5741
Primate Embryo Gene Expression Resource
R24 OD012221

Research Emphasis/Objectives

Primate Embryo Gene Expression Resource (PREGER) advances the study of nonhuman primate reproductive biology by providing gene expression data for rhesus monkey oocytes, preimplantation embryos, ovarian cells, and stem cells, with the broad mission of enabling researchers to incorporate a nonhuman primate model into their research programs. The resource also supports studies of environmental factors affecting these cells. The resource encompasses a growing mRNA expression database, with qRT-PCR and array hybridization data, and will soon include RNAseq data. New and emerging components include a new protein expression database for mammalian oocytes and embryos, a pathway/network analysis database, and a reproductive toxicology database. Other components include links to related websites, protocols, publications, and utilities for data analysis.

Services Provided

qRT-PCR, expression array, RNAseq, amplified cDNA library construction.

Training

The resource also provides an annual Mammalian Gamete and Embryo Molecular Biology Laboratory Training Course, and will soon provide online videos and slide presentations as tutorials.

Contact Information

Department of Animal Science
Michigan State University
474 S. Shaw Lane
East Lansing, MI 48824
Referral Center for Animal Models of Human Genetics Disease

P40 OD011189

Research Emphasis/Objectives

The overall objective of this project to serve as a national referral and resource center to discover, characterize, maintain colonies of, and develop treatments for hereditary disorders in large animals (dogs and cats) that are homologous to those found in human patients. The naturally occurring animal models to be sought, and those currently available, represent true orthologs of their respective human disease, involving defects in homologous genes and resulting in the same molecular, biochemical, pathological, and clinical phenotype as in human patients. While numerous naturally occurring models of disease have been identified and proven critical for preclinical trials on efficacy and safety, the rate at which new mutations are found and characterized is limited. Therefore, we will now also create canine and feline models that bear the same genetic mutation as found in human diseases using CRISPR/Cas9 genome editing. These large animal models can be generated quickly, will be completely orthologous to the human system, and will be maintained in breeding colonies and disseminated to other investigators. Both newly discovered and generated models allow for the study of disease pathogenesis and the evaluation of the safety and efficacy of gene, stem cell, small molecule, and protein-based therapies prior to clinical trials in human patients.

The critical barriers to developing effective treatment for genetic disease are 1) the lack of natural history studies due to the relatively low incidence and the heterogeneity of disease in human patients, 2) an insufficient understanding of disease pathogenesis 3) the paucity of validated surrogate markers of disease that can be monitored as secondary clinical endpoints, and 4) the dearth of candidate compounds which substantially improve neurological disease in animal models. The Referral Center approaches these barriers first by utilizing unique, long-lived, animal models of disease for which breeding colonies and natural history data exist. Second, our well-characterized models allow for the identification and validation of biochemical and imaging surrogate markers of disease due to their large size and accurate recapitulation of human disease. These biochemical markers will also provide insight into disease pathogenesis. Third, studies in murine models have identified substantial therapeutic effects of candidate vectors and compounds that can then be evaluated in large long-lived pre-clinical animal models. Fourth, is the ability to repeatedly sample blood, urine, CSF, cardiac and ocular function, and use non-invasive imaging methods to quantify the efficacy of therapy.

Current Research

Current projects involve the characterization of animal models with inborn errors of metabolism that are potential targets for research on gene and drug therapy include:

Models Studied in the Dog

Cystinuria, Epidermolysis Bullosa, Epilepsy, Exfoliative Cutaneous Lupus Erythematous (aka Lupoid Dermatosis), Factor VII, VIII, and IX Deficiencies,  Fucosidosis, Globoid Cell Leukodystrophy, Golden Retriever X-linked Muscular Dystrophy, Ichthyosis, Iron-Refractory Iron-Deficiency Anemia, Juvenile Dilated Cardiomyopathy, Lethal Acrodermatitis, Mucopolysaccharidosis  IIIB,  Non-syndromic Neuroepithelial Deafness, Phosphofructokinase Deficiency, Predisposition to Avian Tuberculosis, Primary Ciliary Dyskinesia, Tricuspid Valve Dysplasia), X-linked Hypohidrotic Ectodermal Dysplasia, and X-Linked Severe Combined Immunodeficiency.

