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Table 2 Cancer Genetics task entity types, reference resources, and definitions.

From: Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013

Type Reference Ontology ID
ORGANISM NCBI taxonomy CARO:0000012
Anatomical entity   
  ORGANISM SUBDIVISION Species-specific CARO:0000032
  ANATOMICAL SYSTEM anatomy CARO:0000011
  ORGAN resources (e.g. CARO:0000024
  MULTI-TISSUE STRUCTURE FMA), derived CARO:0000055
  TISSUE resources (e.g. CARO:0000043
  DEVELOPING ANATOMICAL STRUCTURE UBERON) UBERON:0005423
  CELL CL CARO:0000013
  CELLULAR COMPONENT GO-CC GO:0005575
  ORGANISM SUBSTANCE FMA etc. CARO:0000004
  IMMATERIAL ANATOMICAL ENTITY FMA etc. CARO:0000007
  PATHOLOGICAL FORMATION - -
  CANCER - -
Molecular entity   
  GENE OR GENE PRODUCT gene, protein, and SBO:0000246
  PROTEIN DOMAIN OR REGION related entity DBs SBO:0000493
  DNA DOMAIN OR REGION   SBO:0000493
  SIMPLE CHEMICAL ChEBI SBO:0000247
  AMINO ACID ChEBI CHEBI:33709
  1. The indentation of the types corresponds to is-a relations. The labels in italics are not annotated types but groupings defined only for organization.