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https://www.ddbj.nig.ac.jp/jga/index-e.html
A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee.
Proper citation: Japanese Genotype-phenotype Archive (JGA) (RRID:SCR_003118) Copy
http://www.humanproteinpedia.org/
A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted.
Proper citation: Human Proteinpedia (RRID:SCR_002948) Copy
http://braininfo.rprc.washington.edu
Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.
Proper citation: BrainInfo (RRID:SCR_003142) Copy
Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Developmental Therapeutics Program (RRID:SCR_003057) Copy
Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available.
Proper citation: Database of Interacting Proteins (DIP) (RRID:SCR_003167) Copy
http://rostlab.org/services/nlsdb/
A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree
Proper citation: NLSdb: a database of nuclear localization signals (RRID:SCR_003273) Copy
http://edoctoring.ncl.ac.uk/Public_site/
Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making
Proper citation: eDoctoring (RRID:SCR_003336) Copy
http://purl.bioontology.org/ontology/CMO
An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.
Proper citation: Clinical Measurement Ontology (RRID:SCR_003291) Copy
http://www.yaleruddcenter.org/
A non-profit research and public policy organization devoted to improving the worlds diet, preventing obesity, and reducing weight stigma.
Proper citation: Yale Rudd Center for Food Policy and Obesity (RRID:SCR_003283) Copy
http://www.brainbank.mclean.org/
Biomaterial supply resource that acquires, processes, stores, and distributes postmortem brain specimens for brain research. Various types of brain tissue are collected, including those with neurological and psychiatric disorders, along with their parents, siblings and offspring. The HBTRC maintains an extensive collection of postmortem human brains from individuals with Huntington's chorea, Alzheimer's disease, Parkinson's disease, and other neurological disorders. In addition, the HBTRC also has a collection of normal-control specimens.
Proper citation: Harvard Brain Tissue Resource Center (RRID:SCR_003316) Copy
Interactive repository of mutations and other allelic variations of the genes involved in the DNA repair disorders, Xeroderma Pigmentosum (XP), Cockayne Syndrome (CS), Trichothiodystrophy (TTD), and other UV-sensitivity disorders. Any omitted data or new data may be submitted by using the on-line data submission form. There is a message board system to support discussions amongst those interested in XP and DNA Repair. RESOURCES * Educational module of the molecular biology of Nucleotide Excision Repair * Introduction to the DNA Repair disorders (XP, CS, TTD, UVs) * Background on each of the XP genes * A searchable database of mutations and sequence variations for the XP genes * Contact point for the submission of new mutation data * Discussion Forums and a Guest Book * Web Links to Additional Resources
Proper citation: Allelic Variations of The XP Genes (RRID:SCR_003376) Copy
http://purl.bioontology.org/ontology/MMO
An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.
Proper citation: Measurement Method Ontology (RRID:SCR_003373) Copy
http://sig.biostr.washington.edu/projects/fm/
A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.
Proper citation: FMA (RRID:SCR_003379) Copy
Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.
Proper citation: Reactome (RRID:SCR_003485) Copy
A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).
Proper citation: Ontology of Vaccine Adverse Events (RRID:SCR_003442) Copy
Videos and podcasts presenting the latest innovative research being conducted by the Stein Institute for Research on Aging medical faculty, with the aim of promoting healthy aging. Additionally, many of the public lectures from the Public Lecture Series are also available on UCSD-TV's website video on demand programming. The Lecture series allows affiliated faculty members of the Stein Institute for Research on Aging and other scientists from the UCSD School of Medicine, as well as individuals from surrounding academic and research institutions, to present the latest findings in their respective fields of expertise and share their present work with the general community. All of these lectures focus on topics related to healthy aging or age-related diseases.