Models Studied in the Cat

Alpha-Mannosidosis, Congenital Hypothyroidism, Glycogen Storage Disease Type IV, Mucolipidosis II, Niemann-Pick Type C disease, Porphyria.

Models Studied in Both the Dog and Cat

Erythrocytic Pyruvate Kinase Deficiency, Leukocyte Adhesion Deficiency, Mucopolysaccharidosis types I, VI, and VII.

Creation of new large animal models using CRISPR/Cas9 genome editing.

While numerous naturally occurring models of disease have been identified, the rate at which new mutations are identified is slow when compared to the rate they can be created using CRISPR/Cas9 genome editing. Therefore, using CRISPR/Cas9 genome editing we will generate new large animal models with orthologous genetic lesions to those found in human disease. With our advisory board, we will prioritize and rank which large animal models should be created based on the need to 1) evaluate experimental therapies prior to beginning clinical trials; 2) better understand disease pathogenesis; 3) develop surrogate markers of disease severity or progression; or 4) perform natural history studies in rare diseases. Contact Dr. Charles H Vite, 215-898-9473; email: vite@vet.upenn.edu.

Gene Cloning and Characterization of Disease-Causing Mutations

This function is limited to genes for diseases in which the studies can lead to further understanding of pathogenesis in ways not possible in human patients, or that are reasonable candidates for gene therapy studies. Contact Dr. Paula Henthorn, 215-898-9061; email: henthorn@vet.upenn.edu.

Gene Therapy

Potential models for research on gene therapy are evaluated in the context of the present status of the field and the availability of other animal models through contacts with other investigators. Contact Dr. Charles H Vite, 215-898-9473; email: vite@vet.upenn.edu.

Services Provided - Consultation and Diagnostic

The center provides consultation, diagnostic services, and preliminary genetic studies to facilitate the discovery and preservation of new and potentially useful dog and cat models. Services depend on the preliminary consultation and evaluation of the potential model by scientists at the Referral Center. The general classes of genetic diseases that are emphasized include:

Hereditary Metabolic Diseases

Includes inborn errors of amino acid, organic acid, carbohydrate, and glycosaminoglycan metabolism; enzyme, receptor, and transporter defects. Contact Dr. Urs Giger, 215-898-8830; e-mail: giger@vet.upenn.edu.

Hereditary Defects in Sexual Development

Includes male and female pseudohermaphroditism, sex reversal, and true hermaphroditism. Contact Dr. Magi Casal, 215-898-0029; e-mail: casalml@vet.upenn.edu.

Hereditary Congenital Malformations

Includes congenital heart disease and anomalies of other organ systems. Particular emphasis is given to isolated malformations or malformation syndromes. Contact DContact Dr. Magi Casal, 215-898-0029; e-mail: casalml@vet.upenn.edu or Dr. Paula Henthorn, 215-898-9061; email: henthorn@vet.upenn.edu.

Hereditary Neurological Diseases

Includes lysosomal storage and other neurological diseases, and epilepsy. Contact Dr. Charles Vite, 215-898-9473; email: vite@vet.upenn.edu.

Clinical Examination

Arrangements for transporting the affected animal to the center are usually the responsibility of the veterinarian or other investigator who makes the referral. Physical examinations and diagnostic laboratory and imaging tests are performed within a sophisticated small animal teaching hospital.

Postmortem/Biopsy Examinations

Biopsy specimens are accepted after initial consultation and offers hisopathological analysis. Complete postmortem examinations include gross and microscopic studies of organs and tissues, electron microscopy, and special histochemical stains. Some tissues may be stored or cells cultured and stored for metabolic, enzyme, and DNA studies.

Metabolic/Biochemical Genetic Disease Screening

This consists of a series of chromatographic and spot tests designed to detect abnormalities in the types or concentrations of metabolites in body fluids or tissues. Urine and serum are usually submitted for initial studies, and abnormal metabolites are further evaluated, as appropriate, by gas/liquid chromatography, amino acid analysis, mass spectrometry, enzyme assay, or other laboratory methods.

Hematologic Evaluation

If the initial evaluation suggests an inherited hematologic defect, appropriate erythrocyte, platelet, leukocyte, and macrophage function tests have been established for further diagnostic evaluation.

