Gustavo Salazar wrote:
Hi Andy,
The way I start to implemented is following the idea of interfaces that
MyDas has. In such a way i just extend the skeleton of MyDas to support
other kind of source called DasWritebackInterface, it allows that every
group implement the writeback in different ways but all of them should
provide the same capabilities(so far I define 3 methods, add, update and
delete)
As the source class can implement more than one interface, my idea for
the query is that the source should implement both the writeback and the
annotation source and in that way the server will use the feature
command to provide the annotations.
do you think that this way will be enough for the hypotetical case that
you describe?
I think this would be best, we just need to figure out how to clearly
identify features from another source that are being annotated (see below).
I've been thinking that the commands in the writeback document should be
extended, because so far the defined commands are DELETES and UPDATES
(no command meaning ADD). An idea that i have is to put a command
SYNONYMS to tag 2 or more features that coming from different servers
and give the same information.
On the other hand a control version for the annotations will be very
useful and in such a case at least 2 new command will be required
getHistorical to get all the meta-annotations done over one feature, and
setCurrent to define which version of the meta-annotations should be used.
I would suggest that ADD functionality can simply be provided by issuing
an UPDATE but with a new feature ID. How did Asia do this? Likewise
setCurrent (e.g. to rollback a change) could be done by the client, by
reinstating the annotation with an UPDATE. I'd like to keep things as
simple as possible, certainly for the client, as in my opinion this has
been key for DAS in the past.
With regards to synonyms, this is a definite issue for DAS which is
probably worthy of its own topic. This was proposed to be fixed via the
METHOD tag (used to identify the "reference" server for the annotation),
but I'm not sure if this has been adopted so far.
By the way, Im not familiar with the Dasmi project, what is the idea of
those rankings?
The idea is that some servers provide interactions (which are
annotations of proteins or domains), and others provide confidence
scores for those interactions which are laid over the top. The
documentation on dasmi.de explains how this works, but IIRC it relies on
the IDs being unique across servers. This isn't guaranteed according to
the DAS spec, so we will likely need to do something about that.
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