Tripal User's Meeting 2021/09/07

Meeting Date
Attendees

Stephen Ficklin, WSU
Meg Staton, UTK
Risharde Ramnath, UCONN & WSU
Irene Cobo, UConn
Chun-Huai Cheng, WSU

Agenda

  1. Reminders
  2. Any Updates from the Advisory Committee?
  3. Next Month's Meeting:  Advisory Committee Meeting.
  4. AgBioData Research Coordinate Network (RCN) Award
    • https://www.nsf.gov/awardsearch/showAward?AWD_ID=2126334&HistoricalAwards=false
    • Monica and Meg are both on the steering committee!
    • Will hold an online meeting in 2022 and there will be some working groups for folks to join.  Meg hopes Tripal can be involved!
      • Meg:  Education
      • Monica: Data Federation
    • Looking to hire a project coordinator.
    • Kick-off meeting was held Sept 1st.
    • Please watch for AgBioData notices and news for further information.
    • Any updates from folks in the leadership team?
    • Chado and the Semantic Web paper
      • If interested please consider volunteering with this.
  5. Tripal Hackathon and PAG Workshop
    • Currently the Tripal Workshop is scheduled with PAG.
    • Due to international travel restrictions, the PMC has decided to hold the annual Hackathon/Codefest online again this year.
    • Suggestions:
      • pre-record talks
  6. Presentation by Stephen Ficklin.  Tripal Network Module Introduction. 
    • Purpose: stores and integrates gene co-expression, protein-protein interaction and other network data within a Tripal site to help researchers explore gene function through relationships. 
    • It is still under development. We are hoping to offer it for use early 2022.
    • History: the module has been in use as a Tripal v2 site at http://gene-networks.org/. The site and the module have languished but with the release of the new KINC workflow (https://kinc.readthedocs.io/en/latest/) we wanted a place to display the networks we and our collaborators are constructing.
    • Features
      • Integrates with the Tripal file module for sharing network files and data with licenses.
      • Designed to support multiple network types with nodes as genomic features:
        1. Gene co-expression
        2. Protein-protein interaction
      • Fully supports controlled vocabularies for edge and node annotations.
      • Supports KINC workflow (https://kinc.readthedocs.io/en/latest/)
      • Database and Code Review
        1. A new set of tables in Chado for storing network data
        2. New Content Type:
          1. Network content types
        3. New Fields
          1. For the Network content type
            1. Network attribute
          2. For the feature-based content types (e.g. gene)
            1. Network Neighborhood Viewer   
        4. New Importers
          1. Imports networks in GraphML format (http://graphml.graphdrawing.org/) 
        5. New Bulk Loader Template
          1. Functional data importer
      • Website Review
        1. Example network data source:
          1. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA301554/ 
        2. Network Content Type
          1. View existing
          2. View creation form
        3. GraphML Loader
        4. Interactive whole network 3D viewer application
          1. Fully Drupal compatible
          2. Uses Plotly for interactive networks
          3. Feature review
            1. Network selection
            2. Network layering
            3. Selected node and edge
            4. Network filtering
            5. Help and info
        5. Interactive gene neighborhood
        6. Web services
    • TODO:
      • selecting networks by data source.
      • Integration of expression data (perhaps in conjunction with the Staton Lab Expression module)
      • Improvements to the gene neighborhood viewer
      • Better graph layouts
      • Bug fixes!
      • Step-by-step installation and usage documentation.
      • Functional enrichment of the filtered network.
    • Thoughts or feature requests?
      • How to do cross-species comparisons.
      • Add the ability to turn on and off node labels
Meeting Type
Users