This page describes the v1 Namespaces. For the most recent version, please see http://resource.belframework.org/belframework/latest-release/namespace/

The BEL Framework includes the following Namespaces.

Gene, RNA, and Protein Abundances

The following Namespaces provide standard vocabularies for designating gene, microRNA, RNA, and protein abundances. Values in the gene vocabularies can also be used to specify abundances of the corresponding RNA and protein coded for by the gene.

Entrez Gene – Identifiers

The NCBI standard for identifying genes by unique identification number. These identifiers can be used to specify gene, microRNA, RNA, and protein abundances. The current version provides identifiers for the following species only:

Homo sapiens, Mus musculus, Rattus norvegicus

Suggested Namespace Identifier:

EGID

Definition

BEL Script

DEFINE NAMESPACE EGID AS URL "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns" 
 	 bel:prefix="EGID"/>
</bel:namespaceGroup>

HUGO Gene Nomenclature Committee – Symbols

Standard approved gene symbols and synonyms for Humans. These identifiers can be used to specify gene, microRNA, RNA, and protein abundances.
Suggested Namespace Identifier:

HGNC

Definition

BEL Script

DEFINE NAMESPACE HGNC AS URL "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns"
     bel:prefix="HGNC"/>
</bel:namespaceGroup>

Mouse Genome Informatics – Symbols

Standard approved gene symbols and synonyms for Mouse. These identifiers can be used to specify gene, microRNA, RNA, and protein abundances.
Suggested Namespace Identifier:

MGI

Definition

BEL Script

DEFINE NAMESPACE MGI AS URL "http://resource.belframework.org/belframework/1.0/namespace/mgi-approved-symbols.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/mgi-approved-symbols.belns"
     bel:prefix="MGI"/>
</bel:namespaceGroup>

Rat Genome Database – Symbols

Standard approved gene symbols and synonyms for Rat. These identifiers can be used to specify gene, microRNA, RNA, and protein abundances. Suggested Namespace Identifier:

RGD

Definition

BEL Script

DEFINE NAMESPACE RGD AS URL "http://resource.belframework.org/belframework/1.0/namespace/rgd-approved-symbols.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/rgd-approved-symbols.belns"
 	 bel:prefix="RGD"/>
</bel:namespaceGroup>

Swiss-Prot – Accession Numbers

Swiss-Prot protein database referenced through Swiss-Prot Accession Numbers. These identifiers can be used to specify gene, protein, and RNA abundances.
Suggested Namespace Identifier:

SPAC

Definition

BEL Script

DEFINE NAMESPACE SPAC AS URL "http://resource.belframework.org/belframework/1.0/namespace/swissprot-accession-numbers.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/swissprot-accession-numbers.belns"
 	 bel:prefix="SPAC"/>
</bel:namespaceGroup>

Swiss-Prot – Entry Names

Swiss-Prot protein database referenced through Swiss-Prot Entry Names. These identifiers can be used to specify gene, protein, and RNA abundances.
Suggested Namespace Identifier:

SP

Definition

BEL Script

DEFINE NAMESPACE SP AS URL "http://resource.belframework.org/belframework/1.0/namespace/swissprot-entry-names.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/swissprot-entry-names.belns"
 	 bel:prefix="SP"/>
</bel:namespaceGroup>

Affymetrix Microarray Namespaces

The following Namespaces provide identifiers for probe sets in Affymetrix arrays or array sets. These identifiers can be used to specify RNA abundances.
Suggested Namespace Identifiers:

HGU133P2 (Human Genome U133 Plus 2.0 Array)
HGU133AB (Human Genome U133 Set)
HGU95AV2 (Human Genome U95Av2 Array)
MG4302 (Mouse Genome 430 2.0 Array)
MG430A2 (Mouse Genome 430A 2.0 Array)
MG430AB (Mouse Expression Set 430)
MGU74ABC (Murine Genome U74v2 Set)
RG2302 (Rat Genome 230 2.0 Array)
RG230AB (Rat Expression Set 230)

Definition

BEL Script (Human Genome U133 Plus 2.0 Array)

DEFINE NAMESPACE HGU133P2 AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133-plus2.belns"

BEL Script (Human Genome U133 Set)

DEFINE NAMESPACE HGU133AB AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133ab.belns"

BEL Script (Human Genome U95Av2 Array)

DEFINE NAMESPACE HGU95AV2 AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u95av2.belns"

BEL Script (Mouse Genome 430 2.0 Array)

DEFINE NAMESPACE MG4302 AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430-2.belns"

