Extract MeSH mappings to external registries / vocabularies

[dhimmel]

MeSH includes some external mappings via the following predicates (from docs):

• meshv:registryNumber: A property of Concepts. A unique identifier from one of these sources: Enzyme Commission (Example: EC 2.4.2.17; Example for Partial enzyme number: EC 1.4.3.-); Chemical Abstracts Service (CAS) (Example: 7004-12-8); FDA Substance Registration System Unique Identifier (UNII) in 10-character format (Example: R16CO5Y76E); or the value of 0 if no match is available from the previous sources. A single MeSH Concept can only have one Registry Number. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords. MUI M0000115 example: 362O9ITL9D.

• meshv:relatedRegistryNumber: A property of Concepts. An additional unique identifier for chemicals, which is sometimes followed by a label in parentheses. Multiple Related Registry Numbers are allowed for each Concept. For example, these might be salts and/or stereoisomers of the parent compound. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords. MUI M0000115 example: 103-90-2 (Acetaminophen). MUI M0068239 example: 75821-71-5 (Ca salt)

• meshv:casn1_label: A property of Concepts. Free-text of the Chemical Abstracts Type N1 Name which is the systematic name used in the Chemical Abstracts Chemical Substance and Formula Indexes. The systematic name is a unique name assigned to a chemical substance to represent its structure. First available in 1995. MUI M0000115 example: Acetamide, N-(4-hydroxyphenyl)-

Here's a query to access these:

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#>
SELECT DISTINCT *
FROM <http://id.nlm.nih.gov/mesh>
WHERE { 
  ?concept_uri rdf:type meshv:Concept.
  ?concept_uri rdfs:label ?concept_label.
  ?concept_uri meshv:identifier ?concept_id.
  VALUES ?predicate_uri {
    meshv:registryNumber
    meshv:relatedRegistryNumber
    meshv:casn1_label
  }
  ?concept_uri ?predicate_uri ?registry_number.
  BIND( STRAFTER(STR(?predicate_uri), "mesh/vocab#") AS ?relationship_type )
  FILTER (?registry_number != "0")
}
ORDER BY ?concept_uri ?predicate_uri ?registry_number

concept_uri	concept_label	concept_id	predicate_uri	registry_number	relationship_type
mesh:M0000001	Calcimycin	M0000001	meshv:casn1_label	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))-	casn1_label
mesh:M0000001	Calcimycin	M0000001	meshv:registryNumber	37H9VM9WZL	registryNumber
mesh:M0000001	Calcimycin	M0000001	meshv:relatedRegistryNumber	52665-69-7 (Calcimycin)	relatedRegistryNumber
mesh:M0000002	Temefos	M0000002	meshv:casn1_label	Phosphorothioic acid, O,O'-(thiodi-4,1-phenylene) O,O,O',O'-tetramethyl ester	casn1_label
mesh:M0000002	Temefos	M0000002	meshv:registryNumber	ONP3ME32DL	registryNumber
mesh:M0000002	Temefos	M0000002	meshv:relatedRegistryNumber	3383-96-8 (Temefos)	relatedRegistryNumber
mesh:M0000011	Abelson murine leukemia virus	M0000011	meshv:registryNumber	txid11788	registryNumber
mesh:M0000055	Abrin	M0000055	meshv:casn1_label	Abrins	casn1_label
mesh:M0000055	Abrin	M0000055	meshv:registryNumber	1393-62-0	registryNumber
mesh:M0000061	Abscisic Acid	M0000061	meshv:registryNumber	72S9A8J5GW	registryNumber
mesh:M0000061	Abscisic Acid	M0000061	meshv:relatedRegistryNumber	113349-29-4 ((Z,E)-isomer)	relatedRegistryNumber

One challenge is that registry numbers appear to be local identifiers without any notation of their source.

[cthoyt]

i was told by the mesh people once that you can use a regex to figure out if xrefs are to CAS or UNII

[cthoyt]

@dhimmel pyobo now implements related logic in https://github.com/pyobo/pyobo/blob/8fc402dcfcd089d6e90c2a6c4a4b6a71629d3a33/src/pyobo/sources/mesh.py#L234-L257