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This page describes the v1 Annotations provided by OpenBEL. Please see http://resource.belframework.org/belframework/latest-release/annotation/ for the most recent version

Annotations provided by OpenBEL

The following Annotations are maintained as .belanno files at http://resource.belframework.org/belframework/1.0/annotation/. Each .belanno file contains a list of values that can be used with the that Annotation type. These annotations must be defined in the header of the BEL document.

Body Region

The BodyRegion Annotation Type is used to annotate a BEL Statement with a body region that the corresponding BEL Statements were observed in. The BEL Framework BodyRegion Annotation Type uses the Body Regions [A01] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch

 Definition

BEL Script

DEFINE ANNOTATION BodyRegion AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-body-region.belanno" 

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="BodyRegion"
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-body-region.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

 SET BodyRegion = "Breast" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="BodyRegion">Breast</bel:annotation>
</bel:annotationGroup> 

Cardiovascular System

The CardiovascularSystem Annotation Type is used to annotate a BEL Statement with a part of the cardiovascular system that the corresponding BEL Statements were observed in. The BEL Framework CardiovascularSystem Annotation Type uses the Cardiovascular System [A07] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

 DEFINE ANNOTATION CardiovascularSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-cardiovascular-system.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="CardiovascularSystem"
 	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-cardiovascular-system.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET CardiovascularSystem = "Endocardium" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="CardiovascularSystem ">Endocardium</bel:annotation>
</bel:annotationGroup>

Cell

The Cell Annotation Type is used to annotate a BEL Statement with a cell type that the corresponding BEL Statements were observed in. The BEL Framework Cell Annotation Type uses the Cell [A11] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch excluding [A11.284].

 Definition

BEL Script

DEFINE ANNOTATION Cell AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-cell.belanno" 

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="Cell"
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-cell.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET Cell = "Epithelial" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="Cell">Epithelial</bel:annotation>
</bel:annotationGroup>

Cell Line

The CellLine Annotation Type is used to annotate a BEL Statement with a cell line that the corresponding BEL Statements were observed in. The BEL Framework CellLine Annotation Type uses American Type Culture Collection (ATCC) Cell Lines.

 Definition

BEL Script

DEFINE ANNOTATION CellLine AS URL "http://resource.belframework.org/belframework/1.0/annotation/atcc-cell-line.belanno" 

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="CellLine" 
 	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/atcc-cell-line.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET CellLine = "Calu-6" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="CellLine">Calu-6</bel:annotation>
</bel:annotationGroup> 

Cell Structure

The CellStructure Annotation Type is used to annotate a BEL Statement with a cellular substructure that the corresponding BEL Statements were observed in. The BEL Framework CellStructure Annotation Type uses the Cell Structure [A11.284] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION CellStructure AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-cell-structure.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="CellStructure" 
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-cell-structure.belanno"/>
</bel:annotationDefinitionGroup
 Examples

BEL Script

SET CellStructure = "Cell Nucleus"

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="CellStructure">Cell Nucleus</bel:annotation>
</bel:annotationGroup>

Digestive System

The DigestiveSystem Annotation Type is used to annotate a BEL Statement with a component of the digestive system that the corresponding BEL Statements were observed in. The BEL Framework DigestiveSystem Annotation Type uses the Digestive System [A03] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION DigestiveSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-digestive-system.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="DigestiveSystem" 
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-digestive-system.belanno"/>
</bel:annotationDefinitionGroup>
 Examples

BEL Script

SET DigestiveSystem = "Intestine, Large"


XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="DigestiveSystem">Intestine, Large</bel:annotation>
</bel:annotationGroup> 

Disease

The Disease Annotation Type is used to annotate a BEL Statement with a disease that the corresponding BEL Statements were associated with. The BEL Framework Disease Annotation Type uses the Diseases [C] branch of the Medical Subject Headings (MeSH).

 Definition

BEL Script

DEFINE ANNOTATION Disease AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-disease.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="Disease" 
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-disease.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET Disease = "Cardiomyopathies" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="Disease">Cardiomyopathies</bel:annotation>
</bel:annotationGroup> 

Embryonic Structure

The EmbryonicStructrure Annotation Type is used to annotate a BEL Statement with an embryonic structure that the corresponding BEL Statements were observed within. The BEL Framework EmbryonicStructure Annotation Type uses the Embryonic Structures [A16] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION EmbryonicStructure AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-embryonic-structure.belanno

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="EmbryonicStructure" 
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-embryonic-strucuture.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET EmbryonicStructure = "Amniotic Fluid" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="EmbryonicStructure">Amniotic Fluid</bel:annotation>
</bel:annotationGroup> 

Endocrine System

The EndocrineSystem Annotation Type is used to annotate a BEL Statement with the endocrine system that the corresponding BEL Statements were observed within. The BEL Framework EndocrineSystem Annotation Type uses the Endocrine System [A06] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION EndocrineSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-endocrine-system.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="EndocrineSystem"
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-endocrine-system.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET EndocrineSystem = "Adrenal Cortex" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="EndocrineSystem">Adrenal Cortex</bel:annotation>
</bel:annotationGroup>

Fluid and Secretion

The FluidAndSecretion Annotation Type is used to annotate a BEL Statement with the fluids and secretions that the corresponding BEL Statements were observed within. The BEL Framework FluidAndSecretion Annotation Type uses the Fluids and Secretions [A12] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION FluidAndSecretion AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-fluid-and-secretion.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="FluidAndSecretion" 
 	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-fluid-and-secretion.belanno"/>
</bel:annotationDefinitionGroup>
 Examples

BEL Script

SET FluidAndSecretion = "Sputum"

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="FluidAndSecretion">Sputum</bel:annotation>
</bel:annotationGroup>

