Ingenuity Knowledge Base

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract The Ingenuity® Knowledge Base is the core technology behind all Ingenuity products. It is a repository of biological interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, metabolites, drugs, and diseases.

These modeled relationships, or Findings, include rich contextual details, links to the original article, and are manually reviewed for accuracy.

The Ingenuity Knowledge Base is used as a starting point for exploration and a bridge between novel discovery and known biology.

When accessed through Ingenuity applications such as IPA - (see G6G Abstract Number 20017U) and Ingenuity Answers (see below...), it provides you with a advanced resource for searching relevant and substantiated knowledge from the literature, and for interpreting experimental results in the context of larger biological systems for greater confidence with research decisions.

Ingenuity Answers - Ingenuity Answers is an advanced search tool that enables you to quickly and reliably answer specific biological and chemical questions by identifying lists of genes (or other biological and chemical objects) that satisfy particular biological criteria.

Ingenuity Answers leverages the Ingenuity Knowledge Base to allow you to ask highly focused questions involving biological details on multiple levels (genes, chemicals, cells, domains, pathways, diseases, and more) and provides answers based on demonstrated and accurate biological relationships, so you have confidence in your search results.

The Ingenuity Knowledge Base is unique because of it’s:

1) Unparalleled structure and contextual details;

2) Expert review process for trusted information; and

3) Broad and timely content.

The Ingenuity Knowledge Base lets you access a wide variety of information in one place, such as:

1) Integrated biological and chemical knowledge including relationships between proteins, genes, metabolites, protein complexes, cells, cellular components, tissues, organs, small molecules, cellular phenotypes, pathways, and disease processes;

2) Comprehensive, species-specific knowledge about gene function and regulation, tissue and cell line expression patterns, clinical biomarkers, subcellular location, mutations, and disease associations;

3) Chemical and drug information for clinical candidates and FDA-approved drugs;

4) Millions of Findings describing physical interactions and regulatory events such as transcription and phosphorylation, extracted from the literature;

5) Representation of biological context, including species specificity, cell and tissue context, subcellular localization, mutations, epigenetic modifications, and experimental conditions;

6) Systematic capture of signaling and metabolic pathway relationships; and

7) Experimentally demonstrated and predicted microRNA-mRNA relationships, including biological roles and potential impacts.

Ingenuity Knowledge Base Highlights --

The Ingenuity Knowledge Base is distinctive because of the accuracy and breadth of biological and chemical knowledge it contains, and because it structures this knowledge in an advanced, detailed way that enables scientific understanding and computation.

Structured information for relevance and better computation.

Ingenuity structures all of the biological and chemical content in the Ingenuity Knowledge Base using the Ingenuity® Ontology. By structuring the content, the manufacturers enable computation and inferencing, ensure semantic and linguistic consistency, and support the integration and mapping of content from multiple sources.

Through Ingenuity applications like IPA and Ingenuity Answers, you can access knowledge and generate hypotheses that are highly relevant to your experimental system.

1) It provides contextual details - Unlike other ontologies, the Ingenuity Ontology is comprehensive. This level of detail helps the manufacturer capture relevant contextual details from the literature such as species specificity, cell type/tissue context, site and type of mutations, direction of change, post-translational modification sites, epigenetic modifications, and experimental methods used.

These contextual details are what make the manufacturers Findings different from other solutions that only report on simple “A to B” relationships. Ingenuity does Not believe that it is sufficient to report a simple “A to B”-type relationship; rather, the manufacturer believes it is critical to reflect additional contextual information about the interaction, e.g. that “transcription factor X increases expression of a gene Y in a specific cell type”.

This type and level of detail is absolutely necessary in order to reflect the complexity of biological knowledge, and is therefore the level of detail the manufacturer captures in the Ingenuity Knowledge Base.

2) It supports computation - The Ingenuity Ontology makes information computationally accessible so you can more rapidly infer novel insights from your own data or get to specific knowledge that is relevant to your research. Ask questions across various types of connections (molecular, cellular, and organismal) and make inferences from one concept to another, or find likely paths between molecular concepts (gene to disease, drug to gene, etc).

3) It provides synonym resolution - The Ingenuity Ontology ensures semantic and linguistic consistency across concepts. The Ingenuity Knowledge Base incorporates processes to resolve synonyms and homographs in order to maintain object identity and remove duplicate objects.

Because the same terms are mapped across databases and concepts, you can integrate disparate information from unrelated disciplines and sources in order to run advanced queries and get precise answers to complex, data-driven questions. It also allows you to take information from multiple sources and related it to your own dataset or questions of interest.

Expert review process for trusted information --

The level of structure in the Ingenuity Knowledge Base is enabled by the manufacturer’s unique knowledge acquisition processes and quality control steps.

All information in the Ingenuity Knowledge Base is manually reviewed by experts to ensure that the content is accurate and detailed, so whether you are using a manually curated relationship from the literature or a relationship described in a 3rd party database, you can trust the quality of information in the Ingenuity Knowledge Base. And you can always link back to the original finding in the original source article.