Cytogenetic Studies

These studies include standard and Giemsa-banded karyotyping and fluorescence in situ hybridization. The studies are conducted when preliminary studies yield sufficient evidence to suspect a chromosomal anomaly or when the physical location of the disease gene locus is to be mapped.

Pedigree Analysis

When family data are available or family studies are possible, the center classifies the phenotype of family members and examines pedigree patterns for consistency with simple and complex modes of inheritance.

Breeding Studies

The center maintains a special canine and feline research colony facility that can house a limited number of affected and potential carrier animals for breeding experiments designed to verify whether a defect is heritable, to determine the mode of inheritance, and to preserve the animal model. These studies depend on whether affected animals and their relatives can be obtained as donations or purchased.

Fees for Diagnostic Services

There is a $50 fee for preliminary urine screening. Clinical appointments with the Genetics, Reproduction, and Pediatric service are ~$100.

Availability of Models to Investigators

Another objective of the center is to establish a breeding colony for each promising model and to serve as a source of animals to be used directly in studies by outside investigators as well as a source of normal dog and cat tissue. Once the initial characterization of the model is completed, breeding stock or semen is available to those who wish to start their own breeding colonies supported by specific separate NIH and other grant funds. We also facilitate contact with and access to large animal models maintained at other institutions and can provide advice on the experimental feasibility of specific animal models. Finally, we act as a center to perform experiments on a fee for service basis for other investigators interested in evaluating therapies using our pre-clinical models of human genetic disease or normal dogs and cats.

Contact Information

Referral Center for Animal Models of Human Genetic Diseases
School of Veterinary Medicine
University of Pennsylvania
3900 Delancey Street, Philadelphia, PA 19104-6051

Charles H Vite, DVM, PhD, Dipl ACVIM (Neurology)
215-898-9473
vite@vet.upenn.edu (link sends e-mail)

Biological Material Resources

Drosophila Genomics Resource Center
P40 OD010949

Research Emphasis/Objectives

The Drosophila Genomics Resource Center (DGRC) collects and distributes reagents and materials essential for Drosophila genomics research, including large clone sets, common transformation vectors, and cell lines. It also tests and refines emerging genomics technologies for Drosophila, supports work on Drosophila cell lines, and advises users in the use of resources.

Services Provided

ESTs and other DNAs

A collection of over 1,000,000 clones is distributed as individual clones and sets. For each clone in the collection, the DGRC website provides relevant references, sequence information, restriction maps, and links to FlyBase entries.

Transformation Vectors

The Center distributes general-purpose transformation vectors for use in flies or in cultured cells.

Cell lines

The DGRC distributes over 100 Drosophila cell lines, provides website support for their use and handling, characterizes newly-added lines, and collaborates with other on-going projects (modENODE, the Drosophila RNAi Screening Resource) to enhance and disseminate systems level information on the cell lines.

Users must create an account prior to purchasing. In addition to purchase orders, online credit card orders are also accepted. Fees are adjusted on an annual basis.

Contact Information

Drosophila Genomics Resource Center
Indiana University
Jordan Hall
1001 East 3rd Street
Bloomington, IN 47405-7005

Principal Investigator

Andrew Zelhof, Ph.D.
Phone: 812-855-0294
Fax: 812-856-9340
Human Tissue and Organ Research Resource
U42 OD011158

Objectives

ORIP supports the Human Tissue and Organ Research Resource (HTORR), a human tissue procurement and distribution program managed by the National Disease Research Interchange (NDRI) . NDRI is a not-for-profit organization with a mission to advance biomedical research and development through the procurement and distribution of human organs, tissues and cells to biomedical researchers in academia, government, and industry.

Services Provided

Donation of tissues and organs, either post-surgery or post mortem, gives individuals and their families an opportunity to leave a meaningful legacy by providing the human specimens needed to advance research and development. Studies with human tissues and organs also serve as important alternatives to the use of live animals in research. By collaborating with the USA’s major organ procurement organizations, tissue banks, eye banks and medical centers, HTORR can provide nearly every anatomical structure, organ and tissue —both diseased and normal—to investigators in support of their research needs.

