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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://www.progenygenetics.com/
Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays.
Proper citation: PROGENY (RRID:SCR_006647) Copy
Study designed to assess the effects of oral supplementation of high doses of macular xanthophylls (lutein and zeaxanthin) and/or omega -3 LCPUFAs (DHA and EPA) for the treatment of AMD and cataract.
Proper citation: AREDS2: The Age-Related Eye Disease Study 2 (RRID:SCR_006306) Copy
https://www.researchmatch.org/
Free and secure registry to bring together two groups of people who are looking for one another: (1) people who are trying to find research studies, and (2) researchers who are looking for people to participate in their studies. It has been developed by major academic institutions across the country who want to involve you in the mission of helping today''''s studies make a real difference for everyone''''s health in the future. Anyone can join ResearchMatch. Many studies are looking for healthy people of all ages, while some are looking for people with specific health conditions. ResearchMatch can help ''''match'''' you with any type of research study, ranging from surveys to clinical trials, always giving you the choice to decide what studies may interest you.
Proper citation: ResearchMatch (RRID:SCR_006387) Copy
Register of clinical trials being undertaken in Australia, New Zealand and elsewhere including trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. In 2007 the ANZCTR was one of the first three trial registries to be recognized by the World Health Organisation International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognizes registries as Primary Registries if they fulfill certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch Studies should be registered prospectively, i.e. before the first patient is recruited. The registry records a trial's * objectives * main design features * sample size and recruitment status * treatments under investigation * outcomes being assessed * principal investigator * contact person Key points about the ANZCTR * Publicly owned, managed by a not-for-profit organization * All details of trials registered on the ANZCTR are made publicly available * Registration is voluntary, but if a registrant chooses to register a trial, certain fields are mandatory * Registration is free of charge * Responsibility for registration lies with the Sponsor
Proper citation: Australian New Zealand Clinical Trials Registry (RRID:SCR_002967) Copy
http://ncim.nci.nih.gov/ncimbrowser/
A wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. NCIm features: * Maps 4,000,000 terms from more than 75 sources into 2,000,000 biomedical concepts that represent their meaning. * Displays preferred terms, synonyms, definitions, and other information from each source. * Links to NCI Thesaurus and other related information sources. * Contains 22,000,000 cross-links between content elements. * Updated frequently by a team of biomedical terminology and subject matter experts. NCIm contains most public domain terminologies from the National Library of Medicine's UMLS Metathesaurus, as well as many other biomedical terminologies created by or of interest to NCI and its partners. Some propriety terminologies are included, with permission, and have restrictions on their use. The current version of the NCI Metathesaurus, based on the UMLS build 2013AA, covers up to National Cancer Institute Thesaurus, 13.12d. A viewer for the UMLS changes document can be downloaded.
Proper citation: NCI Metathesaurus (RRID:SCR_003565) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. In this web site you will find the central European database of OECI-TuBaFrost collecting the information of biobanks or in the project support environment on human material; i.e., frozen tumor tissue specimens, pathology blocks, blood samples in different forms, cell lines, Tissue Micro Arrays, etc. Our goal is by centralizing the tumor tissues information to facilitate the search of doctors / researchers for tumor materials, which they need for their cancer research there with facilitating cancer research. OECI members only can participate in the OECI-TuBaFrost exchange platform, or those introduced by an OECI member. We are a group of pathology and research departments as well as bio-bankers in clinical based biobanking based in comprehensive cancer centers or hospitals with a competence in comprehensive cancer care across Europe. Each participating institute is involved in cancer research resulting in innovative procedures, new drugs, improved diagnosis and new insights in disease development. The overall result is better care and treatment for cancer patients. To maximize the scientific value of the human tissue samples, information about the clinical status of the patient in combination with the quality and type of samples is very important. A TuBaFrost electronic database will securely store all this information. Within the closed project supporting environments, the data collected will include: * Diagnosis - identification of the type of cancer * Type of tissue collected - the origin, i.e. breast, skin, colorectal * Quality of tissue collected - collection and storage details The tissue is stored in the hospital where the donor was diagnosed/treated. It stays there until it is used or sent to another hospital or research center within the TuBaFrost group. The electronic database will track samples throughout the network. The tissue is not sold. The exchange of tissue to other hospitals is regulated by a contract, which uses the national regulations of the country supplying the tissue. Tissue samples within the TuBaFrost collection will only be used for research, which has been approved by ethics committees. This ensures that the tissue is only used for the best quality research and only for the specific reasons given to the ethics committee.
