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Write tutorial on finding secondary IDs #18

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DeniseSl22 opened this issue Jun 3, 2021 · 1 comment
Open

Write tutorial on finding secondary IDs #18

DeniseSl22 opened this issue Jun 3, 2021 · 1 comment

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@DeniseSl22
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Something for Lucas to work on @Chris-Evelo

Common problem in metabolomics PW analysis:

  • Metabolite datasets have outdated/secondary IDs, which don't map to the PW data.
  • Example 1: HMDB01046 "OLD HMDB structure" is part of WP1600 (see image below).

image

  • Example 2: HMDB04161 "OLD && SECONDARY HMDB structure" (not part of PW). SO HMDB04161 should be mapped to HMDB0004160 (but this might need Secondary/primary labeling added in mapping files @egonw ).
@DeniseSl22
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For example 2, the idea of the tutorial would be to find if the IDs are in the mapping file, and if not, replace them manually (for now).
Example 1 + 2 could also benefit from finding out if the IDs are even part of the WP Approved Collection (so when the ID is in the mapping database, match it against WP content, maybe through SPARQL endpoint?)

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