Try Our Tools: Getting started with NCIBI tools
- Exploratory analysis
- Conceptual literature searches
- Databases
- Other
Use this tool |
If you want to: |
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ConceptGen (tool) Related gene lists to enriched concepts and other genes enriched for the given concept. |
Find concepts related to your list of genes Statistically validate enriched concepts Find genes enriched for the same concept as your genes |
MetScape Plug in for Cytoscape (tool) Displays interactive networks of compounds, enzymes, reactions. |
Query a compound or list of compounds Explore reactions and pathways. Add in your own data Use other plugins for time series analysis |
MiMI Plug in for Cytoscape (via Cytoscape) Displays molecular networks in Cytoscape. |
Query on a list of genes Explore gene product interactions Characterize interactions conceptually Link to literature and sub-graph matches with KEGG Use other plugins for clustering Import your own data |
MiMI Web (tool) Retrieves details integrated from numerous databases on genes, interactions, pathways, and literature |
Query on genes, compounds, keywords Characterize genes conceptually Add in your own data Find interactions and related articles Link to protein interaction networks |
SAGA via the MiMI Plug in for Cytoscape (tutorial) Matches Cytoscape sub-graphs to KEGG pathways. |
Explore KEGG pathways that match selected sub-networks in Cytoscape. For a large sub-network, run the Tale.algorithm (no UI) |
Use this tool |
To do the following, all at once |
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Relates gene lists to enriched MeSH terms and retrieves literature for selected gene-MeSH relationships. |
Find 2+ genes that are enriched for the same Medical Subject Heading (MeSH) terms Link to related literature for gene-MeSH associations. |
Gene2MeSH** (tool) Relates 1 gene to its enriched MeSH terms or 1 MeSH term to its genes, and retrieves associated articles |
Find enriched Medical Subject Heading (MeSH) terms for a gene Find all genes enriched for a specific MESH term. Link to the PUbMed literature related to various gene-MeSH associations. |
Metab2MeSH** (tool) Relates 1 metabolite to its enriched MeSH terms or 1 MeSH term to its metabolites, and retrieves associated articles |
Find enriched Medical Subject Heading (MeSH) terms for a metabolite Find all metabolites enriched for a specific MESH term. Link to the PUbMed literature related to various metabolite-MeSH associations. |
MiSearch (tool) Ranks orders retrieved articles from PubMed based on a self- customized personal profile. |
Create personal profiles for PubMed searchers. Rank order retrieved articles based on articles retrieved and viewed in earlier searches on the given topic (profile). |
PubAnatomy(tool) Provides new ways to explore relationships among anatomical structures, pathophysiological processes, gene expression levels and protein-protein interactions in the context of Medline literature and experimental data. |
Query on genes and/or concepts and filter retrieved articles Visually analyze brain regions, genes, and gene expression levels related to retrieved articles Identify connected conceptual relationships, associated genes and interactions |
PubOnto (tool) Provides multiple ontologies from the Open Biomedical Ontology to help researchers explore literature from different perspectives |
Quickly locate and filter articles by concepts, e.g. Gene Ontology (GO), Phenotype Ontology, Environment Ontology or Foundational Model of Anatomy Ontology (FMA) Link to related literature |
** MeSH stands for Medical Subject Heading, the National Library of Medicine’s hierarchical system for classifying texts and assigning keywords characterizing the content. MeSH terms provide insight, for example, about diseases that an article examines.
