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Table 1 Definition of new classes

From: Nanopublications for exposing experimental data in the life-sciences: a Huntington’s Disease case study

Class

URI

Definition

subclass of

subclass of URI

chromatin_region

biosemantics:chromatin_region

A region of chromatin, likely to

biological_region

so:SO_0001411

  

be involved in a biological process

  

chromatin_state

biosemantics:chromantin_state

Annotation of chromatin states, defined by

feature_attribute

so:SO_0000733

  

combinations of chromatin modification patterns

  
  

(described in publication by Ernst et al. Nature, 2011)

  

active_promoter

biosemantics:active_promoter

Open chromatin region, associated with promoters,

chromatin_state

biosemantics:chromatin_state

  

transcriptionally active, defined by the most highly

  
  

observed chromatin marks : H3K4me2,H3K4me3, H3K27ac,

  
  

H3K9ac

  

weak_promoter

biosemantics:weak_promoter

Open chromatin region, associated with promoters,

chromatin_state

biosemantics:chromatin_state

  

weak transcription activity, defined by the most highly

  
  

observed chromatin marks : H3K4me1, H3K4me2,H3K4me3,

  
  

H3K9ac

  

poised_promoter

biosemantics:poised_promoter

Open chromatin region, associated with promoters,

chromatin_state

biosemantics:chromatin_state

  

described as a bivalent domain that has strong signals

  
  

of both active and inactive histone marks. Most highly

  
  

observed histone marks: H3K27me3, H3K4me2, H3K4me3

  

heterochromatic

biosemantics:heterochromatic

Closed chromatin formation, transcriptionally inactive.

chromatin_state

biosemantics:chromatin_state

  

It is associated with none histone marks

  
  1. Prefix biosemantics: http://rdf.biosemantics.org/ontologies/chromatin#.
  2. Prefix so: http://purl.obolibrary.org/obo/.