Proper citation: OECI - Tubafrost: The European Human Frozen Tissue Bank (RRID:SCR_004280) Copy
http://angioma.org/pages.aspx?content=105&id=92
Angioma Alliance has established a DNA/Tissue Bank and matching clinical database for cerebral cavernous malformations (CCM, cavernous angioma, cavernoma). Our goal is to create the world''s largest collection of CCM genetic samples with matching clinical data to be used as a resource to drive research. We are recruiting individuals with a history of cerebral cavernous malformations to participate in the study. Qualified participants donate a blood sample and complete a comprehensive questionnaire or interview. Blood donation kits will be sent in the mail for participants to take to their doctor, clinic or blood draw center to have their blood drawn. The kit is then mailed to a private lab where the sample is processed. If a surgery is scheduled, the Angioma Alliance DNA/Tissue Bank will work with the participant, the surgeon, and the hospital to coordinate tissue donation. If surgery scheduling allows, dry ice will be shipped to the hospital facility along with a tissue collection kit for use and return to the private lab. The Angioma Alliance DNA/Tissue Bank will attempt to acquire Institutional Review Board approvals at facilities where this is required. The Angioma Alliance BioBank will follow up with participants on a yearly basis to update their clinical information. If the participant has not already had documented genetic testing, we will test their DNA sample for possible CCM1, CCM2, or CCM3 mutation or CCM2 exon 2-10 deletion. If additional causative genes are identified for the illness, we will also test for mutations on these. Participants will not be informed of the results of testing, but if a mutation or deletion is found, they will be informed that results can be released to a diagnostic laboratory in order to obtain follow-up confirmatory clinical diagnostic testing. This could mean a substantial cost savings to the patient whose insurance does not cover genetic testing or who is uninsured. All researchers requesting the use of DNA and/or Tissue samples from Angioma Alliance must complete an application form and material transfer agreement.
Proper citation: Angioma Alliance DNA/Tissue Bank and Patient Registry (RRID:SCR_004390) Copy
http://www.rrcancer.ca/en/publique/accueil
An infrastructure to allow Quebec researchers to have at their disposal tumor banks and the services that support large scale research in genomics and proteomics. The database and the tissue bank of the research network was created to allow rapid access to biological samples and their clinical data. It is spread out over many hospital institutions (in Montreal, Quebec and Sherbrooke). The members of the RRCancer-BTD supply normal, benign and malignant samples from routine surgeries and blood tests. Blood and tissue samples are collected by the provincial biobanks on a regular basis and are coded, classified and stored. The samples can be supplied to a researcher either fresh or frozen or blocks of paraffin or on slices. The sharing of information and biological material is managed according to ethical rules and contributes to increasing the value of research in Quebec. The network has mobilized a significant number of researchers in the area of cancer that unite their efforts to pursue high caliber multidisciplinary research. They are a group of researchers from many different Qu��bec Universities all working in the branch of cancer research. They are located in four hospital centers in Quebec, namely the University of Montreal Hospital Centre (CHUM), the University of Quebec Hospital Centre (CHUQ), the University of Sherbrooke Hospital Centre (CHUS) and the McGill University Hospital Centre (CUSM), as well as in the affiliated research and university centers (Sacr��-Coeur, Maisonneuve-Rosemont and the Montreal Jewish Hospital). The collaborative efforts created and maintained in this network have allowed transfer of knowledge and the sharing of cutting edge technologies. RRCancer favors multidisciplinary cancer research in both fundamental and clinical scopes. The network is based on the desire researchers to work together to prevent cancer and improve therapeutic strategies, all the while continuing the very important task of raining new specialists and graduate students.
