Tripal Users Meeting 2021/3/02

Agenda

1. Reminders
   • Tripal Dev meeting every Monday
     • Location: https://gather.town/app/6QHlnxNUK2JBVKKF/tripaldev
     • Time: https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+Development+Meeting&iso=20210201T17&p1=1440&ah=2 
     • Activities: https://docs.google.com/document/d/1KKRzPffcV1PkBXohLiAAo1CFhQL9u927NjoMPCN52q8/edit#heading=h.n42jpnjoy4z5 
2. TAC Announcements (Jill)
   • Tripal White paper is in the last bit of edits--working on trimming the text. 
   • Link will be placed https://docs.google.com/document/d/1w24HzOBJFKG4q3kvgAGwpEWEBgw9773jTcIqMp7bxsg/edit#
   • Please check authors, funding in acknowledgment section
   • Last chance to make minor edits.
3. Demonstration of the Tripal File Module and request for input
   • https://github.com/tripal/tripal_file
   • For sharing data files with collaborators through a Tripal site
   • Working towards FAIR data standards for making files available:
     • Files are findable and accessible via Tripal's content web services.
     • Metadata about files use globally unique controlled vocabularies. These metadata can be assigned as properties of each file.
     • License and usage details can be assigned to each file.
   • There is online documentation available through readthedocs: https://tripal-file.readthedocs.io/en/latest/ 
   • Needs Tripal version 3.6 or higher (currently use the dev branch until 3.6 is released)
   • Uses a number of custom tables to associate files with various chado data
   • Handles a lot of file metadata including the license for the data 
   • Use the Tripal ontology loader to import the EDAM vocabulary (it will be added to the drop-down for you)
   • Creates a file and license Tripal Content Type to allow adding through the UI.
   • First add your License for the file (examples in the document)
   • Next, create the file page: 
     • the types are available via EDAM, 
     • you can use contacts to associate the source of the file (create the contact first)
     • Supports both local and remote locations for the file
   • If the file is associated with Tripal pages (chado data) then the link to those pages will appear on the file page.
   • The license is actually embedded on the file page including the human-readable description
   • If you use the Tripal Managed File Interface to handle your files for download then the size and md5sum will be provided to the user.
   • You can associate a file with a Tripal content page, you edit it and scroll down to the file section near the bottom and select the file to be associated. For example, go to the analysis page from the Tripal Tutorial and clicked edit then select the file on the analysis edit page.
     • Note: Add the field to the content type by clicking “Find new fields” on the Manage fields page for the content type you want to add it to.