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protein-protein interactions

concepts

metabolomics

gene co-occurence
in literature

ConceptGen

ConceptGen Screen Shot Find biomedical concepts enriched for a list of genes or associations between concepts based onoverlapping genes. Read more

This tool allows you to search by: concept (e.g. disease, keyword, cell process, drug name), gene list
Examples of search terms: prostate cancer, cell cycle

LRpath

ConceptGen Screen Shot Find key pathways and other biological concepts affected in gene expression arrays. Read more



This tool allows you to search by:
gene list


Examples of search terms:
brca2, 675, FBgn0036605
Website | User Manual Website | Video Tutorial

Gene2MeSH

Find Medical Subject Headings (MeSH terms) Gene2MeSH Screen Shotenriched for a particular gene or genes enriched for a particular MeSH term. Read more.


This tool allows you to search by:
gene, disease, keyword
Examples of search terms: csf1r,"bipolar disorder"

Metab2MeSH

Metab2MeSH Screen ShotFind Medical Subject Headings (MeSH terms) enriched for a particular compound or compounds enriched for a particular MeSH term. Read more.

This tool allows you to search by: compound, keyword, disease
Examples of search terms: insulin, diabetes
Website | Web Service Website | Web Service

Cytoscape Plugin for MiMI

Cytoscape MiMI Plugin Screen ShotVisualize gene interaction networks based on merged interaction data from MiMI. Read more.


This tool allows you to search by:
gene(s)
Examples of search terms: pparg


MiMI

MiMI Screen ShotFind protein interactions, pathways, compounds, literature, and genes merged from multiple sources. Read more.

This tool allows you to search by: gene, gene listcompound, concept (e.g. disease, keyword, cell process)
Examples of search terms: pwp1, nucleus
Launch tool | User Manual Website | Web Service | User Manual

PubAnatomy

PubAnatomy Screen ShotProvides 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. Read more.

This tool allows you to search by: genes and/or concepts
Examples of search terms: schizophrenia, bipolar disorder


Metscape

MetScape Screen ShotVisualize metabolomics and expression profiling data in the context of human metabolism and display related information about genes, enzymes, reactions, compounds and pathways. Read more.

This tool allows you to search by: compounds or genes and KEGG IDs and Entrez gene IDs can be entered
Examples of search terms: C00024, 5105
Website | User Manual Launch tool | User Manual

PubOnto

Cytoscape MiMI Plugin Screen ShotProvides multiple ontologies from the Open Biomedical Ontology to help researchers explore literature from different perspectives. Read more.


This tool allows you to search and filter by:
concepts, e.g. Gene Ontology (GO), Phenotype Ontology, Environment Ontology or Foundational Model of Anatomy Ontology (FMA).

Examples of search terms: brain, prostate cancer


Website
To access data

If you want to

Use this database

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 database

(Web service interface)

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 a full-text article/set of articles

Query for all the full-text articles that mention a gene/set of genes (symbols/synonyms) / metabolites

NCIBI Pubmed Central database

(Web service interface)

Contains all full-text biomedical
articles from the Pubmed Central Open Access (PMCOA) database, with source files
downloaded monthly and updated to the database. Also contains additional data from natural language processing. Raw data are available via a SOAP interface. 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

Natural Language Processing (NLP) techniques in PubMed and PubMed Central databases

(Web service interface)

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 detailed information on a Gene

View relationships amongst genes and to get access to supporting PubMed articles

NCIBI GENE database

Contains Gene data from public sources. Available as a part of the MiMI data offering and through the MimiWeb website.

To query on specific Metabolomics including reactions, and compounds

To view chemical make up of compounds

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.

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

NCIBI MiMI database

(Web service interface)

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. Web service access to the MiMI database is available here. MimiWeb is the web interface to MiMI.

These Resources

Help you to

MiSearch image website
user manual

MiSearch
ConceptGen Screen ShotRanks orders retrieved articles from PubMed based on a self- customized personal profile.

Read more about MiSearch

Create personal profiles for PubMed searchers.

Rank order retrieved articles based on articles retrieved and viewed in earlier searches on the given topic (profile).

BioSearch2d image website


ConceptGen Screen ShotBiosearch2D

Relates gene lists to enriched MeSH terms and retrieves literature for selected gene-MeSH relationships.

Read more about BioSearch2D

Find 2+ genes that are enriched for the same Medical Subject Heading (MeSH) terms

Link to related literature for gene-MeSH associations.

SAGA image launch tool
tutorial (pg. 10)

SAGA via the MiMI Plug in for Cytoscape

Matches Cytoscape sub-graphs to KEGG pathways.

Read more about SAGA

Explore KEGG pathways that match selected sub-networks in Cytoscape.

For a large sub-network, run the Tale.algorithm (no UI)

Clairlib image website

Clairlib

A library of natural language processing (NLP) modules

 

Plugin to external software to simplify a number of generic tasks in Natural Language Processing (NLP)

 

ConceptSignature image  

ConceptSignature (ConSig)
(In Development)

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

GIN-NA logo website

Gene Interaction Network Analysis (GIN-NA)

Analyzes molecule interactions networks.

 

Rank molecules in a network based on graph centrality measures and second neighbor statistics

 

Build disease-specific networks

 

MARKIT image website
user manual

Markit

Narrows gene lists by Bayesian analysis.

Read more about Markit

Run a Bayesian Network analysis on a long gene list with expression values to identify those likely to occur together

MEAD icon  

MEAD

An underlying natural language processing (NLP) summarizer. It is used by MiMI in its BioNLP searches.

Read more about MEAD

Sort excerpt semantically, mined through natural language processing (NLP)

PEBL tools icon website
user manual

PEBL

 

A python library and command line application for learning the structure of a Bayesian network given prior knowledge and observations.

Read more about PEBL

Set up and run a Bayesian network analysis

 

View likely associations in obseration and intervention data

 

Analze results graphically and statistically