Software:KnetMiner
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| Knetminer logo.png | |
|---|---|
| Content | |
| Description | Knowledge Network Miner |
| Data types captured | Knowledge Discovery and Visualisation |
| Contact | |
| Research centre | Rothamsted Research |
| Laboratory | Bioinformatics |
| Primary citation | doi:10.1111/pbi.13583 |
| Release date | October 2013 |
| Access | |
| Website | knetminer |
| Tools | |
| Web application | KnetMiner Gene View
KnetMiner Evidence View KnetMiner Network View Ondex-knet-builder data integration platform |
| Miscellaneous | |
| Software license | MIT |
| Software versioning | Yes |
| Data release frequency | Quarterly |
| Version | 4.0 (June 2020) |
| Curation policy | Manual Curation |
Knowledge Network Miner (KnetMiner)[1][2] is a system of tools used to integrate, search and visualize biological Knowledge Graphs (KGs). It assists scientists in searching across large biological databases and literature to find links between genes, traits, diseases, and other information types.
Current KnetMiners (non-exhaustive list)
KnetMiner KGs are built using the company’s data integration platform KnetBuilder and provided in OXL, Neo4j and RDF graph formats. It makes use of FAIR data[3] principles and supports the use of a range of biological data formats. The KnetMiner API provides web endpoints to search the KG with genes and keywords, returning the knowledge in graph format. KnetMiner was initially created via collaboration of researchers at Rothamsted Research and has since expanded and initiated a spin-out process. KnetMiner filed for the KnetMiner trademark on November 25, 2021 and was entered into the register on May 6, 2022.[4]
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. It includes the following:
- Triticum aestivum
- Arabidopsis thaliana
- Oryza sativa japonica
- SARS-CoV-2
- Fusarium graminearum
- Fusarium culmorum
- Zymoseptoria tritici
KnetMiner has been involved in a number of 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 to obtain network views for certain searches.
Funding
KnetMiner is funded by the Biotechnology and Biological Sciences Research Council, a UK research council.[1]
References
- ↑ 1.0 1.1 Hassani‐Pak, Keywan; Singh, Ajit; Brandizi, Marco; Hearnshaw, Joseph; Parsons, Jeremy D.; Amberkar, Sandeep; Phillips, Andrew L.; Doonan, John H. et al. (2021-03-22). "KnetMiner: a comprehensive approach for supporting evidence‐based gene discovery and complex trait analysis across species" (in en). Plant Biotechnology Journal 19 (8): 1670–1678. doi:10.1111/pbi.13583. ISSN 1467-7644. PMID 33750020.
- ↑ Hassani-Pak, Keywan (2017). "KnetMiner - An integrated data platform for gene mining and biological knowledge discovery". Bielefeld University, Bielefeld. https://pub.uni-bielefeld.de/record/2915227.
- ↑ 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). doi:10.1515/jib-2018-0023. ISSN 1613-4516. PMID 30085931.
- ↑ "Search for a trade mark - Intellectual Property Office" (in en). https://trademarks.ipo.gov.uk/ipo-tmcase/page/Results/1/UK00003725755.
- ↑ 5.0 5.1 Hearnshaw, Joseph; Brandizi, Marco; Singh, Ajit; Hassani-Pak, Keywan. "Rothamsted Answers White House Call For Coronavirus Data Help". Rothamsted Research. https://www.rothamsted.ac.uk/news/rothamsted-answers-white-house-call-coronavirus-data-help.
- ↑ "Artificial-intelligence tools aim to tame the coronavirus literature". Nature. https://www.nature.com/articles/d41586-020-01733-7.
- ↑ Adamski, Nikolai M; Borrill, Philippa; Brinton, Jemima; Harrington, Sophie; Marchal, Clemence; Bentley, Alison R; Bovill, Wiliam D; Cattivelli, Luigi et al.. A roadmap for gene functional characterisation in wheat. doi:10.7287/peerj.preprints.26877v2. https://repository.rothamsted.ac.uk/download/3d37885124927531c464121fa1419dadcc56736bd3c66c6b1e19c6e11d36b3ed/3487288/Table2_Natural_variation_wheat_roadmap.pdf.
- ↑ Harrington, Sophie A.; Backhaus, Anna E.; Singh, Ajit; Hassani-Pak, Keywan; Uauy, Cristobal (2019). Validation and characterisation of a wheat GENIE3 network using an independent RNA-Seq dataset. doi:10.1101/684183.
- ↑ 9.0 9.1 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. doi:10.3389/fpls.2019.01325. ISSN 1664-462X. PMID 31681395.
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