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Entity identifiers

TwinCell names proteins in the interactome with a fixed string format. You will see these ids in API results, causal paths, and influence matrices.

Grammar

ENTITY_ID ::= SYMBOL "|" TYPE
SYMBOL    ::= HGNC-style gene symbol (2–20 characters)
TYPE      ::= "PROTEIN"
  • Separator — a single pipe character (|), not a slash or space.
  • TYPE — for targets and protein nodes, always PROTEIN (uppercase).
  • SYMBOL — standard HGNC gene symbols: letters, digits, and hyphens; must start with a letter. Ensembl ids (ENSG…), RefSeq accessions (NM_…), and similar identifiers are not valid.

Valid examples

Id Role
BRAF|PROTEIN Target protein
STAT3|PROTEIN Target protein
TYK2|PROTEIN Protein on a causal path

Bare symbol convenience (SDK)

When you pass a target to target_validation() or related methods, you may supply either the full id or the gene symbol alone:

tc.target_validation(target="BRAF", ...)      # SDK sends BRAF|PROTEIN
tc.target_validation(target="BRAF|PROTEIN", ...)

This shortcut applies only to protein targets, not to DEG lists.

Invalid examples

Value Problem
BRAF Missing |PROTEIN when calling the REST API directly (use the SDK convenience above, or send the full id)
braf|PROTEIN Symbols are case-sensitive; use BRAF
ENSG00000157764|PROTEIN Ensembl id, not an HGNC symbol
BRAF|RNA Targets must be PROTEIN entities
BRAF-PROTEIN Wrong separator (must be |)
NOTATARGET|PROTEIN Valid format but unknown to the interactome → failed prediction with target_not_in_interactome