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protein-protein interactions

concepts

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ConceptGen 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	Metab2MeSH Find 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 \| User Manual	Website \| Web Service
Gene2MeSH Find Medical Subject Headings (MeSH terms) enriched 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"	MiMI Find 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
Website \| Web Service	Website \| Web Service \| User Manual
Cytoscape Plugin for MiMI Visualize 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	Metscape Visualize 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
Launch tool \| User Manual	Launch tool \| User Manual
PubAnatomy 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. Read more. This tool allows you to search by: genes and/or concepts Examples of search terms: schizophrenia, bipolar disorder	PubOnto Provides 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 \| User Manual	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.

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user manual

MiSearch
Ranks 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

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.

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)

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 (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

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

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

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)

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