[MOBY-l] Apologies, a hint for MIPS-Service substitutions, and an invitation

[Mark]

Hi all!

It would appear that, for the past few months, all of the DragonDB moby  
services have been down... because of a missing "use" statement in my  
Service daemon!  Spank me later... but accept my apologies in the  
meantime...though I guess I must be the only person who uses them given  
that nobody complained ;-)  LOL!  Anyway, several of the Moby demo  
workflows (e.g. the ones that return images of Snapdragon mutations) will  
now function again properly!

Unfortunately, we've lost *all* of our MIPS services, and many of those  
are components of the various demo workflows, since the MIPS services have  
historically been the most reliable of all Moby services.

Because I needed them for a course I am teaching on Monday, I've  
"replaced" two of the dead MIPS services with ~equivalent services that  
wrap TAIR.  The Global_Keyword search against mutant phenotypes is now  
available from the arabidopsis.org authority (I should probably ask TAIR  
if they mind me referencing their authority name... but it does wrap their  
web interface so I thought I should acknowledge them as the authority for  
that service even though they don't host it!).  I am also retrieving  
sequences based on AGI locus codes from arabidopsis.org rather than from  
MIPS.  Here are the two substitution services:

getAGILocusCodes provided by: mips.gsf.de can be replaced by  
getAGI_LocusCode_by_Keyword provided by: arabidopsis.org

getEmblDNASequence provided by: mips.gsf.de can be replaced by  
getTAIR_SequenceByAGI_LocusCode provided by: arabidopsis.org

If you make these substitutions in your own workflows you will likely find  
that your workflows suddenly come back to life!


IF ANYONE NEEDS REPLACEMENT SERVICES FOR THE OTHER CURRENTLY DEAD MIPS  
SERVICES PLEASE TELL ME and I'll do my best to code them up for you (if  
possible).  It only took a few minutes to wrap TAIR as Moby services, so  
I'm happy to do this for you if you need it.

In addition, MIPS provided an EMBL ID retrieval based on keyword, and that  
fed-into a MIPS sequence retrieval based on EMBL ID.  This pair of  
services can also be replaced by the two above, since they're just a  
different namespace/id route to the same data.

This all brings me to my final comment - I currently have two  
summer-students who are working on the problem of automated workflow  
repair (i.e. finding equivalent services to fix broken workflows).  We're  
going to be inviting everyone to participate in a Moby Service Annotation  
Jamboree later this summer.  It will be a "virtual" jamboree - just come  
to the website.  We'll have an interface there through which you can  
deeply annotate Moby services (inputs, outputs, underlying resources,  
service types, authorities, etc.) with the goal of improving service  
discovery.  I encourage all Moby users to participate and improve the  
quality of our service annotations!  At a minimum, I hope that the current  
service providers will visit the website and annotate their own services  
:-)

Best wishes everyone!

Mark




-- 
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Mark Wilkinson
Heart + Lung Research Institute
Centre for High Throughput Biology
UBC