5.7-RC

Quick start with Docker:

1. Download and expand the zip
2. cd docker
3. ./docker-run.sh

The latter will launch a small/demo dataset, see the documentation for using real data.

See the revision history for a list of new features and changes.

5.6

Quick start with Docker:

1. Download and expand the zip
2. cd docker
3. ./docker-run.sh

The latter will launch a small/demo dataset, see the documentation for using real data.

See the revision history for a list of new features and changes.

5.6-RC

Quick start with Docker:

1. Download and expand the zip
2. cd docker
3. ./docker-run.sh

The latter will launch a small/demo dataset, see the documentation for using real data.

See the revision history for a list of new features and changes.

5.0

KnetMiner 5.0

What's new?

KnetMiner 5.0 comes with a number of new features, speed improvements and a new freemium/premium version.

Key Features

1. KnetMiner (https://knetminer.com) now also offers a range of Free and Pro features. The free version is a perfect starting point for using or testing the platform with a small number of genes. The Pro version enables searching the knowledge graph with any number of genes, creating very large gene networks and storing as many networks as you wish.
2. The gene list search feature has received a major performance enhancement. It now supports wildcards (eg. search for all TPS* genes) and can perform a novel KG enrichment analysis.

3. The Evidence View has seen major upgrades to allow users download the content and to generate gene networks for multiple enriched terms.

4. The Network View has been vastly improved as well, with auto-filtering when the knetworks are too big and a new feature to export the content of the network (all visible genes) as a table.

5. The network visualisation (knetmaps.js) has been enhanced with better node labelling to highlight important parts of the graph and to distinguish genes from different species by taxID. A new type of edge (dashed lines) has also been introduced to flag relationships which need to be treated with caution.

6. KnetMiner generated gene networks can be easily saved to KnetSpace (https://knetminer.com/beta/knetspace/) and shared with colleagues and published online.

References and further details:

1. Latest KnetMiner publication: https://onlinelibrary.wiley.com/doi/10.1111/pbi.13583
2. KnetMiner covid19 data note: https://f1000research.com/articles/10-703/v1

Software improvements and bug fixes

Search and analysis

• Free and Pro KnetMiner features added. Free users are those without a KnetSpace account or those on a KnetSpace Free Plan wile Pro users are subscribers of the KnetSpace Pro plan. Under the free version, users can search KnetMiner with upto 20 genes in their gene list and visualize a knetwork of max. 10 genes. Pro users can search KnetMiner with no limits on gene list size and can render knetworks to analyse upto 200 genes at once.
• Search results messages now show detailed information such as number of linked, unlinked and not-found user genes based on user query and gene list, and also the time taken for the query to run.
• Error messages now return more detailed and user-friendly information.
• Users can now directly add/omit evidence terms to their search box from Evidence View.
• Evidence view table can now be downloaded by users as a tab-delimited file.
• Users can render a combined knetwork of multiple evidence terms from Evidence View.

KnetMiner API

• New explainer implemented for KnetMiner genepage API that analyses the user query to generate a word summary of what the resulting knetwork contains.
• KnetMiner knowledge graph (dataset) version now added to latestNetworkStats API to have it displayed in release_notes html page.

KnetMiner back-end

• Migration to Java 11. Now you do need Java >= 11 to make knetminer work If you use Docker, our images use the right Java version automatically.
• Big refactoring of the OndexServiceProvider component.
• Wildcards now supported in the Gene List Search box (eg, 'MYB*', 'TT?')
• knetminer-base image removed, now there are only two docker image levels.
• Migration from Travis to GitHub Actions for CI builds.
• KnetMiner now allows developer users to enable/disable knetspace login in their KnetMiners, and to enable/disable or re-route google analytics (keywords, gene lists, QTLs) to an Amazon S3 bucket as a set of useful metrics for internal analysis.
• Extensive review of the codebase file structure and names.
• Third-party dependency updates.

Network View (KnetMaps.js)

• Users can now export all visible genes and associated information as a tab-delimited file
• Network View now auto-filters large knetworks to let users visualize subsets and avoid browser issues.
• The network visualization now has more advanced node labelling to highlight important parts of the graph and to distinguish genes by taxID as well, by coloring gene node labels appropriately, which is highly useful for multi-species KGs.
• Network visualization now uses "dashed" edges to flag relationships that are not abdolute and need to be treated with caution.
• Multiple new data sources hyperlinks added/updated to enable users to explore ARA-GWAS, ENSEMBL_PLANTS, wheat-expression, ARA-PHENO and other sources.

