Tools   Select Another Resource Report Type

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

Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH''''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.

Proper citation: NCBI Structure (RRID:SCR_004218) Copy   

•   Source: SciCrunch Registry

http://www.ihop-net.org/UniPub/iHOP/

Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.

Proper citation: Information Hyperlinked Over Proteins (RRID:SCR_004829) Copy   

•   Source: SciCrunch Registry

http://impactstory.org/

A web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile.

Proper citation: ImpactStory (RRID:SCR_002632) Copy   

•   Source: SciCrunch Registry

http://www.chibi.ubc.ca/WhiteText/

Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.

Proper citation: Automated recognition of brain region mentions in neuroscience literature. (RRID:SCR_002731) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rentrez/index.html

Software package provides R interface to NCBI EUtils API, to search databases like GenBank and PubMed, process of those searches. Provides functions that work with NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases.

Proper citation: rentrez (RRID:SCR_021062) Copy   

•   Source: SciCrunch Registry