MariaKim at 17:30, 15 September 2025

2025-09-15T17:30:22Z

← Older revision		Revision as of 17:30, 15 September 2025
Line 15:		Line 15:
	<nowiki>---------------------------------------------------------------------------</nowiki>		<nowiki>---------------------------------------------------------------------------</nowiki>

	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'''

DaniallMasood: New page for keywords

2025-09-15T16:52:00Z

New page for keywords

New page

<nowiki>---------------------------------------------------------------------------</nowiki>

== BiomarkerKB Controlled Vocabulary ==
Biomarker Knowledgebase Project

<nowiki>---------------------------------------------------------------------------</nowiki>

=== 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

<nowiki>---------------------------------------------------------------------------</nowiki>

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

<nowiki>---------------------------------------------------------------------------</nowiki>

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; <nowiki>https://biomarkerkb.org/canonical/AN4824</nowiki>

//

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; <nowiki>https://biomarkerkb.org/canonical/AN6278</nowiki>

//

ID metabolite

AC BM-0003

DE A small molecule involved in metabolism.

HI metabolite

EQ CHEBI:25212; metabolite

EX UREA; <nowiki>https://biomarkerkb.org/canonical/AN6341</nowiki>

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; <nowiki>https://biomarkerkb.org/canonical/AN6729</nowiki>

//

ID DNA

AC BM-0005

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

HI DNA

EQ MESH:D004247; DNA

EX cfDNA; <nowiki>https://biomarkerkb.org/canonical/AN6380</nowiki>

//

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; <nowiki>https://biomarkerkb.org/canonical/AN6498</nowiki>

//

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; <nowiki>https://biomarkerkb.org/canonical/AN6280</nowiki>

//

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; <nowiki>https://biomarkerkb.org/canonical/AN6187</nowiki>

//

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 <nowiki>https://data.oncomx.org/allbiomarkers/biomarker/A0076</nowiki>

//

=== Biomarker Reporting Terms Controlled Vocabulary File ===
Biomarker Knowledgebase Project

<nowiki>---------------------------------------------------------------------------</nowiki>

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

<nowiki>---------------------------------------------------------------------------</nowiki>

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

<nowiki>---------------------------------------------------------------------------</nowiki>

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; <nowiki>https://biomarkerkb.org/canonical/AN6278</nowiki>

//

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; <nowiki>https://biomarkerkb.org/canonical/AN6351</nowiki>

//

ID presence of

AC RT-0006

DE Indicates that the assessed entity is present.

HI presence

EX presence of rs180177132 mutation in PALB2;

EX <nowiki>https://biomarkerkb.org/canonical/AV9568</nowiki>

//

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; <nowiki>https://biomarkerkb.org/canonical/BB1486</nowiki>

//

Controlled Vocabulary and Keywords - Revision history

MariaKim at 17:30, 15 September 2025

DaniallMasood: New page for keywords