fix ids conflicting with readded methods and scales

[bellerbrock]

Description

I ran into problems with some terms while trying to open the obo file in protege and then save again in obo format.

I removed two invalid scale definitions, and reassigned unused ids to new traits and variables whose ids were conflicted with some re-added scale and method ids. Also checked in spbase to make sure there weren't any measurements associated with the changed variables.

Closes #7

Checklist

• [x] An OBO file generated from an OWL file
• [x] New terms
  • [x] The relevant issue has been closed.
  • [ ] Further work is required.
• [ ] Term updates
  • [ ] The relevant issue has been closed.
  • [ ] Further work is required.
• [x] CHECKS
  • [x] New variables have a parent trait ID
  • [x] New variables have methods and scales
  • [x] The OBO file has been validated
  • [x] checked in sweetpotatobase
  • [ ] checked CropOntology

[cooperl09]

Is this ok to merge? @nmenda