MeSH resources (2026 update)

mesh-builds turns NLM MeSH XML and tree files into three R-ready tables: a descriptor thesaurus (terms and concepts), a supplementary concept thesaurus (SCR terms), and a tree table that links descriptors to tree numbers and high-level category labels. The pipeline is in descriptor-records-trees.Rmd; the RDS outputs power the R package puremoe.

May 2026: built from MeSH desc2026, supp2026, and mtrees2026 (newterms release).

MeSH ontology

Based on MeSH files desc2026, mtrees2026 & supp2026.

descriptor-terms

Raw data

readRDS('data/data_mesh_thesaurus.rds') |>
  head() |> knitr::kable()

DescriptorUI	DescriptorName	ConceptUI	TermUI	TermName	ConceptPreferredTermYN	IsPermutedTermYN	LexicalTag	RecordPreferredTermYN
D000001	Calcimycin	M0000001	T000002	Calcimycin	Y	N	NON	Y
D000001	Calcimycin	M0000001	T001124965	4-Benzoxazolecarboxylic acid, 5-(methylamino)-2-((3,9,11-trimethyl-8-(1-methyl-2-oxo-2-(1H-pyrrol-2-yl)ethyl)-1,7-dioxaspiro(5.5)undec-2-yl)methyl)-, (6S-(6alpha(2S*,3S*),8beta(R*),9beta,11alpha))-	N	N	NON	N
D000001	Calcimycin	M0353609	T000001	A-23187	Y	N	LAB	N
D000001	Calcimycin	M0353609	T000001	A 23187	N	Y	LAB	N
D000001	Calcimycin	M0353609	T000003	Antibiotic A23187	N	N	NON	N
D000001	Calcimycin	M0353609	T000003	A23187, Antibiotic	N	Y	NON	N

descriptor-tree-numbers

Raw data

readRDS('data/data_mesh_trees.rds') |>
  head() |> knitr::kable()

DescriptorUI	DescriptorName	tree_location	code	cats	mesh1	mesh2	tree1	tree2
D000001	Calcimycin	D02.355.291.933.125	D	Chemicals and Drugs	Organic Chemicals	Ethers	D02	D02.355
D000001	Calcimycin	D02.540.576.625.125	D	Chemicals and Drugs	Organic Chemicals	Lactones	D02	D02.540
D000001	Calcimycin	D03.633.100.221.173	D	Chemicals and Drugs	Heterocyclic Compounds	Heterocyclic Compounds, Fused-Ring	D03	D03.633
D000001	Calcimycin	D04.345.241.654.125	D	Chemicals and Drugs	Polycyclic Compounds	Macrocyclic Compounds	D04	D04.345
D000001	Calcimycin	D04.345.674.625.125	D	Chemicals and Drugs	Polycyclic Compounds	Macrocyclic Compounds	D04	D04.345
D000002	Temefos	D02.705.400.625.800	D	Chemicals and Drugs	Organic Chemicals	Organophosphorus Compounds	D02	D02.705

supplemental-terms

Raw data

readRDS('data/data_scr_thesaurus.rds') |>
  head() |> knitr::kable()

DescriptorUI	DescriptorName	ConceptUI	TermUI	TermName	ConceptPreferredTermYN	IsPermutedTermYN	LexicalTag	RecordPreferredTermYN
C000002	bevonium	M0040005	T070005	bevonium	Y	N	NON	Y
C000002	bevonium	M0040005	T000946882	2-(hydroxymethyl)-N,N-dimethylpiperidinium benzilate	N	N	NON	N
C000002	bevonium	M0040001	T070001	Acabel	Y	N	TRD	N
C000002	bevonium	M0040002	T070002	CG 201	Y	N	LAB	N
C000002	bevonium	M0307342	T337342	bevonium sulfate (1:1)	Y	N	NON	N
C000002	bevonium	M0402330	T070003	bevonium methyl sulfate	Y	N	NON	N

Maintained outputs

list.files('data', pattern = 'data_.*\\.rds$')
# [1] "data_mesh_thesaurus.rds" "data_mesh_trees.rds" "data_scr_thesaurus.rds"

Notes & useful links:

• MeSH XML data elements

• XML elements as RDF

• Utility functions

• Supplementary Concept Records

‘SCR records are created for some chemicals, drugs, and other concepts such as rare diseases. They are labeled as “MeSH Supplementary Concept Data” and the unique ID begins with the letter “C.”’

‘Supplementary Concept Records - these are not full MeSH Headings and do not fall under the MeSH tree hierarchy. Many times they are used to identify substances that are not included in the MeSH terms.’

‘These do not belong to the controlled vocabulary as such and are not used for indexing MEDLINE articles; instead they enlarge the thesaurus and contain links to the closest fitting descriptor to be used in a MEDLINE search. Many of these records describe chemical substances.’