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https://swisstree.vital-it.ch/

Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure.

Proper citation: SwissTree (RRID:SCR_015881) Copy   

•   Source: SciCrunch Registry
  

https://pmlivingbiobank.uhnresearch.ca/

Core provides services for the use of Xenograft (PDX) models listed in open global catalogue of PDX models for comprehensive search and attribute filtering support for clinico-pathological and molecular data. Molecular data and visualization of profiled models could be accessed through the institute's portal.

Proper citation: University Health Network Princess Margaret Living PDX Core Facility (RRID:SCR_027523) Copy   

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https://dmportal.biodata.pt/

Portuguese distributed infrastructure for biological data and Portuguese node of ELIXIR.

Proper citation: BioData Management Portal (RRID:SCR_023138) Copy   

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https://dwc.tdwg.org/

Natural history collections. Offers a stable, straightforward and flexible framework for biodiversity data. Community-developed biodiversity data standard. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing identifiers, labels, and definitions. Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, samples, and related information.

Proper citation: Darwin Core (RRID:SCR_016778) Copy   

•   Source: SciCrunch Registry
  

http://www.genesis-sim.org/hbp/

Software system to assist computational neuroscientists in interacting with databases of models and with neural simulation packages such as GENESIS. There are three components in the system: a user interface, a database server, and a global registry and repository. The collection of software tools with a graphical user interface enables users to interact over the WWW with databases of models and data. It provides facilities for searching multiple remote databases for model components based on various criteria; visualizing the characteristics of the components retrieved; creating new components, either from scratch or derived from existing models; combining components into new models; linking models to experimental data as well as online publications; and interacting with simulation packages such as GENESIS to simulate the new constructs. Although the initial version uses GENESIS as the simulator, the design permits the use of multiple simulation systems, with or without the use of a database. This allows modeling at multiple levels of scale from the molecular level, through the subcellular (e.g. ion channel), single cell, and network levels, to the systems level (e.g. relating models to fMRI studies). The system is intended to help users create and organize models and to interact with databases of models and neuronal simulation software. More specifically, the Modeler's Workspace is designed to provide the following: * Search and retrieval facilities for interacting with databases of models and other information; * Facilities for creating, editing and visualizing the characteristics of models; * Facilities for combining model components together and translating them into formats suitable for simulation systems such as GENESIS and NEURON; * Facilities for managing a personal database where a user can collect models and other objects; and * Collaboration facilities for connecting one or more users together, to allow them to simultaneously edit objects in a shared database and communicate with each other using real-time chat. The Modeler's Workspace is written in Java for portability and extensibility. It is modular in design and uses pluggable components for supporting different data formats, which means that new data types can be supported by loading an appropriate plug-in. To increase the probability that the Modeler's Workspace will be compatible with future databases and tools, they are using the eXtensible Markup Language (XML) as the interchange format for communicating with databases.

Proper citation: GENESIS Neural Database and Modelers Workspace (RRID:SCR_002357) Copy   

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http://www.pharmgkb.org/

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

Proper citation: PharmGKB (RRID:SCR_002689) Copy   

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http://www.gene-talk.de

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations.

Proper citation: GeneTalk (RRID:SCR_005231) Copy   

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https://www.brain-score.org/

Platform provides accurate, machine-executable computational models of how the brain gives rise to the mind. Enables researchers to quickly get a sense of the alignment of their model(s) to neural and behavioral measurements, and provides these models to experimentalists to prototype new experiments and make sense of biological data. All code is open-source and community members may choose to make their data or model weights fully public.

Proper citation: Brain Score (RRID:SCR_027769) Copy   

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https://ftp.ncbi.nlm.nih.gov/pub/mhc/mhc/Final%20Archive/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019 Database was open, publicly accessible platform for DNA and clinical data related to human Major Histocompatibility Complex (MHC). Data from IHWG workshops were provided as well., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dbMHC (RRID:SCR_002302) Copy   

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http://www.jisc.ac.uk/whatwedo/programmes/mrd/clip/webtracks.aspx

This project will develop an approach and mechanism to address the construction and propagation of linked data in the context of research and academic endeavour. The proposed work will build experiments in previous projects (Claddier, StoreLink) to develop a peer-to-peer protocol to underpin the construction of a web of linked data. This set of semantically annotated links between data resources forms a graph of citation and provenance and the project will build value added services to exploit these features. The project will address the following specific objectives: * To specify and implement the Intercom Protocol so that it can communicate a range of types of semantic links between resources via a secure communication mechanism. * To develop a practical working scenario involving data repositories, publication repositories, open science notebooks and publishers. * To develop aggregation techniques supporting added value services in search and impact analysis. * To evaluate of the approach with the identified stakeholders groups.

Proper citation: Webtracks (RRID:SCR_006615) Copy   

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http://t1dbase.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.