Hemic and Immune System

The HemicAndImmuneSystem Annotation Type is used to annotate a BEL Statement with the hemic and immune system components that the corresponding BEL Statements were observed within. The BEL Framework HemicAndImmuneSystem Annotation Type uses the Hemic and Immune Systems [A15] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION HemicAndImmuneSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-hemic-and-immune-system.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="HemicAndImmuneSystem" 
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-hemic-and-immune-system.belanno"/>
</bel:annotationDefinitionGroup>
 Examples

BEL Script

SET HemicAndImmuneSystem = "Erythrocytes" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="HemicAndImmuneSystem">Erythrocytes</bel:annotation>
</bel:annotationGroup>

Integumentary System

The IntegumentarySystem Annotation Type is used to annotate a BEL Statement with the integumentary system components that the corresponding BEL Statements were observed within. The BEL Framework IntegumentarySystem Annotation Type uses the Integumentary System [A17] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION IntegumentarySystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-integumentary-system.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="IntegumentarySystem"
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-integumentary-system.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET IntegumentarySystem = "Hair Follicle" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="IntegumentarySystem">Hair Follicle</bel:annotation>
</bel:annotationGroup> 

Musculoskeletal System

The MusculoskeletalSystem Annotation Type is used to annotate a BEL Statement with the musculoskeletal system components that the corresponding BEL Statements were observed within. The BEL Framework MusculoskeletalSystem Annotation Type uses the Musculoskeletal System [A02] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION MusculoskeletalSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-musckuloskeleta-system.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="MusculoskeletalSystem"
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-musckuloskeleta-system.belanno"/>
</bel:annotationDefinitionGroup>
 Examples

BEL Script

SET MusculoskeletalSystem = "Muscle, Smooth" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="MusculoskeletalSystem">Muscle, Smooth</bel:annotation>
</bel:annotationGroup> 

Nervous System

The NervousSystem Annotation Type is used to annotate a BEL Statement with the nervous system component that the corresponding BEL Statements were observed within. The BEL Framework NervousSystem Annotation Type uses the Nervous System [A08] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION NervousSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-nervous-system.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="NervousSystem"
 	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-nervous-system.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET NervousSystem = "Astrocytes" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="NervousSystem">Astrocytes</bel:annotation>
</bel:annotationGroup> 

Respiratory System

The RespiratorySystem Annotation Type is used to annotate a BEL Statement with the respiratory system component that the corresponding BEL Statements were observed within. The BEL Framework RespiratorySystem Annotation Type uses the Respiratory System [A04] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION RespiratorySystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-respiratory-system.belanno" 

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="RespiratorySystem"
 	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-nervous-system.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET RespiratorySystem = "Bronchioles" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="RespiratorySystem">Bronchioles</bel:annotation>
</bel:annotationGroup> 

Sense Organ

The SenseOrgan Annotation Type is used to annotate a BEL Statement with the sense organ that the corresponding BEL Statements were observed within. The BEL Framework SenseOrgan Annotation Type uses the Sense Organs [A09] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION SenseOrgan AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno" 

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="SenseOrgan"
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno"/>
</bel:annotationDefinitionGroup> 
 Example

BEL Script

SET SenseOrgan = "Meibomian Glands" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="SenseOrgan">Meibomian Glands</bel:annotation>
</bel:annotationGroup>

Species

The Species Annotation Type is used to annotate a BEL Statement with the species that the corresponding BEL Statements were observed in. The BEL Framework Species Annotation Type uses NCBI Taxonomy IDs in order to standardize the format and representation of species annotations.

 Definition

BEL Script

DEFINE ANNOTATION Species AS URL "http://resource.belframework.org/belframework/1.0/annotation/species-taxonomy-id.belanno" 

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="Species" 
 	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/species-taxonomy-id.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET Species = "9606" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="Species">9606</bel:annotation>
</bel:annotationGroup> 

Stomatognathic System

The StomatognathicSystem Annotation Type is used to annotate a BEL Statement with the stomatognathic system component that the corresponding BEL Statements were observed within. The BEL Framework StomatognathicSystem Annotation Type uses the Stomatognathic System [A14] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION StomatognathicSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="StomatognathicSystem"
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET StomatognathicSystem = "Masseter Muscle" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="StomatognathicSystem">Masseter Muscle</bel:annotation>
</bel:annotationGroup> 

Tissue

The Tissue Annotation Type is used to annotate a BEL Statement with the tissue type that the corresponding BEL Statements were observed within. The BEL Framework Tissue Annotation Type uses the Tissues [A10] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION Tissue AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno" 

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition bel:id="Tissue" 
	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno"/>
</bel:annotationDefinitionGroup>
 Examples

BEL Script

SET Tissue = "Myoblasts, Cardiac" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="Tissue">Myoblasts, Cardiac</bel:annotation>
</bel:annotationGroup> 

Urogenital System

The UrogenitalSystem Annotation Type is used to annotate a BEL Statement with the urogenital system component that the corresponding BEL Statements were observed within. The BEL Framework UrogenitalSystem Annotation Type uses the Urogenital System [A05] sub-branch of the Medical Subject Headings (MeSH) Anatomy [A] branch.

 Definition

BEL Script

DEFINE ANNOTATION UrogenitalSystem AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno"

XBEL

<bel:annotationDefinitionGroup>
	<bel:externalAnnotationDefinition 
	 bel:id="UrogenitalSystem" 
 	 bel:url="http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno"/>
</bel:annotationDefinitionGroup> 
 Examples

BEL Script

SET UrogenitalSystem = "Kidney" 

XBEL

<bel:annotationGroup>
	<bel:annotation bel:refID="UrogenitalSystem">Kidney</bel:annotation>
</bel:annotationGroup> 
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