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This document lists the biomarker entity types used in the BiomarkerKB | This document lists the biomarker entity types used in the BiomarkerKB curation system. When a biomarker entity is paired with measurable.txt terms (increase, decrease, presence, absence etc.), they form the biomarker. The biomarker entity types are: | ||
curation system. When a biomarker entity is paired with measurable.txt terms (increase, decrease, presence, absence etc.), they form the biomarker. The biomarker entity types are: | |||
''' * gene''' | ''' * gene''' | ||
Latest revision as of 17:30, 15 September 2025
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BiomarkerKB Controlled Vocabulary
Biomarker Knowledgebase Project
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Biomarker Entity Types Controlled Vocabulary File
Description: Controlled vocabulary of biomarker entity types used in BiomarkerKB.
Name: biomarker_entity_types.txt
Release: 2025_09_02
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This document lists the biomarker entity types used in the BiomarkerKB curation system. When a biomarker entity is paired with measurable.txt terms (increase, decrease, presence, absence etc.), they form the biomarker. The biomarker entity types are:
* gene
* 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
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
AC BM-0001
DE Nucleic acid sequences that function as units of heredity and which code for
DE the basic instructions for the development, reproduction, and maintenance
DE of an organism.
HI sequence
EQ MESH:D008969; Molecular Sequence Data
EQ SO:0000704; gene
EX BRCA1; https://biomarkerkb.org/canonical/AN4824
//
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.
HI protein
EQ MESH:D011506; Proteins
EQ PR:000000001; protein
EX Interleukin-6; https://biomarkerkb.org/canonical/AN6278
//
ID metabolite
AC BM-0003
DE A small molecule involved in metabolism.
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.
HI glycan
EQ CHEBI:167559
EX N-glycan; https://biomarkerkb.org/canonical/AN6729
//
ID DNA
AC BM-0005
DE A polymer of deoxyribose-containing nucleotides linked by phosphodiester bonds.
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.
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.
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.
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.
HI image
EQ NCIT:C48179; Image
EX presence of ground-glass opacity;
EX https://data.oncomx.org/allbiomarkers/biomarker/A0076
//
Biomarker Reporting Terms Controlled Vocabulary File
Biomarker Knowledgebase Project
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Description: Controlled vocabulary of standardized terms used to describe
biomarker status, behavior, or detection in curated data entries.
Name: measured.txt
Release: 2025_09_09
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This document lists the controlled reporting terms used to describe
biomarkers in the BiomarkerKB curation system. These nouns are used
in fields like `biomarker` to standardize natural language descriptions and
can be modified using adjectives (“significant”, “gradual”, etc).
These terms are classified into categories such as:
* increased
Each entry consists of the following line codes:
---- ---------- --------------------------- ---------------------------------
Code Name Content Occurrences
---- ---------- --------------------------- ---------------------------------
ID Identifier Reporting term Once; starts an entry
AC Accession Unique identifier (RT-xxxx) Once
DE Definition Definition/description 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 Optional; zero or once
NT Notes Optional; zero or once; line
wrapping possible
// Terminator End of entry Once; ends an entry
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ID increased
AC RT-0001
DE Indicates an assessed biomarker entity level is higher than normal by
DE a clinically relevant degree.
HI abundance
EQ PATO:0002300; increased quality
EX increased IL6 level; https://biomarkerkb.org/canonical/AN6278
//
ID decreased
AC RT-0002
DE Indicates an assessed biomarker entity level is lower than normal by
DE a clinically relevant degree.
HI abundance
EQ PATO:0002301; decreased quality
EX decreased albumin level; https://biomarkerkb.org/canonical/AN6351
//
ID presence of
AC RT-0006
DE Indicates that the assessed entity is present.
HI presence
EX presence of rs180177132 mutation in PALB2;
EX https://biomarkerkb.org/canonical/AV9568
//
ID difference
AC RT-0007
DE A statistic that is a subtraction of one quantity from another.
HI expression
EQ STATO:0000613; difference
EX differential expression of TNMD; https://biomarkerkb.org/canonical/BB1486
//