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Add MESH xrefs #146

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GoogleCodeExporter opened this issue Jun 4, 2015 · 4 comments
Closed

Add MESH xrefs #146

GoogleCodeExporter opened this issue Jun 4, 2015 · 4 comments
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auto-migrated autoclosed-unfixed This issue has been closed automatically. Priority-Medium Type-Defect

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@GoogleCodeExporter
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Email on CL list:

> I have been looking at the MeSH terms for some CL nodes and I wonder whether 
there are missing mappings.
>
> For example for CL:0000746, there is not any mesh dbxref. Querying the mesh 
web page, I found "Myocytes, Cardiac" (Tree Number(s): A07.541.704.570, 
A10.690.552.750.570, A11.620.500).
>
> Are there some other files that provide more CL to MeSH mappings?
>
> Many thanks for the help.
>
> Kind regards,
> Ioannis

Original issue reported on code.google.com by cmung...@gmail.com on 21 Jul 2014 at 8:22
@GoogleCodeExporter
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Note: should probably use D numbers like D001253 rather than tree numbers

Original comment by cmung...@gmail.com on 21 Jul 2014 at 8:24

@GoogleCodeExporter
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I am also interested in MeSH cross-references. I see two problems with the 
current state of MeSH information in CL:

1. Many MeSH terms are identified using tree numbers when unique ids are 
preferable.

2. Only one term (`CL:0002211`) has a MeSH xref. However, hundreds of terms 
cite MeSH as the source of their definition or synonym, so why isn't this 
information cross-referenced?

I reported [similar issues for 
UBERON](https://github.com/obophenotype/uberon/issues/698) and was encouraged 
to post here.

Original comment by daniel.h...@gmail.com on 20 May 2015 at 6:57

@GoogleCodeExporter
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I have extracted the MeSH citations in CL descriptions and synonyms (as well as 
the single MeSH xref) and mapped them to MeSH unique ids. Several tree numbers 
used no longer correspond to terms in the current MeSH release.

The results are available here:
https://github.com/dhimmel/uberon/blob/89f4d8c59772e5a2071f5390484712e197fa5200/
data/CL-mesh-map.tsv

The analysis notebook is here:
https://github.com/dhimmel/uberon/blob/89f4d8c59772e5a2071f5390484712e197fa5200/
mesh-map.ipynb

Original comment by daniel.h...@gmail.com on 21 May 2015 at 12:21

@gouttegd gouttegd mentioned this issue Sep 28, 2021
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gouttegd commented Nov 1, 2021

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed – we are now getting some resources to deal with such issues.

@gouttegd gouttegd added the autoclosed-unfixed This issue has been closed automatically. label Nov 1, 2021
@gouttegd gouttegd closed this as completed Nov 1, 2021
@bgyori bgyori mentioned this issue Apr 24, 2022
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