BEL Script (Mouse Genome 430A 2.0 Array)

DEFINE NAMESPACE MG430A2 AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430a-2.belns"

BEL Script (Mouse Expression Set 430)

DEFINE NAMESPACE MG430AB AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-moe430ab.belns"

BEL Script (Murine Genome U74v2 Set)

DEFINE NAMESPACE MGU74ABC AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-mg-u74abc.belns"

BEL Script (Rat Genome 230 2.0 Array)

DEFINE NAMESPACE RG2302 AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-rat230-2.belns"

BEL Script (Rat Expression Set 230)

DEFINE NAMESPACE RG230AB AS URL "http://resource.belframework.org/belframework/1.0/namespace/affy-rae230ab-2.belns"

XBEL (Human Genome U133 Plus 2.0 Array)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133-plus2.belns" 
	 bel:prefix="HGU133P2"/>
</bel:namespaceGroup>

XBEL (Human Genome U133 Set)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133ab.belns" 
	 bel:prefix="HGU133AB"/>
</bel:namespaceGroup>

XBEL (Human Genome U95Av2 Array)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u95av2.belns" 
	 bel:prefix="HGU95AV2"/>
</bel:namespaceGroup>

XBEL (Mouse Genome 430 2.0 Array)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430-2.belns" 
	 bel:prefix="MG4302"/>
</bel:namespaceGroup>

XBEL (Mouse Genome 430A 2.0 Array)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430a-2.belns"
	 bel:prefix="MG430A2"/>
</bel:namespaceGroup>

XBEL (Murine Genome U74v2 Set)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-mg-u74abc.belns" 
	 bel:prefix="MGU74ABC"/>
</bel:namespaceGroup>

XBEL (Rat Genome 230 2.0 Array)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-rat230-2.belns" 
	 bel:prefix="RG2302"/>
</bel:namespaceGroup>

XBEL (Rat Expression Set 230)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/affy-rae230ab-2.belns" 
	 bel:prefix="RG230AB"/>
</bel:namespaceGroup>

Molecular Abundances

The following Namespaces provide standard vocabularies for designating molecule abundances.

Chemical Entries of Biological Interest – Identifiers

Chemical Entities of Biological Interest (ChEBI) database referenced through the standard ChEBI identifier.
Suggested Namespace Identifier:

CHEBIID

Definition

BEL Script

DEFINE NAMESPACE CHEBIID AS URL "http://resource.belframework.org/belframework/1.0/namespace/chebi-ids.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/chebi-ids.belns" 
	 bel:prefix="CHEBIID"/>
</bel:namespaceGroup>

Chemical Entries of Biological Interest – Names

Chemical Entities of Biological Interest (ChEBI) database referenced through the standard name for each compound.
Suggested Namespace Identifier:

CHEBI

Definition

BEL Script

DEFINE NAMESPACE CHEBI AS URL "http://resource.belframework.org/belframework/1.0/namespace/chebi-names.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/chebi-names.belns"
	 bel:prefix="CHEBI"/>
</bel:namespaceGroup>

Biological Processes and Pathologies

The following Namespaces provide standard vocabularies for identifying biological processes such as diseases and pathologies. These identifiers can be used to specify biological processes and pathologies.

Gene Ontology (GO) Biological Process – Names

Gene Ontology database for biological processes referenced through the standard name.
Suggested Namespace Identifier:

GO

Definition

BEL Script

DEFINE NAMESPACE GO AS URL "http://resource.belframework.org/belframework/1.0/namespace/go-biological-processes-names.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/go-biological-processes-names.belns"
	 bel:prefix="GO"/>
</bel:namespaceGroup>

Gene Ontology (GO) Biological Process – Accession Numbers

Gene Ontology database for biological processes referenced through the standard GO accession number.
Suggested Namespace Identifier:

GOAC

Definition

BEL Script

DEFINE NAMESPACE GOAC AS URL "http://resource.belframework.org/belframework/1.0/namespace/go-biological-processes-accession-numbers.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/go- \
	 biological-processes-accession-numbers.belns" bel:prefix="GOAC"/>
</bel:namespaceGroup>

Medical Subject Headings (Disease)

U.S. National Library of Medicine provided vocabulary for disease. This Namespace provides the Main Heading for each disease in the Diseases [C] tree. These identifiers can be used to specify pathologies. Suggested Namespace Identifier:

MESHD

Definition

BEL Script

DEFINE NAMESPACE MESHD AS URL "http://resource.belframework.org/belframework/1.0/namespace/mesh-diseases.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/mesh-diseases.belns" 
	 bel:prefix="MESHD"/>
</bel:namespaceGroup>

