KnetMiner Service
KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is
used by scientists in academia and industry to accelerate gene-trait discovery research.
KnetMiner offers features such as keyword, gene list and genome region search, query
refinement, gene ranking, gene set enrichment analysis and interactive visualisation of
knowledge networks and genomic information.
KnetMiner also offers a set of high-level web API endpoints to access and visualise the
knowledge networks from other applications.
The data that power the web application are also available as FAIR data, through
linked data and knowledge graph endpoints.
Keywords
agricultural science,
genetics, computational biology,
data management, FAIR data,
biology.
Provider
KnetMiner is provided by the KnetMiner Team
at Rothamsted Research.
Inputs
KnetMiner is based on many life science data sources and services, depending on the specific
dataset instance that is served. The most common ones are:
- ENSEMBL Plants
- UniProt
- TAIR
- PubMed
- Reactome
- GeneOntology
- Crop Ontology
- Plant Trait Ontology
- Phenotype Ontology
Organisms
KnetMiner has instances that focus on many different organisms, including:
- Arabidopsis (Arabidopsis thaliana)
- Wheat (Triticum aestivum)
- Rice (Oryza sativa)
- Tomato (Solanum Lycopersicum)
- Potato (Solanum tuberosum)
- Barley (Hordeum vulgare)
- Maize (Zea mays)
- Fusarium (Fusarium graminarearum)
- Human (Homo Sapiens)
- COVID-19
Outputs
KnetMiner allows for the exploration of network knowledge. Its main outputs are
a web application allowing for searching genes and related molecular entities, plus
machine-readbale data in the form of knowledge graphs,
which are published according to the FAIR data principles.
Data are available through these channels:
In the first two cases, the knowledge graph services, the data are based on the KnetMiner ontology, which is being mapped to
schema.org and bioschemas
(see the AgriSchemas project for details).
The types from the KnetMiner ontology are also used by the APIs. The latter are based on REST-like invocations, which return a mix of CSV and JSON as output.
There is a network view API (corresponding to the knowledge graph visualisation in the web application), which returns its results
in a JSON format that is compatible with the Cytoscape CX
version 1. We plan to migrate to a more recent version in future. The application has also a "Save Network" button next to the
network view, which allows for downloading a list of dispalyed genes, in CSV format.