Proper citation: Cancer Research Network of the FRSQ (RRID:SCR_004225) Copy
The purpose of the Multidisciplinary Gynecologic Cancer Translational Research Tissue Bank is to provide investigators with primary human tissue for research projects relating to gynecologic cancer. Priority for samples is given to the MD Anderson scientific community. This tissue bank handles the consent, collection, processing, storage and distribution of primary gynecologic tumor samples as well as ascites, blood and urine of gynecologic cancer patients.
Proper citation: MD Anderson Gynecologic Cancer Tissue Bank (RRID:SCR_005004) Copy
http://www.erasmusmc.nl/pathologie/clinicalpathology/tissuebank/161255/?lang=en
The Erasmus MC Virtual Tissue Bank is embedded in the department of Pathology. The collection is meant for medical research purposes only. This concerns a typical clinical based pathology biobank. Tissue samples left over from surgical resection specimen are stored under liquid nitrogen and can be requested by Erasmus MC scientists for medical scientific experiments. An application has been developed to enable scientists to search the collection on-line and request tissue samples over the Erasmus MC Intranet. Every request shall be judged according to procedures determined by the Erasmus MC Tissue Bank. A growing need is anticipated for large collections of well-diagnosed fresh frozen tumor tissue and, if available, corresponding pre-malignant and normal tissue samples. Scientific research on patient residual material has to comply with strict rules and regulations. Equipment The Erasmus MC Tissue bank manages the PALM microdissection laser for the center for Biomics, which is available through the center for Biomics ONLY after having followed an introduction course. Additionally, a complete TMA (Tissue Micro Array) platform, fully funded by the Josephine Nefkens Stichting, consisting of a Beecher Automated Tissue Arrayer ATA 27 and a Virtual Microscope or Nanozoomer from Hamamatsu and Medical Solutions with TMA analyses software strongly supports translational research on tissue samples. Complete histologic Images from the Virtual Microscope are available within the Erasmus MC Intranet or available on the Internet either by overview or a direct example.
Proper citation: Erasmus MC Tissue Bank (RRID:SCR_004945) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. A clinical database and PTB were created in 1990 and 2000, respectively, to collect clinical information and biospecimens from patients with suspected or confirmed pancreatic cancer, other pancreatic diseases, and tumors of the duodenum, ampulla of Vater, and distal bile duct. Standard procedures for biospecimen collection and data entry were developed. The use of human tissue for research is an invaluable tool to understand the basic mechanisms of tumor biology, which will hopefully lead to the development of new therapeutic approaches to pancreatic cancer treatment. The cornerstone of any large translational research program is the development of an accurate and comprehensive tumor bank. All tumors removed in the operating room are sampled for careful pathologic study and the remainder of the tumor is promptly stored in our Pancreas Tissue Bank (PTB) to be used for research. Other samples, including blood, pancreatic juice and biopsy material, can also be utilized to identify early markers for pancreatic cancer. The molecular profile of tumors in the PTB can be linked to information in our clinical database to provide insight on the relationship between molecular events and clinical outcome. Patients may contribute to the tissue banking effort by choosing to participate in select research protocols. Protecting patient privacy is of great importance and thus, to maintain the confidentiality of health information, the PTB complies with all federal and institutional regulations governing research with human participants.
