We ask researchers wishing to contribute data to FuTRES to use the following procedure to provide data.

Contributing Data to FuTRES

FuTRES is partnering with GEOME to help users load and validate data. General instructions on using GEOME are available on the GEOME Getting Started and a short youtube video on Loading FuTRES data into GEOME. Please reach out to our team with any questions!

FuTRES will deliver all processed trait data via an application programming interface (API), web interface, and R package by Summer of 2019. Currently, code and configuration files for our data processing pipeline can be found at fovt-data-pipeline, which contains all of the settings for processing incoming datasets and aligning with the FuTRES ontology for vertebrate traits (FOVT).

Contents:

Video on Loading Data into GEOME (video)

Generating a template

1. Go to GEOME and create an account
2. Create a project and join the FuTRES Team
   • Naming convention: FuTRES_taxon_contributor_locality_time.period
   • It is up to the user to choose projects / expeditions (datasets) as necessary
     • e.g., each expedition could be a site and each project a collection
     • the organization of expedition (datasets) can be however you would like (e.g., by site or time). FuTRES API already searches based on taxonomy and measurement.
3. Fill in project metadata
   • project title
   • project description
   • visibility (public/private)
     • Note that even if projects are public, expeditions can be private
   • principle investigator
   • principle investigator affiliation
   • citation
     • This is needed if your license is CC BY or BSD
4. Select the template generator to create a spreadsheet for entering data
   • Select terms
   • Export to a spreadsheet application
     • Speadsheet has:
       • Instructions
       • Template (required field in red)
       • Controlled vocabulary
       • Definition for attributes
     • Note that licensing is assumed to be CC0, unless specified as CC BY or BSD
5. Fill in expedition (dataset) metadata
   • expedition title
     • Naming convention: FuTRES_taxon_contributor_locality_time.period_version number or date
   • expedition code
   • if expedition can be public or private

Formatting data

1. Check out the RShinyApp developed by P. Gyawali.
2. Read the “readme” file to learn the data formats we can use, dependencies needed, and limits of the app.
3. For now, we cannot map your terms to the accepted trait terms, please see the term list on GEOME (see above).
4. Please send recommendations or issues to the RShinyFuTRES repository.

Uploading and validating data

1. Upload to GEOME under your project in FuTRES Team Project
   • Can load multiple spreadsheets at one time under same expedition name
   • Will give a warning if something is wrong, but not fatal (can ignore; use your discretion)
   • Will give an error if a value in a field is wrong (e.g., a string where numbers should be)
2. Fill in expedition metadata
   • expedition title - Naming convention: FuTRES_taxon_contributor_locality_time.period_version number or date
   • expedition code
3. Name your expedition:
   • FuTRES_taxon_contributor_locality_time.period and version number or date

Requesting trait terms

1. Check that the term is not currently there
   • Click on measurementType DEF of template
2. Go to FuTRES Ontology of Vertebrate Traits (FOVT)
3. Create a New issue
   • Needs:
   • term label
   • synonyms
   • Parts of the term
     • anatomical feature
     • anatomical points and/or anatomical axis
     • measurement (e.g., width, length, etc.)
   • reference for measurement (illustration if have it)
   • attribution (ORCID id)