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http://www.phenogo.org

PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA).

Proper citation: PhenoGO (RRID:SCR_013646) Copy   

•   Source: SciCrunch Registry

http://rose.man.poznan.pl/aars/index.html

The AARSs database is the collection of amino acid sequences of all published AARSs. Currently it contains 1047 primary structures of cytoplasmic and organellar AARSs from various organisms. The entries are grouped according to AARS amino acid specificity. They are based on EMBL/SWISS-PROT format. Each includes the AARS amino acid sequence, its SWISS-PROT name and the accession number, a short description of the sequence, its source (organism name with taxonomic classification) and bibliographic information. For the enzymes whose sequences were determined at the nucleotide level, the appropriate EMBL/GenBank or TIGR entries are included, and for those with already known 3D structure, the cross-references to the Brookhaven Protein Data Base are indicated. The partial sequences of AARSs are also included in the database. According to the original SWISS-PROT description, some of the entries have been marked as putative or probable.

Proper citation: Aminoacyl-tRNA synthetase database (RRID:SCR_013498) Copy   

•   Source: SciCrunch Registry

http://www.lsbm.org/site_e/database/index.html

It is a comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of thousands of genes are measured with oligo-nucleotide DNA microarray "GeneChip". All gene expression data in this database is produced by LSBM (Laboratory for Systems Biology and Medicine) and the collaborators. SBM DB provides two different databases: A reference database for fur expression analysis (RefEXA) and LSMB GeNet, a database of various organisms, tissues, and experiences. RefEXA provides a comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with GeneChip HG-U133A, can help investigation of Human disease. LSMB provides

Proper citation: SBM DB (RRID:SCR_013491) Copy   

•   Source: SciCrunch Registry

http://www.echinobase.org/

Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology.

Proper citation: EchinoBase (RRID:SCR_013732) Copy   

•   Source: SciCrunch Registry

http://jcggdb.jp/rcmg/glycodb/Ms_ResultSearch

A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans.

Proper citation: Glycan Mass Spectral Database (GMDB) (RRID:SCR_014667) Copy   

•   Source: SciCrunch Registry

https://www.nist.gov/srd/nist-standard-reference-database-1a-v14

A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals.

Proper citation: Mass Spectral Library (RRID:SCR_014668) Copy   

•   Source: SciCrunch Registry

http://db.systemsbiology.net/kaviar/

A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants.

Proper citation: KAVIAR (RRID:SCR_013737) Copy   

•   Source: SciCrunch Registry

http://hbatlas.org

A data repository containing transcriptome and associated metadata for the developing and adult human brain. It provides genome-wide, exon-level transcriptome data from both sexes and multiple ethnicities.

Proper citation: Human Brain Transcriptome (RRID:SCR_013742) Copy   

•   Source: SciCrunch Registry

http://supfam.org/SUPERFAMILY/dcGO/

A database of domain-centric ontologies on functions, phenotypes, diseases and more. As a biomedical ontology resource, dcGO integrates functional, phenotypic, disease, and drug information. As a protein domain resource, it includes annotations to both the individual domains and supra-domains. Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes). Users can mine and browse through resources.

Proper citation: dcGO (RRID:SCR_014392) Copy   

•   Source: SciCrunch Registry

https://www.nursa.org/nursa/transcriptomine/index.jsf

A database of tissue specific nuclear receptor transcriptomes based on annotated published genome wide transcriptional profiling experiments in the field of nuclear receptor signaling. Queries can include single and multiple genes, Gene Ontology terms, disease terms, and uploaded custom gene lists.

Proper citation: NURSA Transcriptomine (RRID:SCR_013746) Copy   

•   Source: SciCrunch Registry

http://user.it.uu.se/~torer/publ/neuro-science.pdf

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database project for the neuroimaging community NeuroGenerator is a database project funded by the European Commission. The overall purpose is to make databases with data in comparable and compatible formats suited for meta research and for making models of the cerebral cortex of the human brain. Researchers can submit their own raw PET-data and fMRI data to NeuroGenerator. The data are analyzed with the statistical software package FSL. In this way databases are produced of PET and fMRI data in standard anatomical format Data as statistical parametric images in standard anatomical format immediately comparable due to the uniform processing Cytoarchitectural data (from post mortem brains) in standard anatomical format.

Proper citation: Neurogenerator (RRID:SCR_013595) Copy   

•   Source: SciCrunch Registry

http://www.kazusa.or.jp/kaos/

This site has been developed by Kazusa DNA Research Institute for the purpose of offering the science community the analyzed sequence data produced by a multi-national Arabidopsis genome sequencing project coordinated by the Arabidopsis Genome Initiatives (AGI). The aim of this service is to enable users to browse the annotated sequence data produced by all the sequencing teams of AGI through an user-friendly graphic display system and search engines. Gene structures proposed on the annotated sequences as well as those predicted by computer programs are presented and each graphic item has a hyperlink to detailed information of the corresponding area. The nucleotide sequence data deposited in GenBank by AGI was downloaded, re-computer-analyzed at Kazusa and parsed results are displayed graphically.

Proper citation: Kazusa Arabidopsis data opening site (RRID:SCR_013511) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/pcp/

A project which systematically preprocess the data from the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI) and openly share the results. Data is currently hosted in an Amazon Web Services Public S3 Bucket and at NITRC.

Proper citation: Preprocessed Connectomes Project (RRID:SCR_014162) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/pd3/

THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan. 5, 2016. Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources.

Proper citation: Parkinsons Disease Discovery Database (RRID:SCR_014160) Copy   

•   Source: SciCrunch Registry

http://www.imodel.org

Database of interactive neural computation computer models at levels ranging from simple linear filters to large-scale networks of spiking units. Interface tools are provided while browsing and exploring models.

Proper citation: iModel (RRID:SCR_014811) Copy   

•   Source: SciCrunch Registry

https://www.crossref.org/services/event-data/

Database of events about articles that is run by CrossRef. It allows users to view social media mentions, news publication references, annotations, and more.

Proper citation: Crossref EventData (RRID:SCR_016281) Copy   

•   Source: SciCrunch Registry

https://www.gem-beta.org/Public/Home.aspx

Database that contains behavioral and social science measures organized by theoretical constructs. GEM is designed to enable researchers to use common measures with the goal of exchanging harmonized data.

Proper citation: Grid-Enabled Measures Database (RRID:SCR_016043) Copy   

•   Source: SciCrunch Registry

https://rtips.cancer.gov/rtips/index.do

Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials.

Proper citation: Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) Copy   

•   Source: SciCrunch Registry

http://mosas.sysu.edu.cn/genome

Database project to document the genome sequence of the Lancelet, a basal extant chordate. Information provided includes reference haploid genome sequence and annotation data, gene models and function, and integrated information from diploid genome sequence and annotation data.

Proper citation: Lancelet Genome Sequence and Annotation Project Database (RRID:SCR_014987) Copy   

•   Source: SciCrunch Registry

http://floresta.eead.csic.es/3dfootprint

Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.

Proper citation: 3D-footprint (RRID:SCR_015713) Copy   

•   Source: SciCrunch Registry