Other updates

• KnetMiner wiki (https://github.com/Rothamsted/knetminer/wiki) updated with new instructions for developers.

Poaceae multi-species knowledge graph

A new multi-species poaceae knowledge graph (KG) integrates a vast amount of: genetic, genomic and literature data from the four most important global cereal crops: wheat, rice, maize, barley, combined with the model plant species Arabidopsis and Brachypodium. We have cleaned, processed, and integrated over 100 datasets which has resulted in a KG of 2 million nodes and 10 million relationships between them. This KG is available through through a paid KnetMiner resource subscribtion (request quote) and our free RDF-SPARQL and Neo4j-Cypher graph query endpoints (https://knetminer.com/data).

4.0

KnetMiner 4.0

What's new?

1. New KnetMiner branding

   • KnetMiner 4.0 sees a major revamp with an all-new website and new branding, logo, fonts, and separated sub- products and services with their own logo, content pages and demos.
   • KnetMiner now on wikipedia.

2. New COVID-19 KnetMiner

   • We have developed a new COVID-19 KnetMiner. Read the full press release here and check out COVID-19 KnetMiner's feature appearance in Nature.

3. Save your knetworks in the all-new KnetSpace

   • KnetMiner users can now save their knowledge networks on KnetSpace (beta), our new collaborative knowledge discovery platform to manage KnetMiner knetworks.
   • New login feature added to KnetMiner with a “Sign in '' button in the header. Users can now sign-in using their KnetSpace username and password (sign-up is very quick). In future, we will add Google login and similar.
   • Previously, users could perform a keyword or gene list search in KnetMiner, generate an initial network for some genes and export a PNG image. As of KnetMiner 4.0, you can save it to your KnetSpace and can edit it anytime in future and share it with your students, colleagues or collaborators to help you find interesting links or curate the network collaboratively (eg hide certain nodes/edges, add labels, change layout).
   • You can give people permissions to either edit your original network or clone it to their own KnetSpace. Once you are happy with a network you can tweet the link or share the interactive network on your own website.
   • To save networks, simply click the new “Save network” button on the KnetMiner Network View tab and provide a name and description. This will quickly save the visible network, its layout and metadata information such as owner, date, version, source, genes, keywords used, etc. to your KnetSpace account.
     

4. Free and Pro user subscription plans

   • We have added Free and Pro subscription plans. Sign-up to KnetMiner and KnetSpace is for free. The Free plan provides all standard KnetMiner features, plus allows users to store a limited number of user knetworks to KnetSpace. The Pro plan provides greater storage and allows users to make their saved Knetworks private. Choose a plan that’s right for you.

5. Neo4j-Cypher integration (beta)

   • The graph traversal code was re-engineered to support the Cypher graph query language. This is the first major milestone to transition towards an alternative graph database backend. Cypher is a more expressive and more standardised query language. This feature is still experimental and requires a separate Neo4j database installation, based on our RDF and Neo4j export tools. The default KnetMiner 4.0 option is to use the old semantic motif search.

References and further details:

• overview of the new Knetminer architecture, https://www.degruyter.com/view/journals/jib/15/3/article-20180023.xml
• Details on the Knetminer backend and sample Cypher motif queries, https://www.slideshare.net/mbrandizi/knetminer-backend-training-nov-2018-124145829
• Real use cases can be found on our dataset files (eg, https://github.com/Rothamsted/knetminer/blob/master/species/wheat-beta/ws/cypher-queries.txt). More documentation will be released soon.

Bug fixes and software improvements

Search

• Searches pertaining to a gene identifier, using the Gene List, are now exact.

API

Several new APIs have been implemented now, including the following:

• API for KnetSpace host url address, as defined in the POM by variable knetminer.knetSpaceHost with the API URL given as /ws/{$speciesName}/ksHost
• API for geneCount added which provides the size of the subgraph (number of nodes, edges) generated by KnetMiner for a given gene list. Given as /ws/{$speciesName}/geneCount?list=
• DataSource information of the knowledge graph including source organisation, database version, provider, species tax ID, date of creation, and species name, is accessible via the /ws/{$speciesName}/dataSource API.