HTORR services focus, primarily, on prospective tissue recoveries to address investigator-driven requests for tissue type, method of preservation and shipping requirements. Researchers can also specify key donor parameters such as age/race/sex, medications and co-morbidities. Interested investigators complete a simple application process and, once approved, are served when tissues matching their requests become available. All tissue acquisition and allocation is conducted in compliance with NDRI’s Quality Management Systems (QMS). For information about how to set up a prospective tissue recovery, please email NDRI Scientific Services Department at researchinquiry@ndriresource.org (link sends e-mail)

HTORR provides specimens to NIH-funded and other academic investigators to facilitate scientific advances in a variety of biomedical platforms including basic research, drug development, drug metabolism/absorption, toxicology and diagnostics across multiple disciplines, such as infectious disease, immunology, cardiology, endocrinology, ophthalmology, nephrology, neurology/neuroscience, regenerative medicine, orthopedics, pathology and pharmacology. Specimens provided by HTORR are utilized in more than 150 peer-review published scientific studies annually. To learn more about NDRI’s services and to browse these publications, please refer to NDRI’s website.

Contact Information

Principal Investigator

Gene Kopen, Ph.D
NDRI, 8 Penn Center
1628 JF Kennedy Boulevard, 15th Floor
Philadelphia, PA 19103
Phone: 800-222-6374 x 271
Neurotropic Viruses
P40 OD010996

Research Emphasis/Objectives

The use of viruses to define the synaptic organization of neuronal circuitry has experienced an explosive growth over the past decade. This experimental approach is the most widely used method to provide a polysynaptic perspective on the functional architecture of the nervous system. Consequently, it has proven to be increasingly popular among neuroscientists whose goal is to define ensemble organization of populations of neurons devoted to specific functions. The mission of this center is to provide a state-of-the-art National Resource Center that: 1) serves as a technical and intellectual resource for those interested in using viral transneuronal tracing; 2) develops improved transneuronal tracing technologies and makes them available to investigators throughout the United States via access to center resources and training; 3) serves as a repository for well-characterized reagents essential to the application of the method; and 4) stimulates collaborative multidisciplinary studies of mechanisms underlying viral neuroinvasiveness and pathogenesis.

Current Research

Research at the Center is focused within two Virus Cores, and a Technology and Resource Core. Reagents produced within the Virus Cores (Alpha Herpesvirus and Rabies Virus Cores) are characterized and developed for research applications in the Technology and Resource Core. Current research focuses on: 1) developing tracing applications with conditional replication of alpha herpesviruses; 2) characterizing the molecular basis of direction selective transport of herpesviruses; 3) constructing and characterizing new recombinant viruses that can be used in complex tracing paradigms and for functional analysis of identified neurons; and 4) defining the distribution of receptors that influence neuroinvasiveness of alpha herpesviruses in the central nervous system.

Services Provided

The center provides reagents and training for those interested in application of the viral transneuronal tracing method.

Contact Information

University of Pittsburgh
Departments of Neurobiology and Neuroscience
4074 Biomedical Science Tower -3
3501 Fifth Avenue
Pittsburgh, PA 15261

Principal Investigators

Peter L. Strick, Ph.D.
Phone: 412-383-9961
Fax: 412-383-9061
J. Patrick Card, Ph.D.
Phone: 412-624-6995
Fax: 412-624-9198

Additional Contact

Amanda Fetsick
Phone: 412-383-9878
Fax: 412-383-9061
Viper Resource Center at Texas A&M University-Kingsville

P40 OD010960

Research Emphasis/Objectives

The National Natural Toxins Research Center (NNTRC), a component of Texas A&M University – Kingsville, is a unique animal and biological material resource center organized to support basic and translational research on venomous snakes and their venoms. The NNTRC has grown to become the only federally funded viper resource center in the U.S., playing a critical role as a provider of high quality single-source venoms and snake-related research materials to national and international biomedical and biological research programs. The goal of the Viper Resource Center is to provide native venoms, purified venom components, cDNA clones, and recombinant venom proteins of the highest quality to support biomedical research.

Current Research

The NNTRC supports a very active and very productive program of toxinology research. Many studies are directly related to isolating and characterizing venom molecules that have biomedical significance. Additional studies are devoted to the development of the molecular technologies that include the construction of snake-venom gland cDNA libraries and the production and characterization of recombinant venom proteins.

