Re: [Obo-discuss] Functional Annotation Tool ?

[Julian H <hum...@ma...>]

I don't know about what other folks see, but this=20
message is virtually unreadable as all the text=20
is run together.  Any possibility of another try?

Julian


At 05:06 PM 7/9/2007, you wrote:
>Hi Mark, On Mon, 2007-07-09 at 10:48 -0400, mark=20
>gibson wrote: > well gee whiz thats something i=20
>never thought of. > so whats the idea here - so=20
>you select a gene in apollo and bring up  >=20
>phenote(menu of some sort) > and phenote then=20
>displays shows that gene in a configured gene=20
>field(?) > and there would then be a go field,=20
>and evidence and bibiography? The idea is to=20
>open Apollo annotation info editor, hit a button=20
>that says "functional annotation editor", and=20
>get a new window that shows : description,=20
>dbxref, and GO terms. Next to these three=20
>fields, it would be possible to add, edit or=20
>delete the information. To add information, up=20
>comes a PheNote-like window, with the Gene=20
>Ontology hierarchy, that can be searched, tab=20
>completed etc. Do you think Apollo and PheNote=20
>can be made compatible to do this "easily" ? > >=20
>that could work - and wouldnt be hard i dont=20
>think - but there would  > be some issues to=20
>think about. > first of all would this be for=20
>one gene at a time - basically a one  > row=20
>phenote - or would you keep phenote up and keep=20
>adding gene  > annotations to it. > > Also how=20
>would you then save this data. Would you > 1)=20
>have phenote send the data back to apollo? >=20
>or > 2) have phenote save the data separately=20
>from apollo? 1) send the data back to apollo and=20
>use the apollo dataadapters. > > The problem=20
>with #1 is that theres no place currently in the=20
>apollo  > datamodel for this kind of data=20
>(though i think there is a catchall  > hash=20
>kinda thingy in there), and of course there isnt=20
>apollo  > dataadapters that deal with it either.=20
>But all that could be added I  > suppose. > I=20
>would have to modify the apollo datamodel and=20
>the apollo dataadapters. So, you are answering=20
>"no" to my question, this possibility does not=20
>already exist. What to do you think? Olivier >=20
>#2 would certainly be simpler, as there=20
>obviously already are phenote  > dataadapters=20
>that can save & read this data. But that might=20
>make for  > a strange user experience that they=20
>have to do 2 separate saves, one  > for apollo=20
>one for phenote. But perhaps there could be=20
>someway of  > having the user hit save and have=20
>both apollo & phenote do their  > saves. But is=20
>it also strange to have 2 different in & outs -=20
>if its  > files you are saving then you have 2=20
>different files being saved  > which could be=20
>confusing. But maybe if you saw it as one app=20
>talking  > to another (a glorious cut & paste)=20
>rather than just one bundled app. > > Also=20
>theres 2 ways these could talk to each other.=20
>You could chuck  > phenote into apollo - either=20
>as a jar or the source itself. Theres  >=20
>synchrony issues there. > > Or alternatively you=20
>can have the 2 apps running separately and  >=20
>talking to each other via http/restful. I=20
>actually just set up such a  > thing in phenote=20
>for BIRNs smart atlas application. Smart atlas=20
>will  > send out http/tag-value data and phenote=20
>listens for http requests  > and picks it up.=20
>And eventually you will be able to webstart=20
>launch  > phenote(configured for smart atlas)=20
>from within smart atlas. > > Mark > > > On Jul=20
>9, 2007, at 12:31 PM, Olivier Arnaiz=20
>wrote: > > > Hello, > > > > I am using Apollo=20
>for structural annotation. I would like to add=20
>a > > functional annotation tool. I need to be=20
>able to annotate GO terms  > > with > > their=20
>evidence codes and bibliographic references, and=20
>I need to be  > > able > > to add a free text=20
>description. > > > > I am aware of Manatee, but=20
>it seems very complicated for our needs. > > > >=20
>Here are the questions: > > > > 1) Is there an=20
>open source tool that will allow us to associate=20
>GO  > > terms > > (and their evidence codes and=20
>the references) to a gene that functions > >=20
>with the same system as PheNote? > > > > 2) I=20
>think it might not be too hard to add these=20
>features to Apollo > > (using existing PheNote=20
>code, Mark?). > > > > Thanks > >=20
>Olivier > > > > > > > > -- > > Olivier=20
>Arnaiz > > Centre de G=C3=A9n=C3=A9tique Mol=C3=A9culaire -=20
>CNRS > > Avenue de la Terrasse - B=C3=A2t. 26 > >=20
>91198 GIF-SUR-YVETTE CEDEX FRANCE > >=20
>http://paramecium.cgm.cnrs-gif.fr > > > > >=20
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Julian Humphries
Digimorph.org
Department of Geological Sciences
University of Texas, Austin, 78712
512-471-3275=20