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MeSH Annual Updates

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filak edited this page Mar 6, 2025 · 39 revisions

MeSH RDF

  1. Download the official MeSH RDF dataset https://github.com/filak/MTW-MeSH/wiki/Loading-MeSH-datasets#get-the-official-mesh-rdf-dataset

  2. ALWAYS perform the checks and resolve any issues in MTW - ie. duplicates, locks, pending changes etc.

  3. Export required output files from MTW - ie. UMLS TSV, MARC file, stats etc.

  4. BACKUP your <mesh> dataset using Fuseki interface

  5. Extract the translation from the backup using mesh-nt2trx tool - run:

     mesh-nt2trx %FUSEKI_BASE%/backups/mesh_YYYY-MM-DD_....nq.gz

  6. Stop MTW Server and MTW Worker services

  7. Go to your <FUSEKI_DATA_DIR> and DELETE the <mesh> directories under datatabases and indexes dirs

  8. Update MTW config file for new target year/period

    <MTW_HOME_DIR>/instance/conf/mtw.ini

  9. Follow the steps in Import the RDF datasets

  10. Clear the MTW cache - delete all files in instance/cache

  11. Start MTW Server and MTW Worker services

  12. Reset the Initial stats in Manage dashboard

UMLS Data exports

NML Bethesda distributes the UMLS MeSH exports as CSV text files usually in autumn.

For better understanding all the data changes it is recommended to upload some of the files to Google Drive sheets and share it with the translating team.

  1. Create a sheet in your Google Drive - ie. MeSH_UMLS_YYYY

  2. Upload the files into lists:

  • deleted_mh.txt => MH_Deleted list

  • new_mh.txt => MH_New list

    DescriptorUI;ConceptUI;Language;Term Type;String;TermUI;ScopeNote;Tree;Change Type;Browser;MTW;TrxTerm;TrxNotes;TrxScopeNote

  • conceptUI_diff.txt => Concepts_Changes - after adding Fx columns select values for TermType filter: MH, PEP, ET

    DescriptorUI;ConceptUI;Language;Term Type;String;ScopeNote;Change Type;Browser;MTW;TrxTerm;TrxNotes

  • changed_marked.txt => MH_Changed list - after adding Fx columns select values for ChangeType filter: UPDATED_MH, UPDATED_MH/UPDATED_ScopeNote, UPDATED_ScopeNote, DELETED_ROW, NEW_ROW

    DescriptorUI;ConceptUI;Language;Term Type;String;TermUI;ScopeNote;Tree;Change Type;Browser;MTW;TrxTerm;TrxNotes

  • ScopeNote_changes.txt => remove empty rows => ScopeNotes_Changed list

    DescriptorUI;ConceptUI;Language;Term Type;String;TermUI;ScopeNote;Tree;Change Type;Browser;MTW;TrxScopeNote;TrxNotes

Functions (Fx) for additional columns

Add filters - Data > Add filter

  • Browser

    =HYPERLINK(CONCAT("https://meshb-prev.nlm.nih.gov/record/ui?ui=",A2),"view")

  • MTW

    =HYPERLINK(CONCAT("https://YOUR-MTW-INSTANCE-HOST/mtw/search/dui:",A2),"mtw")

Translation strategy

You can use the following strategy to prioritize the work on the translation (in combination with the MTW Dashboard):

  1. MH_New - Term Type MH - translate main heading term (and scope note if applicable)
  2. MH_New - Term Type PEP - translate terms
  3. MH_Changed - Term Type MH - revise main heading term (and scope note if applicable)
  4. MH_Changed - Term Type PEP - revise terms
  5. MH_New - Term Type ET - translate terms
  6. MH_Changed - Term Type ET - revise terms
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