KnetMiner back-end

• KnetMiner can now be customised and deployed with a subset of genes. For example, we limited the COVID-19 KnetMiner to call 8,000 human genes as the seed. The path to the seed gene list can be defined in the main KnetMiner POM file variable knetminer.backend.seedGenesFile. This means only the seed genes will appear in the KnetMiner search index. The default is to index all genes. Refer to this commit.
• Users may now define the number of Publications exported in knowledge subgraphs by altering the main POM configuration variable defaultExportedPublicationCount. The default is set to 20 most recent publications.
• The unconnected filter prior to JSON export was extended with additional concept classes
• Metadata information for the knowledge graph can now be defined in the KnetMiner dataset/species POM.

Network view

• Updated to KnetMaps.js v2.0.2.
• Save PNG and JSON have been replaced with a ‘Save Knetwork’ button, as described in the KnetSpace integration section.
• More data sources URLs added to support rendering of new data types.
• Custom branding and fonts packaged for KnetMaps as well via gulp-configs.
• Keyword highlighting logic updated and limited only to primary colours and some shades.

v3.2

New features/enhancements

• New genepage design using KnetMiner look & feel
• New analytics logger for genome, network and genepage modes
• Network View legend was enhanced
• Release Notes stats table was expanded with further graph analytics
• New search button
• Updated footer

v3.1

New features/enhancements

• Evidence View - Legend can be used to filter based on Evidence #373
• Evidence View - Sort table by p-value if available #310
  
• API - provide support for phrase query keywords using double-quotes #374
• Performance - Faster and more responsive when many parallel searches #352
• Docker - Deployment has been significantly improved see #wiki
• Docker - Deployment in AWS Elastic Beanstalk has been updated see #wiki
• Network View (KnetMaps) - Selected genes show highlighted labels as default #394
• Network View - Legend can be used to add and hide nodes from network #408
  

Bug fixes

• Network View - Highlighting keywords in Network fails when multiple keywords found side-by-side #311
• Gene View - Number of evidences shown in legend was not correct #375
• Gene and Evidence View - Table header remains when scrolling #371
• Evidence View - Wrong loading message fixed #369
• Search - Bug with spaces in Gene List box fixed #355
• Search - Issue with many parallel searches was fixed #352
• Search - Null pointer exception for some rare gene-keyword combinations #401
• Search - Concept accessions are not searched, eg no hits returned for "TO:0000286" #345
• Google Analytics can now show the correct country of API users #350
• Legends were missing some icons; fixed

v3.0

Key Features

• Better Gene List & Genome Region Search. You have a list of genes and no clue what they do? Just paste your gene ids/names into the Gene List box (without any keyword) and let KnetMiner provide a summary of all information it has for your genes, their location, enriched linked terms and allow you to view their knowledge network. Genes won't be ranked and only paths from gene to trait and phenotype nodes will initially be shown. If you combine your gene list with keywords, KnetMiner will be able to rank your gene list based on relevance and highlight the most interesting paths of the knowledge network.
• New Web API access. KnetMiner knowledge networks can now be searched and visualized through API calls. For example, check out the MFT gene in araknet, wheatknet or riceknet. Adding a keyword argument to the URL will do some smart filtering and display the most interesting paths connecting genes and keywords (see example). You can embed similar code snippets into your own website.
• Smart Publication filtering. Some genes are linked to hundreds of papers. KnetMiner will now only show the most recent 20 publications in GeneView (Evidence box) and in NetworkView. This change will help you to get quicker to most recent research papers and has significantly improved the KnetMiner loading time.
• Deploy your own KnetMiner with Docker. KnetMiner is now available as a Docker image that can be easily deployed on your own server or in the AWS Elastic Beanstalk. To host your own private or public KnetMiner, you will need to create or clone one of the existing my_species (see example) folder. You can build your own my_species knowledge network or ask us to build one for you as a service.

