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http://www.nactem.ac.uk/GREC/

A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format

Proper citation: GREC Corpus (RRID:SCR_006719) Copy   

•   Source: SciCrunch Registry
  

http://www.innatedb.com

Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.

Proper citation: InnateDB (RRID:SCR_006714) Copy   

•   Source: SciCrunch Registry
  

https://school.wakehealth.edu/departments/pathology/comparative-medicine/vervet-research-colony

NIH funded national research resource to provide biomedical research community with access to US born, known age, pedigreed, genomically sequenced, pathogen free Caribbean origin vervet monkeys also known as African green monkeys. Provides access to animals, extensive multisystem clinical phenotyping, sample and data repositories, expertise in use of nonhuman primate models for translational studies, serves as platform for training veterinarians and other professionals in biomedical research, husbandry, clinical care, and the colony behavioral management.

Proper citation: Wake Forest Vervet Research Colony (RRID:SCR_006678) Copy   

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http://www.ars-grin.gov/

Web server to provide germplasm information about plants, animals, microbes, invertebrates and access to databases that maintain passport, characterization, evaluation, inventory, and distribution data for the management and utilization of national germplasm collections. Under control of the U.S. Department of Agriculture's Agricultural Research Service to support the National Genetic Resources Program (NGRP). Operated by the Database Management Unit of the National Germplasm Resource Laboratory in Beltsville, Maryland.

Proper citation: Germplasm Resources Information Network (RRID:SCR_006675) Copy   

•   Source: SciCrunch Registry
  

http://www.asn-online.org/

Society leading the fight against kidney disease by educating health professionals, sharing new knowledge, advancing research, and advocating the highest quality care for patients. To accomplish its mission, ASN will: # Educate health professionals by increasing the value of ASN education. # Share new knowledge by improving the quality and expanding the reach of ASN''s communications, including maintaining the premier publications in kidney disease. # Promote the highest quality care by serving as the professional organization informing health policy in kidney disease. # Advance patient care and research in kidney disease by strengthening the pipeline of clinicians, researchers, and educators. To accomplish this goal, ASN will: ## Implement a strategy to increase interest in nephrology careers, which includes promoting diversity within the nephrology workforce. ## Help fund travel to ASN educational activities for physicians and researchers training in the field of kidney disease. ## Use the ASN Grants Program to support outstanding research and foster career development. # Continue to bolster the ASN infrastructure, which includes: ## Increasing diversityincluding age and experience, ethnicity, and genderat all levels of the society. ## Providing avenues for helping ASN members facilitate professional exchange. ## Expanding ASN membership. ## Increasing the ASN Council-Designated Endowment Fund (independent of operational budget) to support grants and other priorities

Proper citation: ASN - American Society of Nephrology (RRID:SCR_006709) Copy   

•   Source: SciCrunch Registry
  

http://www.berkeleybop.org/

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site.

Proper citation: Berkeley Bioinformatics Open-Source Projects (RRID:SCR_006704) Copy   

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http://www.ebi.ac.uk/gwas/

Catalog of published genome-wide association studies. Genome-wide set of genetic variants in different individuals to see if any variant is associated with trait and disease. Database of genome-wide association study (GWAS) publications including only those attempting to assay single nucleotide polymorphisms (SNPs). Publications are organized from most to least recent date of publication. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator). Works with HANCESTRO ancestry representation.

Proper citation: GWAS: Catalog of Published Genome-Wide Association Studies (RRID:SCR_012745) Copy   

•   Source: SciCrunch Registry
  

http://www.lifetein.com

Contract research organization based in Somerset, New Jersey, founded in 2008. Supports research teams with peptide synthesis, conjugation, protein services, antibody services, and selected chemistry projects. LifeTein operates as a focused laboratory team, allowing direct communication and continuity across projects.

Proper citation: LifeTein (RRID:SCR_012626) Copy   

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http://www.brain.northwestern.edu/index.html

The Cognitive Neurology and Alzheimer's Disease Center (CNADC) is a multidisciplinary organization dedicated to conducting research to discover how the brain coordinates mental functions such as memory, language, attention, and emotion; transferring the benefits of this research to patients with brain diseases that impair cognitive function; and training researchers and clinicians who want to work in this field. The CNADC's mission is to investigate the neurological basis of cognitive function, to elucidate causes of dementia, and to ensure that the patients and their families are the beneficiaries of resultant discoveries. * Clinical Services: Neurobehavior and Memory Health Clinical Services * Annual Grant Opportunities: Annual Core Pilot Project Funding Opportunities * Research Areas & Faculty: Alzheimer's Disease / Primary Progressive Aphasia / Frontal Dementia, Brain Endowment (Brains are permanently stored, and requests for tissue for research purposes are submitted to Dr. Bigio for review by the Northwestern Alzheimer's Disease Center); Cognitive Brain Mapping Group, Volunteer For A Study * Fellowships: Neuropathology Fellowship, Behavioral Neurology & Neuropsychiatry Fellowship * Training Programs: Mechanisms of Aging and Dementia (M.A.D.) Training Program; Training Program in the Neuroscience of Human Cognition