Proper citation: MD Anderson Pancreas Tissue Bank (RRID:SCR_004983) Copy
https://www.stanleygenomics.org/
The Stanley Online Genomics Database uses samples from the Stanley Medical Research Institute (SMRI) Brain Bank. These samples were processed and run on gene expression arrays by a variety of researchers in collaboration with the SMRI. These researchers have performed analyses on their respective studies using a range of analytic approaches. All of the genomic data have been aggregated in this online database, and a consistent set of analyses have been applied to each study. Additionally, a comprehensive set of cross-study analyses have been performed. A thorough collection of gene expression summaries are provided, inclusive of patient demographics, disease subclasses, regulated biological pathways, and functional classifications. Raw data is also available to download. The database is derived from two sets of brain samples, the Stanley Array collection and the Stanley Consortium collection. The Stanley Array collection contains 105 patients, and the Stanley Consortium collection contains 60 patients. Multiple genomic studies have been conducted using these brain samples. From these studies, twelve were selected for inclusion in the database on the basis of number of patients studied, genomic platform used, and data quality. The Consortium collection studies have fewer patients but more diversity in brain regions and array platforms, while the Array collection studies are more homogenous. There are tradeoffs, the Consortium results will be more variable, but findings may be more broadly representative. The collections contain brain samples from subjects in four main groups: Bipolar Schizophrenia, Depression, and Controls Brain regions used in the studies include: Broadman Area 6, Broadman Area 8/9, Broadman Area 10, Broadman Area 46, Cerebellum The 12 studies encompass a range of microarray platforms: Affymetrix HG-U95Av2, Affymetrix HG-U133A, Affymetrix HG-U133 2.0+, Codelink Human 20K, Agilent Human I, Custom cDNA Publications based on any of the clinical or genomic data should credit the Stanley Medical Research Institute, as well as any individual SMRI collaborators whose data is being used. Publications which make use of analytic results/methods in the database should additionally cite Dr. Michael Elashoff. Registration is required to access the data.
Proper citation: Stanley Medical Research Institute Online Genomics Database (RRID:SCR_004859) Copy
http://nif-apps1.crbs.ucsd.edu/smabiomarkers/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A publicly available tool that contains data from the BforSMA clinical study ( ClinicalTrials.gov, NCT00756821 ), a pilot study to identify candidate biomarkers in blood or urine from a wide range of Spinal Muscular Atrophy (SMA) patients that associate with disease severity. It is hoped that the identification of candidate biomarkers will lead to clinical efficacy and longitudinal natural history studies to verify these markers and enable their use as validated pharmacodynamic markers, longitudinal progression markers, or surrogate endpoint measures in clinical trials.
Proper citation: BioMarkers for SMA Data Portal (RRID:SCR_004920) Copy
The Stanford University HIV Drug Resistance Database is a curated public database designed to represent, store, and analyze the different forms of data underlying HIVs drug resistance. HIVDB has three main types of content: (1) Database queries and references, (2) Interactive programs, and (3) Educational resources. Database queries are designed primarily for researchers studying HIV drug resistance. The interactive programs and educational resources are designed for both researchers and those wishing to learn more about HIV drug resistance. 1.DATABASE QUERY AND REFERENCE PAGES Genotype-Treatment Correlations This Genotype-Treatment section of the database links to 15 interactive query pages that explore the relationship between treatment with HIV-1 antiretroviral drugs (ARVs) and mutations in HIV reverse transcriptase (RT), protease, and integrase. There are five types of interactive query pages: Treatment Profiles (Protease and RT inhibitors) Mutation Profiles (Protease and RT mutations) Detailed Treatment Queries (Protease, RT, and integrase inhibitors) Detailed Mutation Queries (Protease, RT, and integrase mutations) Mutation Prevalence According to Subtype and Treatment Genotype-Phenotype Correlations The main page of the Genotype-Phenotype Correlations section links to four interactive query pages: three dynamically updated data summaries and one regularly updated downloadable dataset. Drug Resistance Positions Query for levels of resistance associated with known drug resistance mutations Detailed