All features and bug fixes

• Search interface:
  • Improved search interface now supporting without-keyword search
  • New search-modes implemented for search with gene-list only, genomic regions only, and gene-list + region-search in addition to existing keyword-centric search-modes
  • New loading spinner to search and view network
  • New search interface layout, icons, post-search auto-scrolling
• Deployment:
  • New deployment framework implemented using Docker
  • Dockerfiles developed to automate building Docker images for KnetMiner for AWS and local deployment.
  • Detailed documentation available at knetminer-docker-docs
  • Build scripts implemented to automate species-specific Dockerfile invocation.
  • npm config tweaked to fix bower errors
• Gene View:
  • Enhancements to Gene Rank calculation
  • 20 most recent publications are shown when you click on a Publication icon
• Evidence View:
  • F-test: P-value added to evidence terms when gene list is provided
  • Network links added to user genes column if gene list is provided
• Network View:
  • 20 most recent publications are shown in network
  • If no-keyword is provided, show initially only paths from gene to Trait and Phenotype nodes
  • If keyword doesn't match any node in path, show initially only paths from gene to Trait and Phenotype nodes
  • Added network loading spinner
  • Updated KnetMaps version for npm and bioJS
• Map View:
  • Improved scaling to fix chromosome overlaps
  • Updated version GenoMap for npm and bioJS
• Back-end API:
  • New API endpoints for different search-modes (gene-list search, region search and gene-list + region-search)
  • Re-structured cleanup of module hierarchy
  • Corrected gene-trait transitions
  • genepage - fixed by serving KnetMaps dist/ over https
• Client GUI
  • relative url's for header logo and ws/ api_url
• Release notes
  • Updates to species/data release notes, fixes added to network stats displayed in release notes

v2.1

Feature_updates:

• KnetMiner UI:
  • Query suggester rendering, and functionality, improved for add/replace search terms/phrases.
  • new example queries added for Wheat, and chromosome map fixed.
• Back-end code:
  • Server-side keyword highlighting implemented to highlight search keyword(s) wherever found in evidence nodes/edges.
  • Analytics added.
  • ondex.version updated from 1.2.1-SNAPSHOT to 2.1.1-SNAPSHOT to use latest dependencies from ondex-knet-builder.
• KnetMaps (Network View) revamp:
  • highlighting implemented to use different colors in network per search keyword.
  • show PMID and PubMed url in relations
  • network preloader fixed.
• Genomaps (Map View) revamp:
  • dropdowns fixed in menu.
• API:
  • Server-side keyword (from url request) highlighted.
  • API analytics added.
  • network/ api_url tweak (relative) for genepage endpoint.
  • Logging fixed.

v2.0

Feature_updates:

• API:
  • Web services endpoints developed for all KnetMiner query "modes".
  • All species instances converted to new code config.: server, client and datasource.
  • New API documentation at https://github.com/Rothamsted/knetminer/wiki/7.-KnetMiner-server-architecture.
  • Search output files no longer saved.
  • Server (back-end/ web services) and client (UI) both now served as Java .war for single-click deployment.
• Genomaps (Map View) revamp:
  • now optimized and packaged via npm, bower and gulp, as a standalone JS tool.
  • restrict to Gene List or QTL regions, if provided.
• KnetMaps (Network View) revamp:
  • now optimized and packaged via npm, bower and gulp, as a standalone JS tool.
  • API: now can also be invoked via "network" mode using wevb services to get JSON back.
  • or via "genepage" endpoint to get packaged KnetMaps visualization.
  • Trait icon changed to TO.
  • Relations to show PMID url in ItemInfo attributes.
• KnetMiner Wheat (new release) developed:
  • with new, updated Map View.
  • new data: SNP, GWAS, CoExp, Tilling, PO.
  • Semantic Motifs updated.
  • updated example queries.
  • new species image.
• Gene View:
  • restrict to Gene List or QTL regions, if provided.
  • QTL, KNETscore removed from View (available in back-end).
  • Trait icon changed to TO in filtering legend.
  • tablesorter restricted to existing columns.
  • interactive legend: revert button to control default ranking (by score) in visible table as well.
• Evidence View:
  • "user genes" can now also be visualized via KnetMaps.
  • Trait icon changed to TO in filtering legend.
• common_server:
  • cyjs_json dependency updated to 2.1.1-snapshot.