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Research Resource Identifiers (RRIDs)

Contract Number: 75N97021P00135


Research Emphasis/Objectives

RRID

The Research Resource Identifiers project, or RRID initiative, aims to promote research resource identification, discovery, and reuse. It helps solve the challenges of reproducibility, efficiency, and connectivity that result from researchers not being precise when citing biological resources. The initiative is based on a concept called an RRID, which is a persistent and unique identifier given to a biological resource. An RRID (example: RRID:MMRRC_031168-UCD) begins with “RRID” and includes other identifying information like the strain and source of the resource. Such a system serves the biomedical community to correctly report, accurately replicate, and more easily extend findings from animal research and allows resource distributors and funding agencies to monitor the use of these key model organisms and other resources.

Services Provided

The Resource Identification Portal community hosts a website (https://scicrunch.org/resources) that displays the proper citations for common research resources. Using this website, authors can find RRIDs by searching for the catalog number of their research resources, clicking on the “How to Cite” button, and copying and pasting the resulting text into their methods section. For resources that are generated de novo and are to be made available as a stable stock, authors are asked to deposit the organism with an appropriate stock center or at least register the information about the animal with the proper authority appropriate for the organism currently available in the Resource Identification Portal (https://scicrunch.org/resources/about/guidelines#organism). These model organism authorities will give authors the proper name and an identifier for the new resource that can then be used to construct its RRID. The portal offers a central location for finding a resource of interest or registering a resource for others to find. The portal relies on the work of many community repositories, such as Addgene, Mutant Mouse Resource and Research Centers, National Swine Resource and Research Center, Bloomington Drosophila Stock Center, and Zebrafish International Resource Center. These community databases are the source for RRIDs of their type. By labeling a research resource with an RRID, researchers can look up information about the resource, as well as find all publications that reference that RRID. This increases transparency in the scientific process and makes it easier to find, report, and track information about resources. A significant number of journals and publishers—including Nature, Cell, Science, and the American Association for Cancer Research—are encouraging the use of RRIDs by authors.

 

Contact Information

Anita Bandrowski, Ph.D.
SciCrunch
P.O. Box 928191
San Diego, CA 92192-8191
anita@scicrunch.com
https://rrid.site

The Monarch Initiative: Linking Diseases to Model Organism Resources

Grant Number: R24OD011883


Research Emphasis/ObjectivesThe Monarch Initiative: Linking Diseases to Model Organism Resources

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. These include 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 website 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, Ph.D.
University of Colorado Denver
Anschutz Medical Campus
Aurora, CO 80045-2570
Phone: 503-407-5970
melissa.haendel@cuanschutz.edu
monarchinitiative.org

Additional Contact

Brandon White
admin@tislab.org

BioGRID: Biological General Repository for Interaction Datasets

Grant Number: R01OD010929


BioGRID LogoResearch Emphasis/Objectives

The Biological General Repository for Interaction Datasets (BioGRID) is an open-access public database that uses structured curation to capture protein, genetic, and chemical interaction data from model organisms and humans. BioGRID currently holds over 2,600,000 interactions curated from both high-throughput datasets and individual focused studies. Complete coverage of the primary literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe), and thale cress (A. thaliana), as well as partial coverage for other model species. Curation of interactions in human cells is focused on aspects of biology that are particularly relevant to human health, including disease-themed projects such as for COVID-19. Comprehensive curation of published genome-wide CRISPR screens systematically captures gene–phenotype relationships.

Services Provided

The BioGRID 4.4 web interface contains new search and display features that enable rapid user queries across multiple data types and sources. BioGRID provides interaction data to the main model organism databases within the Alliance of Genome Resources, including SGD, PomBase, TAIR, Wormbase and FlyBase, as well as to meta-databases such as NCBI, UniProt, and PubChem. The entire BioGRID 4.4 data collection may be downloaded without restriction 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

Mike Tyers
Senior Scientist
Peter Gilgan Centre for Research and Learning
The Hospital for Sick Children
686 Bay Street
Toronto
ON M5G 0A4
Canada
mike.tyers@sickkids.ca
thebiogrid.org
support@thebiogrid.org

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

Grant Number: U42OD010983


Research Emphasis/Objectives

The Informatics, Coordination and Service Center (ICSC) is located at the University of California, Davis, and serves as the centralized support center for the MMRRC (Mutant Mouse Resource & Research Centers) consortium. 

Services Provided

The ICSC is responsible for providing bioinformatics, website functionality and maintenance, strain acquisition, coordination and curation, and customer service to support the MMRRC Centers.

Contact Information

MMRRC-ICSC
c/o Mouse Biology Program
University of California, Davis
2795 Second Street, Suite 400
Davis, CA 95618
mmrrc.org

Principal Investigator

Ian Korf, Ph.D.
Phone: 530-757-5710
Fax: 530-757-3284
service@mmrrc.org

Strain Acquisition Coordinator

sacoord-comment@mmrrc.org

Customer Service

Phone: 800-910-2291 (North America) or 530-757-5710 (International)
Fax: (530) 757-3284
service@mmrrc.org

BioGRID: Biological General Repository for Interaction Datasets

Grant Number: R01 OD010929

BioGRID LogoResearch 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

http://thebiogrid.org/

biogridadmin@gmail.com

Principal Investigator

Mike Tyers

Phone: 416-586-4800

mike.tyers@gmail.com

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