Phenotype Queries Queries for levels of resistance associated with individual mutations or mutation combinations at all positions of protease, RT, and integrase Patterns of Drug Resistance Mutations Downloadable Reference Dataset Genotype-Clinical Correlations This part of the database has two main sections: Clinical Trials Datasets Summaries of Clinical Studies References This part of the database has two main sections: one with summaries of the data from each of the references in HIVDB and one in which every primate immunodeficiency virus sequence in GenBank is annotated according to its presence or absence in HIVDB. Studies in HIVDB GenBank <=> HIVDB New Submissions Approximately every three months, the New Submissions section lists the studies that have been entered into HIVDB. The study title links to the introductory page of the study in the References section. Database Statistics (http://hivdb.stanford.edu/pages/HIVdbStatistics.html) 2. INTERACTIVE PROGRAMS HIVDB has seven main interactive programs. 1. HIVdb Program Mutation List Analysis Sequence Analysis HIVdb Output Sierra Web Service Release Notes Algorithm Specification Interface (ASI) 2. HIValg Program 3. HIVseq Program 4. Calibrated Population Resistance (CPR) tool 5. Mutation ARV Evidence Listing (MARVEL) 6. ART-AiDE 7. Rega HIV-1 Subtyping tool Three programs in the HIV Drug Resistance Database share a common code base: HIVseq, HIVdb, and HIValg. HIVseq accepts user-submitted protease, RT, and integrase sequences, compares them to the consensus subtype B reference sequence, and uses the differences as query parameters for interrogating the HIV Drug Resistance database (Shafer, D Jung, & B Betts, Nat Med 2000; Rhee SY et al. AIDS 2006). The query result provides users with the prevalence of protease, RT and integrase mutations according to subtype and PI, nucleoside RT inhibitor (NRTI), non-nucleoside RT inhibitor (NNRTI), and integrase inhibitor (INI) exposure. This allows users to detect unusual sequence results immediately so that the person doing the sequencing can check the primary sequence output while it is still on the desktop. In addition, unexpected associations between sequences or isolates can be discovered by immediately retrieving data on isolates sharing one or more mutations with the sequence. There are three ways in which the HIVdb program can be used: (i) entering a list of protease and RT mutations, (ii) entering a complete sequence containing protease, RT, and/or integrase, and (iii) using a Web Service. HIVdb is an expert system that accepts user-submitted HIV-1 pol sequences and returns inferred levels of resistance to 20 FDA-approved ARV drugs including 8 PIs, 7 NRTIs, 4 NNRTIs, and - with this update - one INI. In the HIVdb system, each HIV-1 drug resistance mutation is assigned a drug penalty score and a comment; the total score for a drug is derived by adding the scores of each mutation associated with resistance to that drug. Using the total drug score, the program reports one of the following levels of inferred drug resistance: susceptible, potential low-level resistance, low-level resistance, intermediate resistance, and high-level resistance. HIValg is designed for users interested in comparing the results of different algorithms or who are interested in comparing and evaluating existing and newly developed algorithms. The ability to develop new algorithms that can be run on the HIV Drug Resistance Database depends on the Algorithm Specific Interface (ASI) compiler (Shafer & Betts JCM 2003). Submission of Sequences and Mutations For each of the three programs, sequences can be entered using either the Sequence Analysis Form or the Mutation List form. 3. EDUCATIONAL RESOURCES HIVDB contains several regularly updated sections summarizing data linking RT, protease, and integrase mutations and antiretroviral drugs (ARVs). These sections include (i) tabular summaries of the major mutations associated with each ARV class, (ii) detailed summaries of the major, minor, and accessory mutations associated with each ARV, (iii) the comments used by the HIVdb program, (iv) the scores used by the HIVdb program, (v) clinical studies in which baseline drug resistance mutations have been correlated with the virological response (clinical outcome) to a specific ARV, (vi) mutations that can be used for drug resistance surveillance, and (vii) a two-page PDF handout. 