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Unbounded 'prefix' variants declared locally by KEGG #7

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jmcmurry opened this issue Mar 31, 2016 · 0 comments
Open

Unbounded 'prefix' variants declared locally by KEGG #7

jmcmurry opened this issue Mar 31, 2016 · 0 comments

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@jmcmurry
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KEGG's gene ids already contain a colon; however, their prefixes correspond to virtually innumerable species.

Normally, I'd recommend respecting the prefix declared by a provider, however, in this Kegg Gene case it would gobble up too many prefixes, many of which may already be in use by others.

Options are:

  1. Live with double prefixes eg. KEGG:hsa:6469
  2. Try to enumerate the prefixes of all known species and declare them as appended to 'KEGG' eg. KEGG-hsa, KEGG-ptr, KEGG-pps etc etc
  3. Convince KEGG's resolver to honor underscore-delimited versions instead
  4. Barring 3, reroute to someone else willing to parse the local ID

@cmungall thoughts?

See for example here.

hsa:6469
ptr:743371
pps:100995872
ggo:101146888
pon:100461003
nle:100582247
mcc:716553
mcf:102120970
rro:104666156
cjc:100395600
mmu:20423
mmu:320038
rno:29499
cge:100773402
ngi:103745341
hgl:101719896
ocu:100352774

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