Broad and timely information --

The Ingenuity Knowledge Base is updated weekly to include information published as recently as the prior week. It is one of the largest knowledge bases of its kind, including modeled relationships between proteins, genes, complexes, cells, tissues, drugs, pathways, and diseases.

It includes information from a wide range of published biomedical literature, textbooks, reviews, internally curated knowledge (such as pathways), and a variety of trusted 3rd party sources and databases.

There are four (4) types of information in the Ingenuity Knowledge Base, and when accessed through Ingenuity applications, you can filter based on the type of information you prefer at a given time.

1) Ingenuity® Expert Findings - Experimentally demonstrated Findings that are manually curated for accuracy and contextual details from the full-text of articles in top journals. These Findings are modeled by Ph.D. scientists who follow a strict content extraction protocol to ensure inclusion of contextual details.

2) Ingenuity® ExpertAssist Findings - Manually reviewed, automatically extracted Findings from the abstracts of a broad range of recently published biomedical journals. The extraction protocol is modeled on the same process used by our Ingenuity Expert Findings, which is the most comprehensive set of biomedical information extraction guidelines of its kind.

Additionally, the information is manually reviewed before it is imported into the Ingenuity Knowledge Base. This means that unlike other automatic approaches, Ingenuity ExpertAssist Findings maintain a very high level of quality, have proper synonym resolution, capture both contextual details and broad functional relationships, and are computationally accessible.

3) Ingenuity® Expert Knowledge - Ingenuity-modeled knowledge such as signaling and metabolic pathways, drug/target/disease relationships, toxicity lists, and more. This information is modeled by an in-house team of Ingenuity experts who manually curate this information and update as needed.

4) Ingenuity® Supported Third Party Information - Manually reviewed content from selected sources and databases.

This includes findings and annotations from major NCBI databases (EntrezGene, RefSeq, OMIM disease associations), targets and pharmacological relevance of FDA approved and clinical trial drugs, clinical biomarkers, Gene Ontology (GO) annotations, a normal gene expression body atlas for over 30 tissues and the NCI-60 panel of cancer cell lines, microRNA-mRNA target databases, GWAS databases, KEGG and LIGAND metabolic pathways and reactions. These sources include:

Entrez Gene; RefSeq; OMIM; GWAS Database; Gene Ontology (GO); Human Metabolome Database (HMDB);

GNF Tissue Expression Body Atlas; NCI-60 Cell Line Expression Atlas; KEGG metabolic pathway information;

LIGAND enzyme/substrate reactions; BIND, DIP, MINT, MIPS, BIOGRID, INTACT, COGNIA protein-protein interactions (updated);

TarBase; TargetScan;;; Mosby’s Drug Consult;

Goodman & Gilman's ‘Pharmacological Basis of Therapeutics’;

DrugBank; Hazardous Substance Database (HSDB); and

Chemical Carcinogenesis Research Information System database (CCRIS).

There is also some specialized content in the Ingenuity Knowledge Base -- This includes:

1) Chemical Content - Information on thousands of compounds, including endogenous chemicals, metabolites, FDA-approved drugs and clinical candidates, and exogenous chemicals and toxicants. Therapeutically relevant knowledge can be integrated within any pathway in IPA, allowing researchers to understand and visualize the biological impact of these compounds, including:

2) Toxicology Content - The Ingenuity Knowledge Base features a large collection of knowledge from the molecular toxicology literature describing the pharmacological and toxicological effects of chemicals in vitro and in vivo. Here are some highlights from the collection of toxicity pathways and lists in the Ingenuity Knowledge Base:

Anti-Apoptosis Aryl Hydrocarbon Receptor Signaling; CAR/RXR Activation; Cholesterol Biosynthesis;

Cytochrome P450 Panel - Substrate is a Fatty Acid; Cytochrome P450 Panel - Substrate is a Sterol;

Cytochrome P450 Panel - Substrate is a Vitamin; Cytochrome P450 Panel - Substrate is a Xenobiotic;

Cytochrome P450 Panel - Substrate is an Eicosanoid; FXR/RXR Activation;

Glutathione Depletion - CYP Induction and Reactive Metabolites;

Glutathione Depletion - Hepatocellular Hypertrophy; Glutathione Depletion - Phase II reactions;

Hepatic Stellate Cell Activation; Hormone Receptor Regulated Cholesterol Metabolism;

Hypoxia-Inducible Factor Signaling; LXR/RXR Activation; Mitochondrial Dysfunction;

Negative APR Proteins; Oxidative Stress; Positive APR Proteins; PPARa/RXR Activation;

Pro-Apoptosis; PXR/RXR Activation; RAR Activation; TR/RXR Activation; VDR/RXR Activation; and Xenobiotic Metabolism.

System Requirements

Contact manufacturer.


Manufacturer Web Site Ingenuity Systems, Inc.

Price Contact manufacturer.

G6G Abstract Number 20018U

G6G Manufacturer Number 101440