[Bioc-devel] arabidopsis annotations
hpages at fhcrc.org
Thu Aug 23 19:09:24 CEST 2007
In the process of migrating the arabidopsis annotations to the new sqlite-based
infrastructure, we found a problem with the current ENZYME/ENZYME2PROBE maps.
We'd like to know what you think (especially if you've been using these maps).
In the ag and ath1121501 packages the ENZYME/ENZYME2PROBE maps are linking probe ids
to enzyme names, and not to EC numbers like in _all_ other chip-based packages.
In addition the man pages for those maps are incorrect: they claim that those 2 maps
are between manufacturer ids and EC numbers (not really a surprise in fact because
AnnBuilder uses the same template as for any other packages to generate the
ENZYME/ENZYME2PROBE man pages).
This is not a satisfying situation and we'd like to improve things a little
bit for the upcoming ag.db and ath1121501.db packages. There are of course different
ways we could address the problem:
A. just fix the man pages:
- pro: easy and 100% compatible with the current (environment-based) ag and
- con: for arabidopsis, the ENZYME/ENZYME2PROBE maps will remain different
from what they are in all other chip-based packages + people that
want the EC numbers still don't have them
B. fix the ENZYME/ENZYME2PROBE maps so that they are consistent with all
other ENZYME/ENZYME2PROBE maps
- pro: consistency across all other chip-based packages
- con: enzyme names are gone so the user code using the ENZYME/ENZYME2PROBE maps
from ag and ath1121501 will need to be modified to work with ag.db and
C. rename the ENZYME/ENZYME2PROBE maps -> ECNAME/ECNAME2PROBE and deprecate the
- pro: use the standard deprecation procedure for a smooth transition period
- con: people that want the EC numbers right now still don't have them (they'll
need to wait BioC 2.2)
D. fix the ENZYME/ENZYME2PROBE maps and add 2 new maps (e.g. ECNAME/ECNAME2PROBE)
for the mapping between probe ids and enzyme names
- pro: consistency and completeness
- con: the user code using the ENZYME/ENZYME2PROBE maps from ag and ath1121501
will need to use the ECNAME/ECNAME2PROBE maps instead (but here the
impact on the user is not as bad as with B since the data they
have been using so far is still available but under different names)
E. anything else?
Thanks for your feedback!
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