[MOBY-l] Service Hierarchy Attempt

[Mark Wilkinson]

Hey Midori,

thanks for jumping on this so quickly!  Jason and I were discussing (albeit
briefly) the option of making STO a DAG rather than a straight hierarchy.  As
I recall we couldn't see any good reason to not go the DAG route, and the
suggestions you make below make it clear that it will be more sensible to go
this route.

Midori Harris wrote:

>  - Does anyone remember why BLAST and Smith-Waterman went under functional
> assignment (which I changed to function prediction)? Smith-Wateramn

They seem to more correctly live under sequence comparison, but they are often
*used* for functional assignment, whether this is biologically valid or not
;-)  If we are using a DAG we can, as you say, make them children of both.
This makes sense to me... any objections?

>  - Should alignment go under sequence comparison (formerly sequence
> similarity)?

I think so.


>  - What do we mean by 'phylogenetic' service? I wanted to make this one
> more verbose but didn't know what we wanted to say. 'Phylogenetic
> comparison'? 'Phylogenetic analysis'?

building phylogenies from sets of input sequences is what I had in mind
there.  Phylogenetic "construction"?


>  - Do we want to include input and output MOBY objects or object classes
> in the definitions?

no.  Services may take many forms of input and output.


> Sorry to dwell on the details so much; its just that this is one area
> where I can make a meaningful contribution to MOBY!

It was great to see this so quickly!  Thanks very much!

I'm compiling a set of  "minutes" from the meeting.  I'll send these to the
list first to make sure I haven't mis-represented anyone, and then will put
them up on the website along with a much more detailed description of what the
project "looks like" at this point.  This will take a couple of days - I'll
try to get it done over the weekend.

Cheers all!

Mark