MESH IDs #132

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cmungall opened this Issue Oct 12, 2012 · 0 comments

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@cmungall
obophenotype member

From Alexander D:

Most of the MESH IDs in CL and UBERON are of the form "MESH:A.XX.XX.XX", with variable number of '.XX's.  For example: 
MESH:A.11.329.228, MESH:A.06.224.365, or MESH:A.13.223.

However, MESH itself omits the period following the A in their IDs for MESH tree numbers.
A11.329.228 [Fibroblasts, http://www.ncbi.nlm.nih.gov/mesh?term=A11.329.228]
A06.224.365 [ Enterochromaffin-like Cells, http://www.ncbi.nlm.nih.gov/mesh?term=A06.224.365]
A13.223 [ Cloaca, http://www.ncbi.nlm.nih.gov/mesh?term=A13.223]

Using the MESH  IDs with the periods after the letter on http://www.ncbi.nlm.nih.gov/mesh yields the result " The following term was not found in MeSH: A.11.329.228." etc.

Using the MESH IDs that do not follow the letter with the period yields the correct search result, http://www.ncbi.nlm.nih.gov/mesh?term=A11.329.228

If one googles the MESH:A.11.329.228 form, lots of ontology related results are returned, but no links to an actual MESH resource.
If one googles the MESH:A11.329.228 form, links to MESH term listings at NCBI and elsewhere are returned.

There are a few MESH IDs in CL with the correct form, probably put there by Terry.  I think the use of the MESH ID form with the period after the letter was an ID format that was used by original developers of the CL and carried on into UBERON.

I think we should fix all these MESH IDs in CL and UBERON to conform to what MESH actually uses.  A simple find and replace.
@cmungall cmungall added a commit that closed this issue Oct 15, 2012
@cmungall cmungall Fixes #132 aee9160
@cmungall cmungall closed this in aee9160 Oct 15, 2012
@cmungall cmungall added a commit that referenced this issue Oct 16, 2012
@cmungall cmungall Fixes #132
    fixes #134
    updated EFO xrefs
    various placode and ganglion fixes
    metadata
    edits from obo-anatomy call. More specific skeletal relation for metacarpals. syn for preax/postax
    Fixes #131
    more pedal digits
    pedal digitl precusors synonyms
    documentation
ae76b47
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