Proper citation: Northwestern University Cognitive Neurology and Alzheimers Disease Center (RRID:SCR_012747) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/intrepid-bioinformatics

Core offers a repository from which researchers can drag and drop genetic sequence data into another application. Core offers a feature-surface to surface interoperation-that enables the system to be the hub for a network of applications researchers need to perform their work; LIMS, analytic tools, content management, workflow engines, visualization, etc. The core's system is optimized for cloud-based operations, and doesn't require users to re-download data.

Proper citation: Intrepid Bioinformatics (RRID:SCR_012625) Copy   

•   Source: SciCrunch Registry
  

http://autodock.scripps.edu/

Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.

Proper citation: AutoDock (RRID:SCR_012746) Copy   

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http://www.scienceexchange.com/facilities/altabioscience

Founded in 1973, AltaBioscience* is recognised world-wide as a leading manufacturing laboratory providing analysis and synthesis of DNA, proteins and other biochemical molecules to researchers in academia, pharmaceutica and the food industry. *An ISO 9001: 2008 certified UK based laboratory offering CD analysis.

Proper citation: AltaBioscience (RRID:SCR_012593) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/university-of-western-sydney

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Portal, Core facility

Proper citation: University of Western Sydney Labs and Facilities (RRID:SCR_012590) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/ExiMiR.html

R functions for the normalization of Exiqon miRNA array data.

Proper citation: ExiMiR (RRID:SCR_012753) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/cnv/

Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).

Proper citation: CNV Workshop (RRID:SCR_012635) Copy   

•   Source: SciCrunch Registry
  

http://www.iucnredlist.org/

A global evaluation of the conservation status of plant and animal species. The IUCN Red List plays a prominent role in guiding conservation activities of governments, NGOs and scientific institutions. The introduction in 1994 of a scientifically rigorous approach to determine risks of extinction that is applicable to all species, has become a world standard. In order to produce The IUCN Red List of Threatened Species, the IUCN Global Species Programme working with the IUCN Survival Commission (SSC) and with members of IUCN draws on and mobilizes a network of scientists and partner organizations working in almost every country in the world, who collectively hold what is likely the most complete scientific knowledge base on the biology and conservation status of species. The IUCN Red List is underpinned by information management tools (the Species Information Service) which facilitate the collection, management and processing of species data from workshop to publication on The IUCN Red List.

Proper citation: IUCN (RRID:SCR_012758) Copy   

•   Source: SciCrunch Registry
  

https://www.scienceexchange.com/labs/virginia-bioinformatics-institute-vt

THIS RESOURCE IS NO LONGER IN SERVCE, documented January 23, 2019. Core functions as a multi-user resource dedicated to the development and application of various high-throughput technologies to aid in the discovery of biological macromolecules. Core provides analysis platforms for DNA (sequencing and genotyping), RNA (gene expression analysis) and proteins (proteomics). They also offer a selection of molecular biology applications (colony picking, cloning, DNA/RNA isolations).

Proper citation: Virginia Bioinformatics Institute (RRID:SCR_012636) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/sylvester-comprehensive-cancer-center-miami

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. With more than 250 physicians and scientists dedicated to cancer care and research, Sylvester is leading the search for a cancer cure. Every day, our physicians and scientists within the cancer center''''s site disease groups and multidisciplinary research programs, are discovering exciting new breakthroughs that are quickly transforming the way cancer patients are diagnosed and treated.

Proper citation: UM Sylvester Comprehensive Cancer Center Labs and Facilities (RRID:SCR_012720) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/motifRG.html

Software tools for discriminative motif discovery using regression methods.

Proper citation: motifRG (RRID:SCR_012602) Copy   

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http://www.scienceexchange.com/facilities/advanced-analytical-testing-service

Advanced Analytical Testing Service (AATS) is dedicated to providing premium testing services for food, dietary supplement, biotechnology and cosmetic industries. AATS is established on our clients'' greatest satisfaction with our sample processing, testing method development and post-testing consultation. Our goal is to report authentic and accurate testing results with optimal quality and minimum turnover time. AATS is FDA registered independent analytical testing provider that is familiar with cGMP, USP and ISO standards. AATS has established full quality system on personnel, training, sample receipt and handling, testing, quality control and documentation. We provide testing results of high quality, because we have a strong quality system built in our testing facilities.

Proper citation: Advanced Analytical Testing Service (RRID:SCR_012723) Copy   

•   Source: SciCrunch Registry