Proper citation: T1DBase (RRID:SCR_007959) Copy   

•   Source: SciCrunch Registry
  

http://www.xpmutations.org

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   

•   Source: SciCrunch Registry
  

https://www.davincieuropeanbiobank.org/

BioBank that collects, stores, processes and distributes biospecimens and the associated data. The biospecimens are human and non-human genetic materials, proteins, cells, tissues and biofluids. The data are the biological information associated to the samples and, in the case of human samples, the clinical information pertaining to the donor. The da Vinci European BioBank (daVEB) is a multicenter biobank with a centralized IT infrastructure and a main repository located at the Polo Scientifico (Scientific Campus of the University of Florence) in Sesto Fiorentino (Florence, Italy). Hosted by the Magnetic Resonance Center (CERM), an expert center on protein structure and metabolomics, daVEB's aim is to host as rich as possible biological human sample collections, stored accordingly to EU guidelines, in order to offer a powerful tool in the study of complex diseases. At the end of July 2011, the da Vinci European BioBank of the Pharmacogenomics FiorGen Onlus Foundation has been audited and got the quality certification according to UNI EN ISO 9001:2008 for Collection, storage and distribution of biological samples and the associated data for scientific research. Besides the samples stored at da Vinci European BioBank in Sesto Fiorentino (Florence), the daVEB is also the administrative biobank for research sample collections that are stored in the delocalized repositories. All the sample collections must be registered in the biobank: * sample collections taken within the regular health care * samples taken from healthy individuals or other persons out of the regular health care * samples that have been taken in hospitals within research protocols on specific pathologies all transferred to daVEB endowed with a transfer agreement signed by the donor. The Research Units actually afferent to daVEB are delocalized in the Florence, Prato, Pisa and Siena provinces. Delocalized repositories are under construction in Tuscany.

Proper citation: da Vinci European Biobank (RRID:SCR_004908) Copy   

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http://www.uniprot.org/help/uniprotkb

Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.

Proper citation: UniProtKB (RRID:SCR_004426) Copy   

•   Source: SciCrunch Registry
  

https://github.com/XSLiuLab/Pep2TCR

Web tool for CD4 TCR specificity prediction and biology applications. Used for accurate prediction of CD4 T cell receptor binding specificity through transfer learning and ensemble approach. Repository comprises codes of Pep2TCR, providing comprehensive guidance for researchers interested in Pep2TCR.

Proper citation: Pep2TCR (RRID:SCR_024721) Copy   

•   Source: SciCrunch Registry
  

http://clinicaltrials.gov/

Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries.

Proper citation: ClinicalTrials.gov (RRID:SCR_002309) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/cgi-bin/sva/sva.pl/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The ENA Sequence Version Archive is a repository of all entries which have ever appeared in EMBL-Bank Sequence Database. You can browse the archive or use the batch retrieval form.

Proper citation: ENA Sequence Version Archive (RRID:SCR_000929) Copy   

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http://www.fimre.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources

Proper citation: Federation of International Mouse Resources (RRID:SCR_006137) Copy   

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http://www.ohsu.edu/xd/education/schools/school-of-medicine/departments/clinical-departments/pathology/research/oregon-brain-bank.cfm

Brain bank that harvests, banks and disperses postmortem tissue for use in brain and medical research. It also provides neuropathologic diagnoses of organic dementia in a cohort of NIH sponsored research subjects. The bank includes tissue primarily from patients with Alzheimer's but also includes Huntington's, Parkinson's, and other disorders.

Proper citation: Oregon Brain Bank (RRID:SCR_013085) Copy   

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http://www.framinghamheartstudy.org/

A longitudinal, epidemiologic study to identify the common risk factors or characteristics that contribute to cardiovascular disease by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms or suffered a heart attack or stroke. Since that time the FHS has studied three generations of participants resulting in biological specimens and data from nearly 15,000 participants. Since 1994, two groups from minority populations, including related individuals have been added to the FHS. FHS welcomes proposals from outside investigators for data and biospecimens. The researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have continued to return to the study every two years for a detailed medical history, physical examination, and laboratory tests, and in 1971, the Study enrolled a second generation - 5,124 of the original participants'''' adult children and their spouses - to participate in similar examinations. In 1994, the need to establish a new study reflecting a more diverse community of Framingham was recognized, and the first Omni cohort of the Framingham Heart Study was enrolled. In April 2002 the Study entered a new phase, the enrollment of a third generation of participants, the grandchildren of the Original Cohort. In 2003, a second group of Omni participants was enrolled. Over the years, careful monitoring of the Framingham Study population has led to the identification of major CVD risk factors, as well as valuable information on the effects of these factors such as blood pressure, blood triglyceride and cholesterol levels, age, gender, and psychosocial issues. Risk factors for other physiological conditions such as dementia have been and continue to be investigated. In addition, the relationships between physical traits and genetic patterns are being studied. FHS clinical and research data is stored in the dbGaP and NHLBI Repository repositories and may be accessed by application. Please check the following repositories before applying for data through FHS. Investigators seeking data that is not available through dbGaP or BioLINCC or seeking biological specimens may submit a proposal through the FHS web-based research application. The FHS data repository may be accessed through this FHS website, under the For Researchers link, then Description of Data, in order to determine if and how the desired data is stored. Proposals may involve the use of existing data, the collection of new data, either directly from participants or from previously collected samples, images, or other materials (e.g., medical records). The FHS Repository also has biological specimens available for genetic and non-genetic research proposals. Specimens include urine, blood and blood products, as well as DNA.

Proper citation: Framingham Heart Study (RRID:SCR_008963) Copy   

•   Source: SciCrunch Registry