Biomarker Entity Types Controlled Vocabulary

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BiomarkerKB Controlled Vocabulary

Biomarker Entity Types Controlled Vocabulary File

Biomarker Knowledgebase Project

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Description: Controlled vocabulary of biomarker entity types used in BiomarkerKB

Name:        biomarker_entity_types.txt

Release:     2025_07_16

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This document lists the biomarker entity types used in the BiomarkerKB

curation system. When a biomarker entity is paired with terms from

measurable.txt (increase, decrease, presence, absence, etc.), they form the

biomarker. The biomarker entity types are:

   * sequence variation

   * protein

   * metabolite

   * glycan

   * DNA

   * RNA

   * cell

   * lipid

   * image

Each entry consists of the following line codes:

 ----  ----------  ---------------------------  -------------------------------

 Code  Name        Content                      Occurrences

 ----  ----------  ---------------------------  -------------------------------

 ID    Identifier  Biomarker entity name        Once; starts an entry

 AC    Accession   Unique identifier (BM-xxxx)  Once

 DE    Definition  Definition/description       Once; line wrapping possible

 UF    Used For    Instructions for use         Once; line wrapping possible

 HI    Hierarchy                                Optional; zero or more

 SY    Synonym                                  Optional; zero or more

 EQ    Equivalent  External identifier with     Optional; zero or more

                     same meaning

 EX    Example     A biomarker that uses        Optional; zero or once; line

                     the indicated entity         wrapping possible

 NT    Notes                                    Optional; zero or once; line

                                                  wrapping possible

 //    Terminator  End of entry                 Once; ends an entry

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ID   sequence variation

AC   BM-0001

DE   For polymers, any difference between the observed order of monomer units

DE   within a polymer chain and the order within a suitably comparable reference

DE   polymer.

UF   Entities that differ when specifically comparing sequence; includes

UF   polymorphisms and mutations of genetic material and proteins.

HI   sequence variation

EQ   SO:0001059; sequence_alteration

EX   presence of rs11571833 mutation in BRCA2;

EX   https://biomarkerkb.org/biomarker/AN7363-3

//

ID   protein

AC   BM-0002

DE   Amino acid chain formed by ribosome-mediated translation of a genetically-

DE   encoded mRNA, and any post-translationally modified derivatives.

UF   Entities that are composed, in whole or in part, of protein; includes

UF   protein complexes and mixed-composition entities such as glycoproteins.

HI   protein

EQ   MESH:D011506; Proteins

EQ   PR:000000001; protein

EX   Interleukin-6; https://biomarkerkb.org/canonical/AN6278

NT   Mixed-composition entities can get multiple entity-type tags; for example,a

NT   glycoprotein would be both ‘protein’ and ‘glycan’.

//

ID   metabolite

AC   BM-0003

DE   A small molecule involved in metabolism.

UF   Entities that are inputs to or outputs from metabolic reactions.

HI   metabolite

EQ   CHEBI:25212; metabolite

EX   UREA; https://biomarkerkb.org/canonical/AN6341

NT   MESH term for metabolite being requested.  

//

ID   glycan

AC   BM-0004

DE   Any oligosaccharide, polysaccharide or their derivatives consisting of

DE   monosaccharides or monosaccharide derivatives linked by glycosidic bonds.

UF   Entities that are composed, in whole or in part, of glycan; includes

UF   protein complexes and mixed-composition entities such as proteoglycans.

HI   glycan

EQ   CHEBI:167559

EX   N-glycan; https://biomarkerkb.org/canonical/AN6729

NT   Mixed-composition entities can get multiple entity-type tags; for example,a

NT   proteoglycan would be both ‘protein’ and ‘glycan’.

//

ID   DNA

AC   BM-0005

DE   A polymer of deoxyribose-containing nucleotides linked by phosphodiester

DE   bonds.

UF   Entities that are composed of DNA when measured in bulk, or that are direct

UF   or proxy measures of gene expression.

HI   DNA

EQ   MESH:D004247; DNA

EX   cfDNA; https://biomarkerkb.org/canonical/AN6380

//

ID   RNA

AC   BM-00096

DE   A polymer of ribose-containing nucleotides linked by phosphodiester bonds.

UF   Entities that are composed of RNA when measured in bulk, or that are direct

UF   or proxy measures of RNA expression.

HI   RNA

EQ   MESH:D012313; RNA

EX   miRNA-21; https://biomarkerkb.org/canonical/AN6498

//

ID   cell

AC   BM-0007

DE   An organism (or part thereof) that is a maximally connected compartment  

DE   surrounded by a plasma membrane.

UF   Entities that are cells; includes cases when ratios between cell types are

UF   measured.

HI   cell

EQ   MESH:D002477; Cells

EQ   CL:0000000; cell

EX   WBC; https://biomarkerkb.org/canonical/AN6280

//

ID   lipid

AC   BM-0008

DE   A class of biomolecules including fats, oils, and certain hormones.

UF   Entities that are lipids.

HI   lipid

EQ   MESH:D008055; Lipids

EQ   CHEBI:18059; lipid

EX   very long chain fatty acid; https://biomarkerkb.org/canonical/AN6187

//

ID   image  

AC   BM-0018  

DE   Any visual display of structural or functional patterns of organs or tissues for

DE   clinical evaluation.  

UF   Entities evaluated via the use of an image.

HI   image  

EQ   NCIT:C48179; Image

EX   presence of ground-glass opacity;

EX   https://data.oncomx.org/allbiomarkers/biomarker/A0076

NT   For type ‘image’, the entity that is being imaged would be indicated as the

NT   sample source.

//

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