Content-Type: multipart/related; boundary=Apple-Mail-29--447815510; type="text/html" --Apple-Mail-29--447815510 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable
Thank you for the script and = all this information, NomiPhenote will be = better than OBOedit going forwards because it spits out a text file that = we can use....Your Pal example is nice: I can = see that it is case insensitive - however, it does not bring back items = where pal is in the middle of the = phrase!
<Screen shot 2010-05-17 at = 2.28.01 PM.png>On May 17, = 2010, at 7:40 AM, Helen Imogen Field wrote:Dear = Nomi
I am trying to persuade my curators to use Phenote for GO as = well as phenotype annotation.
One very powerful feature of OBO = edit and QuickGO is their search capablity
- putting = in bits of words (like 'reg' for regulation)
- putting things in = incorrect order (like 'death cell' which should return cell death).
- = misspelt items (American spelling = etc)Phenote already can do = the first of these. If you start typing in one of the term boxes = in the Annotation Editor, it will offer you a pulldown list of terms = that include the sequence of letters you've typed--for = example:<phenote-new-config>If you select one of the terms = from the list, the Term Info window will show you more information about = the selected term.Phenote is not currently set = up to handle the other two search capabilities you = mentioned.There are several items on the = Phenote request tracker asking for more advanced search capability in = Phenote. I will try to determine whether these capabilities are = desired by the current highest-priority Phenote-using project, and if = so, I will be happy to work on this.If we can get these right I think we could make great = use of Phenote... particularly because it is so configurable and because = it delivers a text file.
Can you let me know how high on the priority = list this search item is? it is a blocker for us! Very few curators = dealing with all and any gene will be familiar with enough terms to get = the search input in = correctly.Right, I = understand. Maybe for now they could use OBO-Edit for that = purpose?In addition I would = like to be able to open it on the command line with the configuration = file of choice - I think I can already do that can't = i?Not really--see forwarded = message below. However, I have made you a modified version of the = phenote script that you can call with a configuration (e.g., hpo or = plant) on the command line. You can use this script to launch Phenote = from the command line (from a Unix-like system, including Mac--it won't = work on Windows). Just put this script in the directory where you = installed Phenote, and make sure it's executable. Launch by saying = "phenote hpo" (or whatever your desired configuration is--leave out the = ".cfg" = part).If I determine that the funded Phenote = users want to be able to change the configuration on the command line, I = can easily make that part of Phenote, but maybe this script will work = for you in the meantime.= NomiBegin forwarded = message:From: Nomi Harris <email@example.com>
= div>Date: April 23, 2010 = 9:45:42 AM PDTTo: Helen Imogen Field <firstname.lastname@example.org>
=Cc: Nomi Harris <email@example.com>
= div>Subject: Re: Using Phenote = API
On Apr 23, 2010, at 1:24 AM, Helen = Imogen Field wrote:Hi = NomiIs there a way = of firing up your latest release on the command line, telling it which = config file to use?
No, but if you want to change = your config without having to start Phenote, you can hand-edit the file = ~/.phenote/conf/my-phenote and put the desired config file name in = there.Also, it would be helpful if it = could restart itself (quickly) when using alternative config files, if = selected from within the application. That way, if my users have a = config for every kind of search they need to do (different items require = quite different searches) then they can see the new set up immediately; = otherwise they would have to restart constantly (which would cause them = to abandon Phenote, I would guess). The other alternative is a = completely generic approach - let me know what you think is the best = workaround.
Phenote was not intended to allow quick = config switching--the assumption was that the user would be working on a = particular project and would select a config for that project and not = need to change the config frequently. I'm afraid there's not a way = to make Phenote restart itself quickly without significant = reworking.
However, I think we can find a way to get you closer = to what you want. Can you explain more about what your users are = searching for? If they need access to a range of different ontologies, = we should be able to make a new hybrid config that pulls together the = ontologies they need.
Another thing you can do to make startup = faster is to turn off auto-updating of ontology files. That is = also controlled by the config file.
Probably the best way to = start is for you to pick a config file that's closest to what you want, = and then we can work together to modify it (add ontologies, turn off = auto-update, etc). Then I can commit your new config file to the = Phenote repository.