1. Drug Resistance Summaries Tabular Drug Resistance Summaries by ARV Class Detailed Drug Resistance Summaries by ARV Drug Resistance Mutation Comments Used by the HIVdb Program Drug Resistance Mutation Scores Used by the HIVdb Program Genotype-Clinical Outcome Correlation Studies 2. Surveillance Drug-Resistance Mutation List Section 3. PDF Handout Grant Support 1. National Institute for Allergy and Infectious Diseases (NIAID, NIH): Online HIV Drug Resistance Database (PI: Robert W. Shafer, MD, 1R01AI68581-01A1), 04/01/06 - 3/31/11 2. National Institute for Allergy and Infectious Diseases (NIAID, NIH) supplement to the grant Identification of Multidrug-Resistant HIV-1 Isolates (PI: Robert W. Shafer, MD, AI46148-01): Supplement provided 1999-2005. 3. NIH/NIGMS Program Project on AIDS Structural Biology Program Project: Targeting Ensembles of Drug Resistant Protease Variants (PI: Celia Schiffer, PhD, University of Massachusetts): 2002-2007 4. University-wide AIDS Research Program (CR03-ST-524). Community collaborative award: Optimizing Clinical HIV Genotypic Resistance Interpretation: Principal Investigators: Robert W. Shafer, MD and W. Jeffrey Fessel MD (Kaiser Permanente Medical Care Program): 2004-2005 5. Stanford University Bio-X Interdisciplinary Initiative: HIV Gene Sequence Analysis for Drug Resistance Studies: A Pharmacogenetic Challenge Principal Investigators: Robert W. Shafer, MD and Daphne Koller, Ph.D. (Computer Science): 2000-2002
Proper citation: Stanford University HIV Drug Resistance Database (RRID:SCR_006631) Copy
http://www.research.va.gov/programs/tissue_banking/als/
A human tissue bank that collects, processes, stores and gives out research specimens for future scientific studies. Presently, the VABBB is obtaining neurologic tissue specimens from Veterans who suffer from amyotrophic lateral sclerosis (ALS) and other illnesses that affect Veterans, along with relevant clinical data, essential for research. Currently, neither the cause nor prevention of ALS is known. Medical researchers are currently examining environmental, toxic, genetic, traumatic, medical, and occupational influences as possible contributors to the development and progression of ALS. Veterans have a higher risk of developing ALS compared with non-Veterans; however, the reasons for this higher risk are currently unknown. Any Veteran with ALS in the U.S. may enroll in the VABBB.
Proper citation: VA Biorepository Brain Bank (RRID:SCR_006546) Copy
https://www.iscaconsortium.org/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 22, 2022. A rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. They improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population. The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. Efforts of the Consortium include: # Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). # Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (which will evolve into a Standing Committee with international representation). # Public Database for clinical and research community: It is essential that publicly available databases be created and maintained for cytogenetic array data generated in clinical testing laboratories. The ISCA data will be held in dbGaP and dbVar at NCBI/NIH and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. # Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of unknown clinical significance.
Proper citation: ISCA Consortium (RRID:SCR_006168) Copy
http://www.ncbi.nlm.nih.gov/clinvar/
Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard.
Proper citation: ClinVar (RRID:SCR_006169) Copy
http://code.google.com/p/neurological-disease-ontology/
An ontology for the representation of the range of clinical and basic science aspects of neurological diseases. ND has a broad scope that includes neurological diseases as well as their associated signs, symptoms, diagnoses, pathologies, etiologies, processes, treatments, and any other aspect of a neurological disease that is or can be encountered in the course of clinical practice or medical research. ND is being built in accordance with the OBO Foundry principles. It is an extension of the Ontology for General Medical Science (OGMS) as well as the Basic Formal Ontology (BFO). ND aims to develop classes utilizing both textual and axiomatized definitions to describe and formalize relations between instances of classes both within the ontology itself as well as between ND and external ontologies such as the: Gene Ontology (GO), Cell Ontology (CL), Protein Ontology (PRO), Chemical Entities of Biological Interest (ChEBI), and Ontology for Biomedical Investigations (OBI).
Proper citation: Neurological disease ontology (RRID:SCR_010284) Copy
http://cahub.cancer.gov/about/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures.
Proper citation: caHUB (RRID:SCR_009657) Copy
http://code.google.com/p/ogms/
An ontology based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop (Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.
Proper citation: Ontology for General Medical Science (RRID:SCR_010384) Copy
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