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http://www.candidagenome.org/

Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome.

Proper citation: Candida Genome Database (RRID:SCR_002036) Copy   

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http://autosnpdb.appliedbioinformatics.com.au

We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The implementation of autoSNPdb allows researchers to query the results of SNP analysis to characterize SNPs between specific groups of individuals or within genes with predicted function. The system is flexible and researchers may add additional levels of annotation, and perform novel queries specific to their area of interest. If you have sequence data you'd like to include please contact Dave Edwards.

Proper citation: autoSNPdb (RRID:SCR_001927) Copy   

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http://www.genet.sickkids.on.ca/cftr/

Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

Proper citation: Cystic Fibrosis Mutation Database (RRID:SCR_000685) Copy   

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http://flybase.org/

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

Proper citation: FlyBase (RRID:SCR_006549) Copy   

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http://androgendb.mcgill.ca/

Comprehensive listing of androgen receptor gene mutations published in journals and meetings proceedings. The majority of mutations are point mutations identified in patients with androgen insensitivity syndrome. Information is included regarding the phenotype, the nature and location of the mutations, as well as the effects of the mutations on the androgen binding activity of the receptor. In light of the difficulty in getting new AR mutations published the curator will now accept new mutations that have not been published, provided that it is from a reputable research or clinical laboratory. The database incorporates information on the exon 1 CAG repeat expansion disease, spinobulbar muscular atrophy (SBMA), as well as CAG repeat length variations associated with risk for female breast, uterine endometrial, colorectal, and prostate cancer, as well as for male infertility. The possible implications of somatic mutations, as opposed to germline mutations, in the development of future locus-specific mutation databases (LSDBs) is discussed.
The database now provides information on the external genitalia and on sex - of - rearing. Additionally, the new version of the database has an entry to show if pathogenicity has been proven. A pdf and fully searchable version of the Database is available for download.

Proper citation: Androgen Receptor Gene Mutations Database (RRID:SCR_006887) Copy   

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http://pga.mgh.harvard.edu/primerbank/

Database of human and mouse primer pairs for gene expression analysis by polymerase chain reaction (PCR) and quantitative PCR (qPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. All primers in PrimerBank were carefully designed to ensure gene specificity. All experimental validation data for mouse primers are available from PrimerBank. You can submit your primers. They will be added to the database once they are properly QCd.

Proper citation: PrimerBank (RRID:SCR_006898) Copy   

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http://locus.jouy.inra.fr/cgi-bin/bovmap/intro.pl

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.

Proper citation: BovMap Database (RRID:SCR_008145) Copy   

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http://code.google.com/p/eagle-i/

Ontology that models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/) and consists of over 3451 classes of which over 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well. The main ontology can be browsed in OntoBee. All purls resolve to OntoBee.

Proper citation: eagle-i research resource ontology (RRID:SCR_008784) Copy   

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http://www.mrc-lmb.cam.ac.uk/genomes/dolop/

DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins.

Proper citation: DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) Copy   

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http://xin.cz3.nus.edu.sg/group/admeap/admeap.asp

A database for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion (ADME) associated proteins. It contains information about known drug ADME associated proteins, functions, similarities, substrates / ligands, tissue distributions, and other properties of the targets. Associated references are also included. Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates. ADME Class Based on their respective role of pharmacokinetics, ADME-associated proteins can be classified into four categories: A: This Category includes proteins involved in the absorption or re-absorption of drugs into systemic system. D: This category includes proteins responsible for facilitating the distribution of drugs from the systemic system to the target sites or away from the target sites back to the systemic system. Certain plasma proteins and intracellular binding proteins may alter free drug concentration by acting as drug storage depot. These proteins thus play a regulatory role in drug distribution and they are thus included in Category D. Based on their role in drug distribution, proteins in this category can be further divided into three groups D1, D2, and D3. The first group D1 includes transporters capable of transporting chemicals across membranes of various tissue barriers from the systemic system into the target sites. Blood-brain barrier and placenta barrier are examples of tissue barrier. Proteins in the second group D2 are responsible for transporting drugs back into the systemic system. Proteins in the third group D3 mainly function as drug storage depot. These include ligand binding proteins in plasma and intracellular proteins. M: Proteins in category M are drug-metabolizing enzymes. These enzymes can be further divided into two separate groups M1 and M2, according to whether the corresponding enzymatic reaction is phase I or phase II. E: This category E includes proteins that enable the excretion or presystemic elimination of drugs. Some proteins belong to more than one category: e.g. P-glycoprotein both limits intestinal absorption and excludes drugs from the brain back to the blood. It thus belongs to both Category E and D. For those proteins capable of transporting natural substrates without literature report of interaction with a drug, a postfix potential is attached to their respective classification to indicate that their specific role in ADME is yet to be confirmed. Use of ADME-AP for commercial purposes is not allowed.

Proper citation: Drug ADME Associated Protein Database (RRID:SCR_013501) Copy   

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http://research.bmh.manchester.ac.uk/bryce/amber

Assisted model building with energy refinement parameter database. Family of force fields for molecular dynamics of biomolecules. Collection of equations and associated constants designed to reproduce molecular geometry and selected properties of tested structures.

