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Overview

The BEL Namespace (.belns) files contain information about the BEL functions that can be used with each value. This 'encoding' information is specified after each value in the namespace, delimited with '|' and is used by the BEL Framework during compilation of BEL documents to enforce BEL function semantics and generate warnings.

  • G - geneAbundance()
  • R - rnaAbundance()
  • P - proteinAbundance()
  • M - microRNAabundance()
  • A - abundance()
  • B - biologicalProcess()
  • O - pathology()
  • C - complex()

This page provides information about how the encodings were determined for BEL namespaces (see also https://github.com/OpenBEL/resource-generator), based on information provided by the naming authority.

EntrezGene

from "type_of_gene"

type_of_geneBEL encoding
protein-codingGRP
miscRNAGR
ncRNAGR
snoRNAGR
snRNAGR
tRNAGR
scRNAGR
otherG
pseudoGR
unknownG (plan change to GRP)
rRNAGR


microRNAs are currently included in "ncRNA". More information is required to assign as "GM"/"GRM". Plan to use type_of_gene = "ncRNA" AND description begins with "microRNA" for future versions of the EntrezGene namespace.

HGNC

from "Locus Type":

Locus TypeBEL Encoding
complex locus constituentGRP
endogenous retrovirusG
fragile siteG
gene with protein productGRP
immunoglobulin geneGRP
immunoglobulin pseudogeneGR
phenotype onlyG
protocadherinGRP
pseudogeneGR
readthroughGR
regionG
RNA, clusterGR
RNA, long non-codingGR
RNA, microGRM
RNA, miscGR
RNA, pseudogeneGR
RNA, ribosomalGR
RNA, small cytoplasmicGR
RNA, small nuclearGR
RNA, small nucleolarGR
RNA, transferGR
RNA, vaultGR
RNA, YGR
T cell receptor geneGRP
T cell receptor pseudogeneGR
transposable elementG
unknownGRP
virus integration siteG
withdrawnOMIT from .belns

MGI

from "Feature Type":

Including only those associated with Marker Types 'Gene' and 'Pseudogene'. See http://www.informatics.jax.org/userhelp/GENE_feature_types_help.shtml for descriptions of Feature Types.

Feature TypeBEL Encoding
geneGRP
gene segmentG
heritable phenotypic markerG
lincRNA geneGR
miRNA geneGRM
non-coding RNA geneGR
polymorphic pseudogeneGRP
protein coding geneGRP
pseudogeneGR
pseudogenic gene segmentGR
pseudogenic regionGR
RNase MRP RNA geneGR
RNase P RNA geneGR
rRNA geneGR
scRNA geneGR
snoRNA geneGR
snRNA geneGR
SRP RNA geneGR
telomerase RNA geneGR
tRNA geneGR
unclassified geneGRP
unclassified non-coding RNA geneGR

RGD

From "GENE_TYPE":

GENE_TYPEBEL Encoding
geneGRP
miscrnaGR
predicted-highGRP
predicted-lowGRP
predicted-moderateGRP
protein-codingGRP
pseudoGR
snrnaGR
trnaGR
rrnaGR

microRNAs are currently included in "ncrna" (previously were "miscrna". More information is required to assign as "GM"/"GRM". Plan to use GENE_TYPE = "miscrna" OR GENE_TYPE = "ncrna" AND NAME begins with "microRNA" for future versions of the BEL RGD namespace.

A few RGD entries have an empty string - no assigned type, and will be conservatively assigned as 'GRP'.

SwissProt

SwissProt is a protein database - all entries are given the encoding "GRP"

Affymetrix Probe Set Namespaces

These namespaces are probe set IDs for RNA measurements - all entries should be given the encoding "R". Another namespace should be used for references to the Gene or Protein term.

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