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cmungall / cell-ontology-DO-NOT-USE

Initial attempt to move repo from gcode. USE OBOPHENOTYPE
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Add MESH xrefs #146

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
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 commented 9 years ago 
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 commented 9 years ago 
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 commented 9 years ago 
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

GoogleCodeExporter commented 9 years ago 
Thanks! We'll try and get these in before the next release

Original comment by cmung...@gmail.com on 9 Jun 2015 at 7:03