Proper citation: AMBER parameter database (RRID:SCR_018815) Copy   

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http://fluency.talkbank.org/

Database for study of development of fluency in both normal and disordered populations. Participants include normally-developing monolingual and bilingual children, children with disfluencies (CWD), adults with disfluencies (AWSD), and second language learners.

Proper citation: FluencyBank (RRID:SCR_016313) Copy   

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http://www.camarades.info/index_files/Protocols.html

A site for sharing meta-analysis protocols for translational neuroscience research. Protocols for systematic review of in vivo data modelling human neurological disease. Making the protocol for your systematic review available to the community has a number of benefits; it provides evidence that prespecified analyses were indeed prespecified; allows others to comment on your approach; provides examples for others planning such reviews; and can help you identify if other reviews in similar areas are already in progress. This site was created to foster collaboration.

Proper citation: CAMARADES Protocols for Systematic Reviews of Animal Studies (RRID:SCR_008970) Copy   

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http://link.springer.com/article/10.1007%2Fs11357-003-0002-y

A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments.

Proper citation: AgingDB (RRID:SCR_010226) Copy   

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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   

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http://c1.accurascience.com/miRecords/

A resource for animal miRNA-target interactions consisting of the Validated Targets component, a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation, and the Predicted Targets component, an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. April 27, 2013, the Validated Targets component of miRecords hosts 2705 records of interactions between 644 miRNAs and 1901 target genes in 9 animal species. Among these records, 2028 were curated from low throughput experiments. The Predicted Targets component of mIRecords integrates the predicted targets of the following miRNA target prediction tools: DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid, and TargetScan/TargertScanS. We would be glad to include your experimentally validated miRNA target data (published or unpublished) into miRecords., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: miRecords (RRID:SCR_013021) Copy   

•   Source: SciCrunch Registry
  

https://bioregistry.io

Open source, community curated registry, meta-registry, and compact identifier resolver. Used for unifying identification of biomedical entities through integrative, open,community driven metaregistry. The registry contains metadata about ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more.

Proper citation: Bioregistry (RRID:SCR_022586) Copy   

•   Source: SciCrunch Registry
  

http://mayoresearch.mayo.edu/mitochondrial-disease-biobank/

A biobank of blood and tissue samples from patients with known and suspected mitochondrial diseases along with data from their families. Samples are used in research to understand the family of mitochondrial disorders such as Alpers' syndrome, encephalopathy, and Friedrieich's ataxia, among many others. The goal of the biobank is to advance the understanding of mitochondrial disease and improve patient care.

Proper citation: Mayo Mitochondrial Disease Biobank (RRID:SCR_010598) Copy   

•   Source: SciCrunch Registry
  

http://vivisimo.com/

Vivisimo''s mission is to help organizations maximize the business value of their information through innovations in search and discovery technology. Building on its other innovations, Vivisimo was first to offer enterprise social search, which lets enterprise users share their knowledge with coworkers by tagging, ranking, and annotating search results. Vivisimo''s founders first developed new ways to categorize search results as a research project at Carnegie Mellon University''s computer science department. After years of product development and further innovations, Vivisimo today offers Velocitya complete enterprise search platform that unifies access to secure business repositories, presents search results with an unmatched user experience, and enables knowledge sharing across an organization. Velocity is making single-search-box access to wide selections of corporate information a reality at organizations large and small. You can install Velocity in minutes, use its web console to configure access to diverse document, email, database, and web page repositories, and import their access rights so that searchers get just what they''re authorized to see and nothing more. Use the console to spotlight high-value information, package repositories into search tabs, enable clustered results by topic or meta-data, enliven the search results with embedded images, and more, all without custom programmingjust configuration.

Proper citation: Vivisimo Document Clustering (RRID:SCR_008247) Copy   

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http://www.masy.com/biopharma-repository/biopharma-repository

Safe and secure environmentally controlled storage for the biotech, pharmaceutical and medical device industries. Masy provides same-day retrieval and shipping of your biomaterials. Our cost-effective repository space is comprised of multiple chamber styles, from walk-in refrigerators / freezers for large containers, to single-shelf storage units for individual vials. Segregated & unsegregated storage is available. Our sophisticated inventory management system utilizes a precise bar-code inventory track-and-trace system with data safely stored on dedicated servers. Critical data access is secured by password protection. Environmental storage condition information and sample access is limited to customer approved personnel only. Our in-house Validation and Calibration teams allow us to offer unique storage conditions. And, we now offer GMP labeling and distribution of clinical samples. Masy is ISO 9001:2009 Certified and NVLAP ISO/IEC 17025:2005 Accredited. Our state-of-the-art facility is conveniently located less than an hour from Metro-Boston, just 15 minutes from the Devens Commerce Park.

Proper citation: BioPharma Storage Facility - Masy Systems (RRID:SCR_004155) Copy   

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