Use this database |
If you want to |
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NCIBI Pubmed database Contains all biomedical articles from the National Library of Medicine's (NLM) Pubmed database, with source files downloaded nightly and updated to the database. Also contains additional data from natural language processing. Data are available in XML format via a web service interface. |
Query for all the genes (symbols/synonyms) / metabolites mentioned in an abstract/set of abstracts Query for all the genes (symbols/synonyms)/metabolites mentioned in abstracts that share an author/MeSH term Query for all the abstracts that mention a gene/set of genes (symbols/synonyms) / metabolites Query for the most relevant genes for abstracts that share a MeSH term Map an abstract to a set of UMLS concepts |
NCIBI Pubmed Central database Contains all full-text biomedical
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Query for all the genes (symbols/synonyms) / metabolites mentioned in a full-text article/set of articles Query for all the full-text articles that mention a gene/set of genes (symbols/synonyms) / metabolites |
MicroArray database Contains Affymetrix datasets from NCBI's Gene Expression Omnibus (GEO) microarray repository. This includes raw CEL files and experiment annotation .soft files downloaded directly from GEO, as well as data processed in our analysis pipeline: normalized data values using RMA, quality control measures, and significance statistics (fold change and p-value) using an empirical Bayes test for differential expression. |
Query for all experiments in which a gene/set of genes was significantly differentially expressed Query for all up/down-regulated genes in a particular GEO experiment Query for all experiments with a keyword in the description Query for the expression profile of a gene/set of genes across all experiments Query for the significance profile of a gene/set of genes across all experiments Query for which genes are most/least often differentially expressed across experiments |
Natural Language Processing (NLP) techniques in PubMed and PubMed Central databases NLP in these databases tags gene names, gene name synonyms, and metabolites from segmented sentences. Protein-protein interactions and their annotations are also extracted. Techniques include sentence segmentation, named entity tagging, and parsing sentences into trees. From trees, the NLP determines phrase structures within sentences and grammatical relationships between pairs of words. Data are available in XML format via a web service interface. |
Query for natural language processing (NLP) extracted sentences, named entity tags, parse trees, or protein interactions from an abstract or full text article |
NCIBI GENE database Contains Gene data from public sources. Available as a part of the MiMI data offering and through the MimiWeb website. |
Query for detailed information on a Gene View relationships amongst genes and to get access to supporting PubMed articles |
NCIBI HUMDB database Contains Metabolomics data from public and internal sources. Integrates Reactions, Compounds, Genes, and Proteins. Available on the web in the MimiWeb Beta website and through the Metscape plugin for Cytoscape. |
To query on specific Metabolomics including reactions, and compounds To view chemical make up of compounds |
NCIBI MiMI database Contains protein, Gene, Pathway and Interaction data integrated together from a number of data sources such as HPRD and KEGG. The database is rebuilt on a regular basis. A web service is currently in development. MimiWeb is the web interface to MiMI. |
Query for genes, proteins, and interactions. View detailed information on genes, proteins and interactions including supporting PubMed articles View pathway and metabolomics information associated with the genes, proteins and interactions |
These Resources |
Help you to |
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Clairlib (download) A library of natural language processing (NLP) modules
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Plugin to external software to simplify a number of generic tasks in Natural Language Processing (NLP)
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ConceptSignature (ConSig) Statistically narrows gene lists by significance. |
Run a statistical analysis on a long gene list genes to identify those more likely to occur together than by chance alone |
Gene Interaction Extraction (GIN-IE) (RSS) Extracts molecule interactions and context information from literature.
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Access GIN-IE's interaction pipeline via an RSS feed Access GIN-IE's interaction data from the NCIBI data repository |
Gene Interaction Network Analysis Analyzes molecule interactions networks.
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Rank molecules in a network based on graph centrality measures and second neighbor statistics
Build disease-specific networks
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Markit (no UI) Narrows gene lists by Bayesian analysis. |
Run a Bayesian Network analysis on a long gene list with expression values to identify those likely to occur together |
MEAD (no UI) An underlying natural language processing (NLP) summarizer. It is used by MiMI in its BioNLP searches. |
Sort excerpt semantically, mined through natural language processing (NLP) |
PEBL (no UI) PEBL (tutorial) A python library and command line application for learning the structure of a Bayesian network given prior knowledge and observations. |
Set up and run a Bayesian network analysis
View likely associations in obseration and intervention data
Analze results graphically and statistically |