Proper citation: Stein Institute for Research on Aging Video Archive (RRID:SCR_003761) Copy
https://sites.google.com/site/p2tconsortium/
A three-member pharmaceutical industry consortium that aims to provide a new platform to improve access to information about clinical trials for patients and providers. The platform aims to enhance the existing clinicaltrials.gov by providing more detailed and patient-friendly information about available trials and embedding a machine-readable target health profile to improve the ability of healthcare software to match individual health profiles with applicable clinical trials. Using clinicaltrials.gov as its foundation and Eli Lilly''''s Application Programming Interface (API), the consortium is focused on creating an open platform to make this data more amenable to patients and providers, as well as creating an opportunity to integrate a patient''''s electronic health record into the clinical trial matching service. This feature will allow patients to search for trials using their own Blue Button data. The following features are planned add-ons to clinicaltrials.gov: * Target Profile is a machine readable query, that can be executed against an electronic file (or record) with patient health data such as an Electronic Health Record (EHR), an Electronic Medical Record (EMR) or Personally Controlled Health Record (PCHR) * Augmented Content is public, IRB approved information about the study that has not been published on clinicaltrials.gov, and that is shared with / targeted for patients with a matching Target Profile. The following are the incremental goals of the consortium: * Advancement of the Lilly API platform to support read/write interaction and additional data objects and information. * The initial 3 sponsor organizations - Lilly, Pfizer and Novartis - will upload Target Profiles for a select set of clinical trials. A Target Profile is a machine interpretable description of the characteristics of patients who may qualify for that trial i.e. a query that can be executed against a patient''''s electronic health record or personal health record. Additionally, sponsors of clinical research studies will also be able to upload Augmented Content to the Lilly Platform to supplement information on clinicaltrials.gov with additional, patient-focused information about the study, e.g., a study brochure and practical information on how to contact investigational sites. * A matching service, developed by Corengi, will compare Target Profiles to a de-dentified personally controlled health record (PCHR), represented by patient''''s Blue Button Plus CCDA XML document. * Integration into a patient community platform from Avado for providing the patient PCHR and presenting the results of the match service. The patient will be able to explore the respective matching studies for additional information and next steps such as contacting a nearby investigator clinic or hospital. The first demo of the prototype was made available on June 2014, built on a database of anonymized patient health records from different clinical research studies sponsored by Lilly, Novartis, and Pfizer. Other website: http://portal.lillycoi.com/
Proper citation: Patients to Trials Consortium (RRID:SCR_003877) Copy
Portal dedicated to the development and application of the latest advances in biomedical and behavioral science knowledge to issues of successful, healthy aging and the prevention and reduction of the burden of disability and disease in late life. Additionally, they provide numerous grants to junior faculty, as well as education programs for doctors and researchers through monthly Grand Rounds. From studying memory to identifying genes with important roles in aging, Stein Institute scientists are continuously pushing the boundaries of knowledge. One of their most promising ongoing projects is the Successful AGing Evaluation (SAGE) Study. SAGE is the only large-scale study on successful aging that considers the impact of positive psychological traits, such as resilience and wisdom, in addition to biological factors, providing a much more complete picture of older adults. Their monthly public lectures presented by renowned physicians and scientists are broadcast on UCSD-TV and have been viewed more than one billion times. This year they partnered with the Clinical and Translational Research Institute and the Osher Lifelong Learning Institute to organize Making Sense of Science, a course for older adults interested in science and health. In addition, They distribute a free monthly newsletter and work extensively with the community, participating in numerous events and conferences.
Proper citation: Stein Institute for Research on Aging (RRID:SCR_003759) Copy
A nonprofit organization representing dialysis facilities and centers throughout the United States. It supports members from all types of providers including freestanding, hospital-based and national chains through the weekly e-mail newsletter, Renal Watch, the Annual Meeting, periodic workshops and other meetings. NRAA members include dialysis provider companies and management consulting companies and other companies involved in the End Stage Renal Disease (ESRD) industry and supportive of the purposes of NRAA. Individuals not directly employed or otherwise involved in companies that are NRAA members may join as individual Associate Members. The purposes for which the NRAA is organized are as follows: # To provide renal administrators the opportunity for gaining continuing education, obtaining peer recognition and expanding development in the profession. # To promote and encourage education and training for renal administrators. # To recognize individuals who have done or are doing noteworthy service in the field of renal administration. # To educate the public and members of governing bodies of health care organizations to understand the issues surrounding the practice of renal administration. # To represent the professional interests of renal administrators as a national representative spokesperson for the development and implementation of public policy. # To act as a resource on local and national ESRD issues.
Proper citation: National Renal Administrators Association (RRID:SCR_003991) Copy
http://www.nimh.nih.gov/educational-resources/index.shtml
A portal to educational resources.
Proper citation: NIMH Educational Resources (RRID:SCR_004045) Copy
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