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http://srv00.recas.ba.infn.it/py_script/REDIdb/overview.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A relational database in which all editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored and maintained in ad hoc designed textual flat files. Individual genes of interest can be searched by appropriate query strings containing the gene name or the intracellular location or the molecular type (as tRNA, rRNA, intron) or the organism or a combination of the previous terms. Moreover, each record of the REDIdb database can be also retrieved according to its specific accession number (more help on how to perform a REDIdb search is available at the ?help? page). To make easier the browsing of each REDIdb entry and quicker the identification of editing sites, two alternative but complementary facilities have been provided either to graphically display genomic and cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are shown by mousing over.

Proper citation: REDIdb- RNA Editing Database (RRID:SCR_013429) Copy   

•   Source: SciCrunch Registry

http://www.msdiscovery.org/research-resources/drug-pipeline

A database providing information about compounds under investigation for therapeutic use. There are currently 44 compounds on record with 100 compounds in the process of being uploaded to the database.

Proper citation: MSDF Drug Development Pipeline (RRID:SCR_013825) Copy   

•   Source: SciCrunch Registry

http://editor.citationstyles.org/about/

A database that contains different CSL citation styles. Styles can be searched by name, journal title, or by example and then viewed or installed. Users can also edit current styles and save them.

Proper citation: CitationStyles (RRID:SCR_014000) Copy   

•   Source: SciCrunch Registry

http://okcam.cbi.pku.edu.cn/

OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families. :We have mapped these genes onto a novel cell adhesion molecule ontology (CAMO) that provides a hierarchical description of cell adhesion molecules and their functions. It is intended to provide a means to facilitate better and better understanding of the global and specific properties of CAMs through their genomic features, regulatory modes, expression patterns and disease associations become clearer. :Cadherins, IgCAMs, Integrins, Neurexins, Neuroligins, Catenins :

Proper citation: Ontology-based Knowledgebase for Human Cell Adhesion Molecules (RRID:SCR_013555) Copy   

•   Source: SciCrunch Registry

http://www.xs4all.nl/~ingenium/dicom.html

Fast error free and transparent compression (>2x) of image data on disk with NKI private or JPEG compression. A database browser and slice viewer integrated in the PACS system with options for: viewing DICOM header, creating BMP files (ideal for slides), sending selected images, printing, database fix tools such as changing patient IDs, deleting and anonymizing studies and series, and splitting and merging series. Uses drag and drop to load DICOM and HL7 files. A simple query/move user interface for diagnostic purposes, to improve your knowledge of DICOM, and to grab missing data from another server. Elementary DICOM print server and client - prints to the default printer. Correct display of JPEG and RLE compressed images in browser. Flexible configuration of JPEG and NKI private compression with optional (de)compression of incoming, dropped, transmitted and archived files. The JPEG compression is done using executables from the OFFIS DICOM toolkit (DCMTK version 3.5.4), developed by Kuratorium OFFIS e.V. A simple DICOM Modality Worklist implementation with HL7 import with configurable translation. A CGI WEB interface with several possible viewers (especially important for the Linux version without a GUI). The server can act as an advanced scriptable DICOM image forwarder and/or DICOM image cache. The server integrates an advanced DICOM viewer based on K-PAC DICOM training and testing Demonstration and research image archives Image format conversion from a scanner with DICOM network access DICOM image viewing and slide making DICOM image selection, (limited) editing, and splitting and merging of series Advanced scriptable image modification, filtering, forwarding and conversion DICOM caching and archive merging DICOM web access for viewing and data management (scriptable)

Proper citation: Conquest DICOM software 1.4.15 (RRID:SCR_013513) Copy   

•   Source: SciCrunch Registry

http://margalit.huji.ac.il/promec/

A compilation of E. coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E. coli chromosome, as well as the actual sequences in the promoter region. The database is currently updated as of July 2000 and includes 471 entries.

Proper citation: PromEC (RRID:SCR_013514) Copy   

•   Source: SciCrunch Registry

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

The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on.

Proper citation: HUGE - Human Unidentified Gene-Encoded large proteins (RRID:SCR_013482) Copy   

•   Source: SciCrunch Registry

http://www.simbiome.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. Simbiome is a curated, online electronic resource that organizes and presents relevant resources for physics-based simulation of biomedical structures and related entities in biology and life sciences.

Proper citation: Simbiome (RRID:SCR_013640) Copy   

•   Source: SciCrunch Registry

http://viroligo.okstate.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of virus-specific oligonucloetides and their primers. It allows users to search based on virus name, PMID, VirOligoID, or taxonomy ID. The VirOligo database is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place. To this end, researchers are also exploring Virus Signature Hybridization (ViSH) and Virus Signature Amplification (ViSA), microarray-based methods for hybridization and PCR amplification. The site employs Universal PCR techniques, a PCR that amplifies DNA fragments from more than one viral species, such as family- or genus-specific PCR.

Proper citation: VirOligo: Virus Oligonucleotide Database (RRID:SCR_013481) Copy   

•   Source: SciCrunch Registry

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://rarge.psc.riken.jp/rartf/

Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available.

Proper citation: RARTF (RRID:SCR_013457) 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://www.lamondlab.com/NOPdb/

It archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene its domain structures and relevant protein homologues across species as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints highlighted by visualization means in the NOPdb provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/ uncharacterized proteins. The NOPdb is searchable by either gene names protein sequences Gene Ontology terms or motifs or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink OMIM and PubMed).

Proper citation: NoPdb: Nucleolar Proteome Database (RRID:SCR_013459) 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://soybeangenome.siu.edu

It provides the mapping of relationships between soybean genomic features in a way that is presentable in GBrowse. It combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. The database is also searchable for listings of these relationships.

Proper citation: The Soybean GBrowse Database (RRID:SCR_013463) Copy   

•   Source: SciCrunch Registry

http://www.cstl.nist.gov/div831/strbase/

A database of information on short tandem repeat systems. It contains facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes.

Proper citation: STRBase (RRID:SCR_013465) 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