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They're in already, only reclassified:
http://www.ebi.ac.uk/efo/EFO_0000222
http://www.ebi.ac.uk/efo/EFO_0000220
We've got lymphoma and leukemia as single terms from the old structure. This division does not represent current medical knowledge on blood cancers, hence the new classification. They still form part of other disease names, e.g. ALL and AML, so should be queryable.
2009-11-17 19:29:51 UTC by tadamusiak
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leukemias - add ALL, AML etc - and their synonyms, we have many of these in the archive.
2009-11-17 17:24:10 UTC by parkinso
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needs a revision for the existing structure of assays, remove re-sequencing from the hierarchy, this is a platform/technology not an assay and add sequencing platform and array platform (or similar) then make cross products with the assays - using some relation to indicated is performed on some platform. OBI may have a better label than platform.
then GEO terms need to be added and or mapped...
2009-11-17 15:46:05 UTC by parkinso
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started some work - use new uploaded file.
2009-11-13 17:30:01 UTC by jamesmalone
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almost done now except for genetic factor and children and external control ratio.
2009-11-13 16:51:44 UTC by jamesmalone
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Complete! Good review Jie, I think I addressed almost all of these except a couple of the definition formats which I was not too concerned about. great stuff cheers!
James.
2009-11-13 16:51:05 UTC by jamesmalone
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All renamed
>rename EFO_0000220 to acute lymphoblastic leukemia
>rename EFO_0000094 to B-cell acute lymphoblastic leukemia
>rename EFO_0000209 to T-cell acute lymphoblastic leukemia
Closing ticket!
James.
2009-11-13 10:42:22 UTC by jamesmalone
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ok so Hematological neoplasm (EFO_0000525) is now obsolete - use the synonym lymphoid neoplasm (EFO_0001642) instead.
I think we should keep leukemia for now - it is a highly searched for class term.
2009-11-13 10:39:03 UTC by jamesmalone
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Helen,
James has obtained these programatically in the past so surely it can be done again. I spend *alot* of time tracking down terms and associated accessions in order to make adding terms to EFO easier and quicker. In addition the roles don't seem to be listed via OLS (I find this is the easiest and least likely tool to crash).
When finding or submitting terms ChEBI is causing me the...
2009-11-10 13:29:15 UTC by eleh
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Ok, the plan is to put it in production under /nfs/ma/ma-subs/AE/subs/onto_tools
James, do you want to drop latest bubastis version in there as well?.
2009-11-09 17:23:28 UTC by tadamusiak
