KMINE Literature Reports

KMINE Literature Reports summarize the relevant literature for bacteria, genes, metabolites pathways, drugs, phenotypes and diseases, or other biomedical terms. All automated literature reports are based on PubMed abstracts and are generated as interactive HTML pages.

The KMINE Literature Reports are generated for a set of concepts that a client has a particular interest in. This Start Set is provided by the client. The Start Set consists of concepts such as human genes, metabolites, pathways, bacteria, bacterial genes, cell types, diseases, drugs, foods and research terms. This report helps in the look-up of the relevant literature for thisStart Set: it displays abstracts about each of these concepts and all inter-connections. Next, relations between the concepts of the Start Set and concepts that are part of our BioSets are described. BioSets are expert-curated sets of different biological concepts that describe a certain topic. Examples of BioSets that can optionally be included are: gut health, skin health, brain health, oncology and immunity. Finally, relations between the concepts of your Start Set and the Discovery Set are described. The Discovery Set contains over 200,000 biological concepts that are the basis of our KMAP database. The above is described in the overview picture below:

The report has been divided into several sections, designed to answer specific questions. These are listed below:

  • What is known about the members of my set?
  • How are the concepts related to each other?
  • Which facts are known about the members of my set?
  • How are my concepts related to BioSets?
  • How is each concept related to new concepts?

TenWise has a large number of precompiled literature reports, created on basis of external concept sets. These include:

  • 4440 reports for regulated gene sets from the molecular signature database (MSigDB).
  • 2417 reports for phenotype & disease related genes sets from the HPO database.
  • 793 reports for metabolites from a set of curated metabolic pathways.
  • 654 reports for human pathways from WikiPathways.
  • 35 custom reports with mixed type concepts gathered by experts, addressing a specific biological field. Examples of these are shown below.

Precompiled literature reports from other external sources can be added on request.

Multi omics gut set
A mixed omics set of concepts related to gut microbiome including organisms, pathways and metabolites.
Read report
Genes & ALS
A set of 10 genes related to general inflammation and to the disease Amyotrophic Lateral Sclerosis.
Read report
Microbes & skin microbiome
A set of micro-organisms related to the skin microbiome.
Read report

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