Services Provided

NNTRC serves as a critical resource for the support of both basic and applied toxinology research. Through the maintenance of a unique collection of venomous snakes and the quality-controlled collection and distribution of venoms, tissues and recombinant DNA libraries to biomedical researchers, the NNTRC has supported a diverse set of outstanding research programs. The NNTRC also provides biological assays, research training, and outreach programs.

Contact Information

National Natural Toxins Research Center
Texas A&M University-Kingsville
975 W. Avenue B., MSC 224
A. L. Kleberg Hall, Rm. 100
Kingsville, TX 78363

Principal Investigator

Elda E. Sánchez, Ph.D.
361-593-3796
Fax: 361-593-3798

Information Resources

BioGRID: Biological General Repository for Interaction Datasets
R24 OD011194

Research Emphasis/Objectives

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID currently holds over 1,400,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 57,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway.

Services Provided

Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.2 web interface contains new search and display features that enable rapid queries across multiple data types and sources. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases. The entire BioGRID 3.2 data collection may be downloaded in multiple file formats, including IMEx compatible PSI MI XML. For developers, BioGRID interactions are also available via a REST based Web Service and Cytoscape plugin. All BioGRID documentation is available online in the BioGRID Wiki.

Contact Information

Mount Sinai Hospital
Lunenfeld-Tanenbaum Research Institute
600 University Avenue
Toronto, Ontario CAN M5G 1X5

 

Mike Tyers
Phone: 416-586-4800

 

Informatics, Coordination and Service Center for the Mutant Mouse Resource and Research Centers
U42 OD010983

Research Emphasis/Objectives

The Informatics, Coordination, and Service Center (ICSC) at UC Davis facilitates the organization and activities of the entire multi-site Mutant Mouse Resource and Research Centers (MMRRC) in its mission to cryopreserve and distribute genetically engineered mouse strains and mouse ES cell lines for the global biomedical research community. Each of the MMRRC's facilities provides the following services: cryopreserve embryos, gametes, or other germplasm of selected strains and stocks of mice, distribute mice as breeding stock to investigators, perform microbiologic and genetic quality control of mice bred, maintained and distributed, develop resources to facilitate mouse-related research, provide contract services for resource preservation and distribution, offer additional related services as specifically provided by individual facilities.

Services Provided

The ICSC accomplishes its goals through a single, centralized set of public and internal services. Publicly, these services present the MMRRC as a unified entity, greatly simplifying brand recognition, the processes of donating and ordering repository materials, and access to documentation supporting best practices with the research materials. This is achieved through the public MMRRC.org web portal with its on line donation, product catalog, and ordering systems as well as a centralized customer service center and a community outreach and marketing program. Internally, the ICSC provides the organizational backbone for all five MMRRC centers. This is accomplished through the hosting of regular teleconferences, the centralized biological annotation of all repository holdings, the archiving of all consortium documentation, and the maintenance of a comprehensive database of all repository holdings and donation and ordering system activity.

Contact Information

Genome and Biomedical Sciences Facility / 4333
University of California
One Shields Ave.
Davis, CA 95616, USA.

 

Ian Korf
Phone: 416-586-4800 or 530-754-4989

 

The Monarch Initiative: Linking Diseases to Model Organism Resources
R24 OD011883

Research Emphasis/Objectives

The Monarch Initiative is the biomedical research community’s most comprehensive cross-species phenotype information resource, delivering powerful computational phenotypic tools. The Monarch Initiative combines structured information about genetics and descriptions of resulting malformations, clinical signs, and symptoms from multiple organisms to increase the utility of animal models and improve our understanding of human diseases.

Services Provided

Since its inception in 2012, Monarch has been a leader in all aspects of phenotype computation, creating and extending multiple ontologies; aggregating substantial bodies of annotations, including over 78,000 disease-gene associations and 1.4 million genotype-phenotype associations from more than 25 primary resources; implementing novel algorithms for phenotypic analysis and applying those algorithms to previously unsolved rare diseases; developing an open web site and computational resources to provide these data to the community; creating visualizations that facilitate the interpretation of the results of phenotypic analyses; and contributing to community efforts aimed at capturing the provenance and research resource information needed to validate phenotype associations.

Contact Information

Melissa A. Haendel
Oregon Health & Science University, Library Operations
3181 SW Sam Jackson Park Rd LIB
Portland, OR
Phone: 503-407-5970