mesh

Converting MeSH to NXOntology

Key features:

• Convert MeSH to a directed acyclic graph that includes Topical Descriptors and Supplemental Concept Records. Data output to mesh_topical_descriptor_descendants.json.gz.

• Create a map of MeSH node to top-level (root) Topical Descriptors. Includes top-level tree numbers for categorization. Data output to mesh_topical_descriptor_descendants_top_level_map.json.gz

• Preserve edges from Supplemental Concept Records (SCRs) to Descriptors that go through an AllowedDescriptorQualifierPair. See nxontology-data/issues/4.

• Extract all MeSH identifiers across RDF classes including many properties / metadata fields. Data output to mesh_identifiers.json.gz.

• Extract MeSH synonyms consisting of Concepts & Terms including whether they are preferred. Concept relations to the preferred concept are exposed. See nxontology-data/issues/7. Data output to mesh_synonyms.json.gz.

• Extract a table of all allowed and disallowed descriptor-qualifier pairs. See nxontology-data/issues/3. Data output to mesh_descriptor_qualifier_pairs.json.gz

Key links:

• HHS/meshrdf GitHub Repository. Relevant issues below (currently offline):

  • Difference between mappedTo and preferredMappedTo predicates?
  • Comment by Dan Davis on creating a TopicalDescriptor Ontology
  • Pagination / offset of results for the SPARQL endpoint is faulty
  • 2022 MeSH descriptor hierarchy contains a cycle

• MeSH RDF Technical Documentation

• MeSH Homepage

• MeSH SPARQL Endpoint

References

Works related to converting MeSH to a directed acyclic graph:

1. Desiderata for an authoritative Representation of MeSH in RDF
   Rainer Winnenburg, Olivier Bodenreider
   AMIA (2014-11-14) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419968/
   PMID: 25954433 · PMCID: PMC4419968

2. Transforming the Medical Subject Headings into Linked Data: Creating the Authorized Version of MeSH in RDF
   Barbara Bushman, David Anderson, Gang Fu
   Journal of library metadata (2015) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749162/
   DOI: 10.1080/19386389.2015.1099967 · PMID: 26877832 · PMCID: PMC4749162

3. MeSHHeading2vec: a new method for representing MeSH headings as vectors based on graph embedding algorithm
   Zhen-Hao Guo, Zhu-Hong You, De-Shuang Huang, Hai-Cheng Yi, Kai Zheng, Zhan-Heng Chen, Yan-Bin Wang
   Briefings in Bioinformatics (2020-03-31) https://doi.org/ghnr5n
   DOI: 10.1093/bib/bbaa037 · PMID: 32232320

4. Semantic Measures Library & ToolKit Medical Subject Headings (MeSH)

5. MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents
   Zhou Jing, Shui Yuxuan, Peng Shengwen, Li Xuhui, Mamitsuka Hiroshi, Zhu Shanfeng
   Institute of Electrical and Electronics Engineers (IEEE) (2015-07) https://doi.org/ghnr5x
   DOI: 10.1109/chicc.2015.7260989

6. pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms
   Zhi-Hui Luo, Meng-Wei Shi, Zhuang Yang, Hong-Yu Zhang, Zhen-Xia Chen
   BMC Bioinformatics (2020-06-18) https://doi.org/ghnvj9
   DOI: 10.1186/s12859-020-03583-6 · PMID: 32552728 · PMCID: PMC7301509

7. Redefining a Thesaurus: Term-Centric No More
   Douglas Johnston, Stuart J Nelson, Jacque-Lynne A Schulman, Allan G Savage, Tammy P Powell
   Proceedings of the AMIA Symposium (1998)
   PMCID: PMC2232255

Key Quotations

Note that MeSH violates a core assumption of ontologies. From the "Contextual hierarchical structure" section of Winnenburg & Bodenreider, 2014:

MeSH also uses a non-standard hierarchical organization. The hierarchy among MeSH descriptors is indicated through "tree numbers" assigned to descriptors. Tree number inclusion reflects that the descriptor with the longer tree number is narrower than that with the shorter tree number. For example, the tree number for Liver [A03.620] has an additional node (.620) compared to that of Digestive System [A03], indicating the narrower relation between the two. Note that tree numbers are not the unique identifiers of descriptors. Descriptors often have multiple tree numbers reflecting particular aspects of the descriptors, each aspect being assigned specific broader and narrower descriptors. For example, the descriptor Eye (D005123) has two tree numbers, A01.456.505.420 and A09.371. In the A01 tree, Eye is narrower than Head [A01.456] and broader than Eyebrows [A01.456.505.420.338] and Eyelids [A01.456.505.420.504], whereas, in the A09 tree, Eye is narrower than Sense Organs [A09] and broader than Eyelids [A09.371.337], Retina [A09.371.729], Uvea [A09.371.894] and nine other descriptors. Note that, although Head is broader than Eye (A01 tree), some descendants of Eye in the A09 tree (e.g., Retina) do not have Head as their ancestor. For all practical purposes, the broader/narrower relationship among MeSH descriptors is not transitive.