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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

http://www.stemcord.com

Not yet vetted by NIF curator

Proper citation: StemCord Cord Blood Bank (RRID:SCR_013502) 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://sbi.imim.es/cgi-bin/archdb/loops.pl

ArchDB is a compilation of structural classifications of loops extracted from known protein structures.
ArchDB includes 4 classifications:
* ArchDB40 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 40% sequence identity.
* ArchDB95 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 95% sequence identity.
* ArchDB-EC is a classification of loops extracted from proteins with known enzymatic function
* ArchDB-KI is a curated classification database of kinase loops EC number 2.7.X.X with functional information of residues.
Futhermore, the functional annotation of residues in this database are further classified in four categories:
1. ATP interaction: for residues involved on ATP binding/interaction.
2. Substrate binding: for residues involved in substrate interaction/binding with the exception of ATP
3. Ion interaction: for residues involved in ion interaction/binding of ions needed for the catalytic mechanism
4. Catalytic: involved in reaction, the stabilization of a transition state or the activation of substrates.
Additionally, three different approaches were applied to identify functional residues of the loops of the sub-classes:
1. Residues found within a cut-off distance of 6���� from an heteroatom, ligand, inhibitor, cofactor or complex partner molecule (protein or DNA), with the exception of D2O or crystallization buffer molecules.
2. Residues identified by functional information from ACTSITE and SITE records in the RCSB protein data bank.
3. Residues identified by the functional annotation collected from the literature and assigned to specific motifs of kinases.
Lastly, the multiple ways to browse and query in ArchDB are:
* Search by sequence: Users can search for classified loop(s) with sequence similarity to a query sequence.
* Search by structure: Users can upload protein coordinates in PDB format and its loops will be extracted and compared with those from the classification. First: structural class is assigned comparing loop geometry and, second: the loop conformation is compared among the subclasses within the assigned class.
* Search subclasses and/or Search Loops: A range of options are offered for subclass or loop searches. Users can query ArchDB asking for subclasses or loops with specific flanking secondary structures, length of loops or phi/psi loop conformation. Also, users can retrieve all subclasses or loops with PDB SITE annotations and contacts with co-crystallized ligands. Finally, users can search for subclasses that have SCOP, GO or EC annotations conserved at different percentage levels.
* Search structures: Users can search for classified PDB structures in ArchDB with specific Sprot. Annotation/Keyword, GO annotation, SCOP and EC codes.
* Specific queries for ArchDB-KI: Users can list functional subclasses or loops classified in ArchKI.
:Sponsors: ArchDB is funded by grants from Fundacin Areces (Spain), Ministerio de Ciencia y Tecnologa Spain (MCYT; BIO2002-03609, BIO2001-246 and BIO2001-264), Centre de Referncia en Biotecnologia Generalitat de Catalunya (CERBA), and the Generalitat de Catalunya
:
:Enzyme-specific classification,
:Kinase proteins, ligand, Protein residue, Protein motif, Protein loop,

Proper citation: ArchDB - Biological Database of Protein Loops (RRID:SCR_013472) Copy   

•   Source: SciCrunch Registry

http://mitodrome.ba.itb.cnr.it/

It has been developed with the aim to annotate the complete set of Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome.

Proper citation: MitoDrome (RRID:SCR_013474) 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.radiometer.dk

Commercial organizations which develops, manufactures, and sells solutions and equipment for blood sampling, blood gas analysis, transcutaneous monitoring, and IT management systems under certain brand names.

Proper citation: Radiometer (RRID:SCR_014772) Copy   

•   Source: SciCrunch Registry

http://www.zeitz-puller.com/

Manufacturer and supplier of the DMZ Universal electrode pullers which produce pipettes and electrodes with a tip diameter down to 0.2 micrometers.

Proper citation: Zeitz (RRID:SCR_014774) Copy   

•   Source: SciCrunch Registry

https://imacel.net/en/

Artificial intelligence image analysis platform that facilitates life science research. It offers data analysis, processing functions, and security features to accelerate research productivity.

Proper citation: IMACEL (RRID:SCR_015868) Copy   

•   Source: SciCrunch Registry

http://www.neuralsignal.org

Public archive of neural signals recorded from various types of cells and sites in neural systems. Any data can be publicly accessed and downloaded, and users can submit their data.

Proper citation: Neural Signal Archive (RRID:SCR_014810) 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

http://www.bml-nmr.org

A collection of experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards.

Proper citation: Birmingham Metabolite Library (RRID:SCR_014666) Copy   

•   Source: SciCrunch Registry

http://mobidb.bio.unipd.it

A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING.

Proper citation: MobiDB (RRID:SCR_014542) 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