Tripal Advisory Commitee Meeting 2020/04/07

Meeting Date
Attendees

Meg Staton, UTK
Noah Caldwell, UTK
Matthew Huff, UTK
Monica Poelchau, USDA-ARS-NAL
Risharde Ramnath, TreeGenes
Ethy Cannon, MaizeGDB
Sean Buehler, UTK/i5k
Katheryn Buble WSU
Lacey-anne Sanderson, USASK
Valentin Guignon, Bioversity-CIAT Alliance

Community Highlights

Please add anything you would like to highlight about your Tripal-based projects: publications, new extension modules, new collaborations, newly funded grants, project update, etc.  We won't talk about these in the meetings but may tweet them from the Tripal twitter account if you approve!

Name

Highlight Description

Can we tweet it? Yes/No

Meg

Advisory committee update - grants and white paper

  

 

Agenda

  1. White Paper (Monica, Ethy, Meg)

    1. Willing to help: Lacey-anne Sanderson

      1. Start by developing an outline

      2. Send out to community and recruit help to write

    2. Other white papers worth reviewing

      1. Agbiodata

      2. LegFed

    3. Who is the audience for our white paper?

      1. Funding agencies

      2. Us! (organizing)

      3. Other dbs?

    4. WP Topics:

      1. Value proposition for community databases (orphan data types, data integration, community communication)

  • Why does Tripal matter, what value does it add, what value do data resources provide.
    On one side, a CMS like Drupal brings a lot in terms of “key-in-hands” website but Tripal brings the link with biological data and visualization/investigation tools.

  • Defining the customer (user): who is Tripal serving
    "User" =  administrators, curators, researchers

  1. Tripal support of FAIR principles

At least partly built-in. What is built in, what do data resources have to do, what remains to be implemented in Tripal.

  1. Community database sustainability

Tripal sustainability ... sustainability of data resources that use Tripal.

  1. Extensions

  • This is a huge strength because it allows every group to truly make it their own. It ensures we can support so many different types of data and researcher needs.

  • This also allows you to get things done without waiting for core developers. It is easier to meet grant needs while still greatly aiding collaboration.

  1. Challenges

    1. Keeping up with Drupal, bringing in groups that won't work with Drupal.

    2. Why is group collaboration difficult?

    3. Expand Drupal use in other countries

    4. Help to guide future development goals

    5. Not all DBs engaged with Tripal

    6. Chado is challenging for new devs

    7. Lack of metadata structure

  2. Tripal community organization

    1. PMC and TAC

    2. AgBioData

    3. International scope

    4. Plant and animal;  model and ag

This is a strength, serves as a model for other open-source projects.

  1. Future development goals

    1. Where are the mods going?

    2. Drupal 8/9 ... beyond?

    3. Different underlying database structures (NoSQL?)

  2. Future support needs

  • Recommendations for support. Depends on audience!

  • How was GMOD supported? How is AGR supported? How to get the same structural support for ag/model organisms?

  1. Example white papers:

    1. The future of legume genetic data resources: Challenges, opportunities, and priorities

  2. AgBioData GFF3 working group (Monica)

    1. Working group motivation and charges, first draft: https://docs.google.com/document/d/1dlL3mYXL32Ng_HMLeWeUNiMncXQ_YWUP9oiHGwJvk3k/edit#

    2. Maggie Woodhouse -  suggested all those working with gff3 have experienced problems and should have a discussion

    3. Scott Cain - updates from AGR on modifications to gff3

    4. We need (yet another ;) working group to provide SOP or extension standard

    5. Working group formed and going to make progress (validation software!)

    6. Starting with protein coding gene

    7. Other use cases coming soon (e.g. QTLs)

    8. Industry interested too.

    9. I5k has a gff to fasta tool - has to make certain assumptions, such as proper use of phase field. https://github.com/NAL-i5K/gff3toolkit

    10. Agbiodata community can give feedback

    11. Email Monica to join working group. (monica.poelchau@usda.gov)

  3. Grants (Anyone)

    1. Transcontinental/International ideas?

      1. Accelnet

      2. https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=505584

    2. NSF Big Network opportunity to support international collaboration

    3. NIFA - CIN Collaboration and Innovation Network - worth a shot?

      1. Originally fairly vague, may be looking for more tools or hypothesis driven work, so may be good for Tripal? Pick a particular innovation. Check RFA for updates

    4. NIFA - Food and Agriculture Cyberinformatics and Tools Initiative

Meeting Type
TAC