how to handle KPMP Specimen and derivatives

[yongqunh]

This is an issue out of a discussion on April 3, 2018 between Jonas M. Carson and Oliver He:

We need to handle KPMP specimen and their derivatives using ontology, e.g., as Dr. Sanjay Jain from UW mentioned:
"Kidney-frozen OCT block Dry ice- sections-RNA/protein/dna/metabolite/fixed-stains-HE/immuno
Kidney-frozen LN2- frozen sections/RNA/protein/dna/metabolite
Kidney-frozen RNAlater- RNA
Kidney-fixed paraffin block-sections-stain-HE/PAS/JMS/Trichrome/immuno
Kidney-fixed cryopreserved frozen OCT block-sections- RNA/fixed-stains-HE/immuno stain-HE/PAS/JMS/Trichrome/immuno
Kidney-dissociated suspension- cells/nuclei-RNA/protein

Once a specimen ID is registered with basic metadata, the user can choose the samples associated with that and add derivatives (how many different tissue pieces made from the parent tissue, what was further derived from them such block, RNA, protein, metabolites etc) and how many aliquots (example-sections or slides, number of RNA aliquots) are made so for subsequent distributions these can be tracked and inventory kept."

For this use case, we can seperate the examples based on categories:

• Freezing methods:
  o OCT block dry ice
  o LN2- frozen
  o RNAlater
• Fixation:
  o paraffin block
  o cryopreserved
• Section:
  o RNA
  o Protein
  o DNA
  o Metabolite
• Staining
  o HE
  o Immune
  o PAS
  o JMS
  o Trichrome
• Dissociated suspension
  o Cell
  o Nuclei-RNA
  o Protein
• Number of aliquots

We may also use the Ontology for BioBanking: http://www.ontobee.org/ontology/OBIB. However, it appears OBIB is not sufficient to handle this issue. We may contact and collaborate with them. Also, such a study may become part of the KTAO. Any suggestions and comments?