Medical Subject Headings (Phenomena & Processes)

U.S. National Library of Medicine provided vocabulary for Phenomena and Processes. This Namespace provides the Main Heading for each biological process and phenomena in the Phenomena and Processes [G] tree. These identifiers can be used to specify biological processes. Suggested Namespace Identifier:

MESHBP

Definition

BEL Script

DEFINE NAMESPACE MESHBP AS URL "http://resource.belframework.org/belframework/1.0/namespace/mesh-biological-processes.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/mesh-biological-processes.belns"
 	 bel:prefix="MESHBP"/>
</bel:namespaceGroup>

Named Complex and Family Abundances

The following Namespaces provide standard vocabularies for encoding scientific findings in BEL, but for which there is no obvious standard vocabulary. These Namespaces are provided and managed by Selventa as part of the BEL Framework infrastructure.

Protein Families

Categorizes proteins into functional families identifiable by a protein family name. There is one of these Namespaces for each Human, Mouse and Rat species. These identifiers can be used to specify protein abundances. Suggested Namespace Identifiers:

PFH (Human), PFM (Mouse), PFR (Rat)

Definition

BEL Script (Human)

DEFINE NAMESPACE PFH AS URL "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-protein-families.belns"

BEL Script (Mouse)

DEFINE NAMESPACE PFM AS URL "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-protein-families.belns"

BEL Script (Rat)

DEFINE NAMESPACE PFR AS URL "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-protein-families.belns"

XBEL (Human)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-protein-families.belns" 
	 bel:prefix="PFH"/>
</bel:namespaceGroup>

XBEL (Mouse)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-protein-families.belns" 
	 bel:prefix="PFM"/>
</bel:namespaceGroup>

XBEL (Rat)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-protein-families.belns" 
	 bel:prefix="PFR"/>
</bel:namespaceGroup>

Named Complexes

Provides commonly used names for some commonly occurring complexes. There is one of these Namespaces for each Human, Mouse and Rat species. These identifiers can be used to specify complex abundances. Suggested Namespace Identifiers:

NCH (Human), NCM (Mouse), NCR (Rat)

Definition

BEL Script (Human)

DEFINE NAMESPACE NCH AS URL "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-complexes.belns"

BEL Script (Mouse)

DEFINE NAMESPACE NCM AS URL "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-complexes.belns"

BEL Script (Rat)

DEFINE NAMESPACE NCR AS URL "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-complexes.belns"

XBEL (Human)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-complexes.belns"
	 bel:prefix="NCH"/>
</bel:namespaceGroup>

XBEL (Mouse)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-complexes.belns" 
	 bel:prefix="NCM"/>
</bel:namespaceGroup>

XBEL (Rat)

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-complexes.belns"
	 bel:prefix="NCR"/>
</bel:namespaceGroup>

Other Namespaces

The following Namespaces are not associated with a particular biological domain.

Medical Subject Headings (Cellular Locations)

U.S. National Library of Medicine provided vocabulary for cellular locations. This Namespace provides the Main Heading for each cellular location in the Cell structure sub-branch [A11.284] of the Anatomy [A] tree. These identifiers can be used within translocation terms and as abundances. Suggested Namespace Identifier:

MESHCL

Definition

BEL Script

DEFINE NAMESPACE MESHCL AS URL "http://resource.belframework.org/belframework/1.0/namespace/mesh-cellular-locations.belns"

XBEL

<bel:namespaceGroup>
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/mesh-cellular-locations.belns" 
	 bel:prefix="MESHCL"/>
</bel:namespaceGroup>

Gene Ontology (GO) Cellular Component – Names

Gene Ontology database cellular components referenced through term names.
Suggested Namespace Identifier:

GOCCTERM

Definition

BEL Script

DEFINE NAMESPACE GOCCTERM AS URL "http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-terms.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-terms.belns"
	 bel:prefix="GOCCTERM"/>
</bel:namespaceGroup>

Gene Ontology (GO) Cellular Component – Accession Numbers

Gene Ontology database cellular components referenced through accession numbers.
Suggested Namespace Identifier:

GOCCACC

Definition

BEL Script

DEFINE NAMESPACE GOCCACC AS URL "http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-accession-numbers.belns"

XBEL

<bel:namespaceGroup> 
	<bel:namespace 
	 bel:resourceLocation="http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-accession-numbers.belns"
	 bel:prefix="GOCCTERM"/>
</bel:namespaceGroup>