Tools   Select Another Resource Report Type

http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=2759&hopt=html

Curated sequence data and related information on organelles from NCBI Refseq for the community to use as a standard. The animal mitochondrial records are considered reviewed; that is, they have been manually curated by the NCBI staff. Other mitochondrial and chloroplast genome records are provisional and are presented with varying levels of review compared to the primary record used to build the RefSeq. Additionally, protein clusters for the metazoan and plastid genomes proteins can be reviewed with Entrez Protein Clusters.

Proper citation: Organelle Genome Resources (RRID:SCR_007838) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/Structure/

A database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB contains experimentally determined biopolymer structures obtained from the Protein Data Bank. MMDB contains a subset of three-dimensional structures obtained from the Protein Data Bank (PDB), excluding theoretical models. MMDB is a database of ASN.1-formatted records. It was designed for flexibility, and as such, is capable of archiving conventional structural data as well as future descriptions of biomolecules, such as those generated by electron microscopy (surface models).

Proper citation: Molecular Modelling DataBase (RRID:SCR_007773) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/sites/entrez?db=journals

The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library''s holdings in LocatorPlus, NLM''s online public access catalog, are also provided.

Proper citation: NLM Catalog (RRID:SCR_004583) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/unigene

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.

Proper citation: UniGene (RRID:SCR_004405) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/nucleotide

Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Proper citation: NCBI Nucleotide (RRID:SCR_004860) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/bioproject

Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.

Proper citation: NCBI BioProject (RRID:SCR_004801) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Wilbur/IRET/PIE/

A web service to extract Protein-protein interaction (PPI)-relevant articles from MEDLINE that provides protein interaction information (PPI) articles for biologists, baseline system performance for bio-text mining researchers and a compact PubMed-search environment for PubMed users. It accepts PubMed input formats including All Fields, Author, Journal, MeSH Terms, Publication Date, Title, and Title/Abstract with Boolean operations (AND, OR, and NOT). However, the output is the list of articles prioritized by PPI confidence rates. Some words (mostly gene/protein names) which contributed for PPI prediction are underlined and linked to Entrez or Entrez Gene. Even though our system focuses on a PubMed search environment, it also provides a CGI access for bio-text mining researchers. Using the CGI program, a list of PubMed IDs can be obtained as a query result, thus it can be utilized as a baseline system performance. PIE the search is based on a winning approach in the BioCreative III ACT competition (BC3)1. For input queries, MEDLINE articles are first retrieved through the PubMed service. PPI scores are calculated for the retrieved articles, and the articles are re-ranked based on scores. To effectively capture PPI patterns from biomedical literature, their approach utilizes both word and syntactic features for machine learning classifiers. Dependency parsing, gene mention tagging, and term-based features are utilized along with a Huber classifier.

Proper citation: PIE the search (RRID:SCR_005296) Copy   

•   Source: SciCrunch Registry

http://www.youtube.com/ncbinlm

Videos from the National Center for Biotechnology Information including presentations and tutorials about NCBI biomolecular and biomedical literature databases and tools.

Proper citation: NCBI YouTube Channel (RRID:SCR_006084) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/genbank/wgs/

Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database.

Proper citation: Whole Genome Shotgun (WGS) Project (RRID:SCR_016637) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission.

Proper citation: tbl2asn (RRID:SCR_016636) Copy   

•   Source: SciCrunch Registry

http://www.journalreview.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. International interdisciplinary Internet based unbiased forum for review of medical literature. Very much like an on-line journal club, we aim to provide a venue which will improve communication amongst physicians and lead to better understanding and interpretation of medical literature. In the academic world, Journal Clubs are a common way to discuss and critically question medical literature. The knowledge gained by this activity can be immeasurable, and often leads to ideas both relating to patient care and to future research. However, many clinicians are unable to participate in these academic activities. In addition, information shared within an individual journal club is seldom disseminated. Here you will find a free, user-friendly website where you can rate and discuss medical literature. It offers innovative and powerful search tools that will allow you to quickly query the medical literature and identify the information you need. In addition, their exclusive tools will help identify the most important and controversial articles. It is their hope to bring both insight and questions to the literature -- both of which will be used to shape future research. Clinicians will have a better understanding of the evidence, and ability to partake in a venue that fosters communication between peers.

Proper citation: JournalReview.org (RRID:SCR_008198) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://biologylabs.utah.edu/jorgensen/wayned/ape/

Software tool for plasmid and sequence editing, annotating and drawing plasmid sequences. Used to view circular or linear maps of DNA sequences. Users can perform virtual digests whereby they select predefined DNA ladder, or specify their own, and visualize theoretical DNA fragments. Used to highlight restriction sites in editing window, accurately reflect Dam/Dcm blocking of enzyme sites, highlighting and drawing graphic maps using feature annotations from genbank and embl files, highlighting text using pre-defined and custom feature libraries, and directly BLASTing selected sequence at NCBI or Wormbase. Runs across Windows, OS X, and Linux/Unix.

Proper citation: A plasmid Editor (RRID:SCR_014266) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

Proper citation: Entrez (RRID:SCR_016640) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pubmedhealth/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 9, 2022. A consumer health database that provides up-to-date information on diseases, conditions, injuries, drugs, supplements, treatment options, and healthy living, with a special focus on comparative effectiveness research from institutions around the world. PubMed Health includes * consumer guides summarizing comparative effectiveness research * fact sheets on diseases and conditions * information on drugs and supplements * encyclopedic overviews of health topics * links to external Web sites PubMed Health has a special focus on comparative effectiveness research, in particular that research which evaluates the available evidence of the benefits and harms of different treatment options for different groups of people. In Comparative Effectiveness Research, experts often synthesize the evidence from dozens, or even hundreds, of individual studies.

Proper citation: PubMed Health (RRID:SCR_000512) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/genbank/dbgss/

Database of unannotated short single-read primarily genomic sequences from GenBank including random survey sequences clone-end sequences and exon-trapped sequences. The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA). It should be noted that two classes (exon trapped products and gene trapped products) may be derived via a cDNA intermediate. Care should be taken when analyzing sequences from either of these classes, as a splicing event could have occurred and the sequence represented in the record may be interrupted when compared to genomic sequence. The GSS division contains (but is not limited to) the following types of data: * random single pass read genome survey sequences. * cosmid/BAC/YAC end sequences * exon trapped genomic sequences * Alu PCR sequences * transposon-tagged sequences Although dbGSS sequences are incorporated into the GSS Division of GenBank, annotation in dbGSS is more comprehensive and includes detailed information about the contributors, experimental conditions, and genetic map locations.

Proper citation: NCBI Genome Survey Sequences Database (RRID:SCR_002146) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gene

Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.

Proper citation: Entrez Gene (RRID:SCR_002473) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/proteinclusters

Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP

Proper citation: Protein Clusters (RRID:SCR_003459) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/homologene

Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.

Proper citation: HomoloGene (RRID:SCR_002924) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/protein

Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

Proper citation: NCBI Protein Database (RRID:SCR_003257) Copy   

•   Source: SciCrunch Registry