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.

Contents:

Generating a template
Formatting data
Uploading and validating data
Requesting trait terms

Generating a template

1. Go to GEOME and create an account
2. Create a project and join the FuTRES Team
   • Project naming convention: FuTRES_taxon_contributor_locality_time.period
   • It is up to the user to choose projects / expeditions (datasets) as necessary
     • the organization of expeditions (datasets) can be however you would like (e.g., by site or time)
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
   • Required terms are automatically populated
   • Select any additional 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

For the FuTRES datastore, data are expected to be in “long” format, where each row is a measurement. This means that there will be repeated data.

Formating

• All column headers use camelCase
• See the template for suggested and required values under “example”.
• All non-required columns need to be removed (not recommended) or moved into a “dynamicProperties” field (recommended)
• Three unique IDs are required:
  • diagnosticID
    • this is unique for every measurement (row)
    • this can be an index or a combination of index + catalog number + institutionID
  • materialSampleID
    • This is unique for every element (e.g., bone) and connects all the measurements on the same element
    • This can be a random indentifier or a combination of element + catalog number + institutionID
  • individualID
    • This is unique for ever individual and connects all the elements of an individual
    • This can be a random identifier or a combination of catalog number + institutionID

We have also created a RShiny App. Read the “readme” file to learn the data formats we can use, dependencies needed, and limits of the app. Please send recommendations or issues to the RShiny FuTRES 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
• Go to the Ontology Lookup Service to look for the term, restricting searches to only include “FOVT”

2. IF the term does not yet exist, go to FuTRES Ontology of Vertebrate Traits (FOVT) and 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)