KnetMiner

Last updated
KnetMiner
Knetminer logo.png
Content
DescriptionKnowledge Network Miner
Data types
captured		Knowledge Discovery and Visualisation
Contact
Research center Rothamsted Research
LaboratoryBioinformatics
Primary citation doi:10.1111/pbi.13583
Release dateOctober 2013
Access
Website knetminer.org
Tools
Web KnetMiner Gene View

KnetMiner Evidence View KnetMiner Network View

Ondex-knet-builder data integration platform
Miscellaneous
License MIT
Versioning Yes
Data release
frequency		Quarterly
Version4.0 (June 2020)
Curation policyManual Curation

Knowledge Network Miner [1] (KnetMiner) [2] [3] is a system of tools used to integrate, search, and visualize biological knowledge graphs (KGs). It is used to search for information across large biological databases and literature to find links between genes, traits, diseases, and other relevant information.

Contents

Current KnetMiners (non-exhaustive)

KnetMiner KGs are built using the data integration platform, KnetBuilder, with output available in OXL, Neo4j, and RDF graph formats. It follows FAIR data [4] principles and supports a variety of biological data formats. The KnetMiner API provides web endpoints that enable users to search for specific genes and keywords, returning results in the form of a knowledge graph.

Originally developed through a collaboration of researchers at Rothamsted Research, KnetMiner has undergone further development and has initiated a spin-out process.

KnetMiner hosts a range of different species, including a knowledge graph dedicated to SARS-CoV-2 [5] [6] in response to the 2020 global pandemic, on Rothamsted Research HPC machines.

Species included in KnetMiner's knowledge graphs:

KnetMiner has been involved in several studies, including studies for wheat, [7] [8] [9] willow, [9] and SARS-CoV-2. [5] It is also being used for exploring pathogen-host interactions in collaboration with PHI-base, soybean loopers, and other species.

API access

KnetMiner uses REST API access to obtain either JSON outputs of each view type or network views for certain searches.

Funding

KnetMiner is funded by the Biotechnology and Biological Sciences Research Council, a UK research council. [2]

References

  1. ↑ "knetMiner".
  2. 1 2 Hassani-Pak, Keywan; Singh, Ajit; Brandizi, Marco; Hearnshaw, Joseph; Parsons, Jeremy D.; Amberkar, Sandeep; Phillips, Andrew L.; Doonan, John H.; Rawlings, Chris (2021-03-22). "KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species". Plant Biotechnology Journal. 19 (8): 1670–1678. Bibcode:2021PBioJ..19.1670H. doi:10.1111/pbi.13583. ISSN   1467-7644. PMC   8384599 . PMID   33750020.
  3. ↑ Hassani-Pak, Keywan (2017). "KnetMiner - An integrated data platform for gene mining and biological knowledge discovery". Bielefeld University, Bielefeld.
  4. ↑ Brandizi, Marco; Singh, Ajit; Rawlings, Christopher; Hassani-Pak, Keywan (2018). "Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach". Journal of Integrative Bioinformatics. 15 (3) 20180023. doi: 10.1515/jib-2018-0023 . ISSN   1613-4516. PMC   6340125 . PMID   30085931.
  5. 1 2 Hearnshaw, Joseph; Brandizi, Marco; Singh, Ajit; Hassani-Pak, Keywan. "Rothamsted Answers White House Call For Coronavirus Data Help". Rothamsted Research.
  6. ↑ Hutson, Matthew (2020). "Artificial-intelligence tools aim to tame the coronavirus literature". Nature. doi:10.1038/d41586-020-01733-7. PMID   34103725.
  7. ↑ Adamski, Nikolai M; Borrill, Philippa; Brinton, Jemima; Harrington, Sophie; Marchal, Clemence; Bentley, Alison R; Bovill, Wiliam D; Cattivelli, Luigi; Cockram, James; Contreras-Moreira, Bruno; Ford, Brett; Ghosh, Sreya; Harwood, Wendy; Hassani-Pak, Keywan; Hayta, Sadiye; Hickey, Lee T; Kanyuka, Kostya; King, Julie; Maccaferri, Marco; Naamati, Guy; Pozniak, Curtis J; Ramirez-Gonzalez, Ricardo H; Sansaloni, Carolina; Trevaskis, Ben; Wingen, Luzie U; Wulff, Brande BH; Uauy, Cristobal. "A roadmap for gene functional characterisation in wheat" (PDF). PeerJ Preprints. doi: 10.7287/peerj.preprints.26877v2 . S2CID   43925415.
  8. ↑ Harrington, Sophie A.; Backhaus, Anna E.; Singh, Ajit; Hassani-Pak, Keywan; Uauy, Cristobal (2020). "The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat". G3: Genes, Genomes, Genetics. 10 (10): 3675–3686. bioRxiv   10.1101/684183 . doi:10.1534/g3.120.401436. PMC   7534433 . PMID   32747342.
  9. 1 2 Alabdullah, Abdul Kader; Borrill, Philippa; Martin, Azahara C.; Ramirez-Gonzalez, Ricardo H.; Hassani-Pak, Keywan; Uauy, Cristobal; Shaw, Peter; Moore, Graham (2019). "A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization". Frontiers in Plant Science. 10 1325. Bibcode:2019FrPS...10.1325A. doi: 10.3389/fpls.2019.01325 . ISSN   1664-462X. PMC   6813927 . PMID   31681395.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.