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@AjitPS AjitPS released this Feb 25, 2019 · 1 commit to knetminer-3.0 since this release

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.
  • 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
  • Release notes
  • Updates to species/data release notes, fixes added to network stats displayed in release notes
Assets 2
Feb 22, 2019
Merge pull request #337 from Rothamsted/knetminer-3.0
Knetminer 3.0

@AjitPS AjitPS released this Sep 12, 2018 · 383 commits to master since this release

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.
Assets 2

@AjitPS AjitPS released this Jul 23, 2018 · 435 commits to master since this release

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.
Assets 2

@AjitPS AjitPS released this Mar 7, 2018 · 630 commits to master since this release

Feature_updates:

  • GeneView:
    • interactive legend developed for filtering using evidence types.
    • concept names (inferred) added to table.
    • tablesorter fixed.
  • common_server:
    • Lucene upgrade to 1.2.1-snapshot and Wheat unit tests m-brandizi
    • mapGene2PathLength created to map geneID and endNodeID with semantic motif's PathLength.
    • generate GeneEvidence Stats summary.
    • upgrade all ondex dependencies in common-server POM to 1.2.1-snapshot.
    • Knetscore - show evidences_linked count in GeneView.tab.
    • Lucene test: load WheatKnet oxl from resources dir.
  • KnetMiner Rice (prototype) config/setup.
  • KnetMaps (Network View):
    • interactive concepts legend added for filtering visible network.
    • stylesheet-mapper xml developed for cytoscape desktop. ajit-singh
    • network PNG export added, file downloader implemented for network JSON export.
  • Fungi KnetMiners config.
Assets 2
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