It is hard to get reliable, detailed answers for biological and chemical questions today. For example, what if you wanted to identify gene sets that met multiple criteria:
Current approaches are time consuming, unreliable, and limited. Some search tools only provide abstracts. With abstracts, there is no way to ensure terms you are searching on are related. For example, you might search for BRCA1 and brain cancer, and find several articles. Without reading each abstract, there is no way to know if there is any connection between those two terms beyond co-occurring in the same abstract. Other tools, such as specialized databases, may be so specific that they only support one or a limited number of questions (e.g. what genes are phosphorylated). Ingenuity Answers was developed to address these challenges.
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.
Get relevant and accurate results by searching the Ingenuity Knowledge Base:
- Leverage actual biological relationships, or findings, in the Ingenuity Knowledge Base (as opposed to other sources that only provide access to documents)
- Gain confidence from searching over demonstrated scientific findings, instead of only predicted annotations
- Take advantage of high-quality knowledge that is manually curated and quality controlled for accuracy
- Access the Ingenuity Knowledge Base’s comprehensive body of biological and chemical knowledge, including peer-reviewed journal findings plus reliable and quality-controlled databases (such as Go, Entrez-Gene, BIND, DIP, ClinicalTrials.gov, OMIM, TarBase, HMDB), so you can easily integrate information about genes, molecules, chemicals, cellular processes, and disease processes in a single tool
- Leverage highly detailed biological knowledge – including information such as mutation details, sites of post-translational modification, expression in particular tissue/cell types, and experimental method – to answer specific research questions
Ask your questions in your way:
- Ask and answer broad or narrow questions – so you can explore possibilities or drill down to specifics
- Leverage follow-up questions and filter your results so you can answer multiple lines of questions involving different combinations of criteria (unlike other search tools that support only limited types of questions)
- Examine a list of genes and identify those that meet your specific biological criteria
- Explore or ask detailed questions about your own lists of genes or chemicals
- Integrate with multiple workflows by importing lists from other tools, or exporting lists from Ingenuity Answers into tools such as IPA, Spotfire, or others
Easy to use:
- Benefit from an intuitive, sentence-style interface that makes asking detailed biological questions simple for all types of researchers
- Quickly find the relationships and information you need without having to understand database structure or query language
- Get quick, relevant answers without scanning documents or performing time-consuming searches
- Access a library of frequently-asked, pre-formulated questions for simple biological discovery
- Easily modify your queries in order to quickly refine and reiterate your questions
- Choose from a simple list of results, or a more detailed list of results that includes supporting evidence such as relationships, references, and related information such as date and experimental method
- Easily export results to Excel and import to other tools as needed
Frequently asked questions
What Types of Questions Can I Ask in Ingenuity Answers?
With Ingenuity Answers you can ask for specific information about a gene such as mutation details, sites of post-translational modification, whether it contains a particular domain, if it is expressed in a certain tissue or cell line, and whether it is associated with a particular disease or phenotype.
Here are some specific examples:
- What genes are expressed in A549 cells?
- What pathogens affect activation of MAP3K genes?
- What are the molecular functions of Notch proteins?
- What cells secrete insulin gene products?
- What gene mutations have been associated with asthma?
- What kinases bind SH2 domain containing proteins?
- What cells express cytokines that activate monocytes or macrophages?
- What chemicals inhibit transcription factors present in the Filoviral-mediated cytokine production pathway?
- What genes, RNAs, or proteins are biomarkers of neurological disorders?
You can also add valuable annotation to your own lists of genes deriving from proprietary investigations such as GWA studies, biomarker development efforts, or target identification:
- Which of my genes of interest are known to be associated with a disease or phenotype?
- Which of my genes of interest have had their gene products detected in cerebrospinal fluid, blood, or saliva?
- Which genes encode proteins that are tyrosine kinases?
- Which genes are expressed in macrophages but NOT red blood cells?
- Which chemicals bind to my list of genes that affect cell death? Are any of these chemicals in clinical trials?
Easily refine and explore questions in Ingenuity Answers by adding multiple follow-up questions and filter your results. Because you can ask multiple lines of questions about a list of genes, you can explore a tremendous amount of information about your biological lists or selected molecules.
How is Ingenuity Answers different from other search tools?
- Ingenuity Answers searches over the actual relationships between objects, not merely co-occurrences in text, so you’re assured that your search results are relevant, related, and actually answering your question.
- Ingenuity Answers searches over scientifically demonstrated knowledge culled from the full text of articles, including figures, and tables – unlike other tools which are limited to searching over predicted annotations or documents.
- Ingenuity Answers lets you link directly to supporting references for findings, so you can see the date, journal, experimental method, and more.
- Ingenuity Answers allows flexible question types across multiple levels of biology, as opposed to other tools which constrain you to a limited number of question types. You can explore possibilities or drill down on specific relationships between genes, molecular, cellular processes, and diseases.
- Ingenuity Answers is the only search tool that leverages the Ingenuity Knowledge Base (see below), so the content being accessed is accurate, comprehensive, and current.
What is the Ingenuity Knowledge Base?
The Ingenuity Knowledge Base is a repository of molecular interactions, regulatory events, gene-to-phenotype associations, and chemical knowledge that provides the building blocks for pathway construction. It is the largest knowledge base of its kind, with millions of findings pulled from the full text of the life sciences literature by Ph.D.-level life scientists, and features the most descriptive and detailed structure, and the highest degree of accuracy.
The Ingenuity Knowledge Base is used as a starting point for exploration of biological and chemical systems and a bridge between novel discovery and known biology. It provides researchers with a tremendous 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.
Learn more about the Ingenuity Knowledge Base, its content, and why it is unique by clicking here.
How can I use Ingenuity Answers and IPA together?
Ingenuity Answers is designed to ask specific and complex questions of the Ingenuity Knowledge Base and rapidly return a list of genes, chemicals, or other biological things that meet a certain biological criteria. Ingenuity Answers also excels at informing users about the properties a particular gene or list of genes might have. IPA is designed to support the analysis, visualization, and exploration of data generated from mammalian systems, and output that information in the form of pathways and functional associations.
In Ingenuity Answers results can be sent directly to IPA (see button import to IPA) for visualization, analysis, or further exploration. Ingenuity Answers can be used to layer additional decision-enabling information onto an imported list of genes or chemicals from IPA that derive from proprietary investigations such as GWA studies, biomarker development efforts, or target identification.