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New ENSEMBL release 87 on 8th December changed naming convention causing organism*() functions to be temporally unavailabe #1

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HajkD opened this issue Dec 13, 2016 · 1 comment

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@HajkD
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HajkD commented Dec 13, 2016

In the new ENSEMBL release 87 on 8th December the naming convention of organisms changed from a scientific name based system, e.g. "Homo sapiens" to a common name based system: "Human" in the biomart description section... thus all organism*() functions did not work anymore and need to be adapted. See changes at http://www.ensembl.org/Homo_sapiens/Info/WhatsNew?db=core#change_2382 .

Thus I will now start working on incorporating these changes.

I apologise for the temporal unavailability for all organism*() functions, but I am shocked myself that ENSEMBL descriptions now use inconsistent descriptions of their BioMart features. E.g. sometimes "Mouse", "Pig", "Human" and sometimes the scientific name, e.g. "Caenorhabditis elegans".

Since internal organism*() functions parse the ENSEMBL biomart descriptions for scientific name conventions, the new ENSEMBL release now caused that the parser doesn't work anymore.
I will try my best to adapt the parser to the new common name convention of ENSEMBL's biomart descriptions.

@HajkD
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HajkD commented Dec 15, 2016

All organism*() functions have been adapted to the new ENSEMBL release 87 notation. All functions work properly now. I will submit the new package version 0.2.1 to CRAN today.

@HajkD HajkD closed this as completed Dec 15, 2016
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