OE IRC 7Feb06

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4:35 PM
midori: Hi - I wondered whether anyone else would be there!
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jrichter: Hi, folks.
midori: Hi
jrichter: We've got a while before we start. I was just testing my timestamp recorder to see if it was working.
hjd: I don't have a mike, so I'll just be listening in Gizmo
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midori: Should I hear anything in Gizmo yet?
4:40 PM
jrichter: No. I still have some prep to do.
midori: oh good
jrichter walks away for a bit
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hjd: watching that vnc screen gives me vertigo
Carol has quit the server saying: Quit: Carol
hjd: lost one already!
Alex_MGI: Not exactly high speed is it?
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gwg: g'day all
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Alex_MGI: Hello
jenclark: hi
4:45 PM
hjd: i'm dl-ing b15 at this moment; ooh; network errror in the vnc!
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midori: yep, I got that too, but managed to log back in
midori: btw, term addition is hosed in b15
gwg: ah good, so no major problems with it, then...
hjd: ooh: new icon; hey, the mac installer works! My dbxrefs are there!
pfey: hi All!
midori: nah, we've got a lot a lot of terms already
midori: harold, will it add a term for you?
gwg:   No point in adding any more really, is there?
hjd: no it won't add any terms; add child does nothing; deleting now, back to 14
4:50 PM
jrichter: Midori - Term addition is hosed?
midori: yes - I put in a bug report - SF 1426025
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hjd: where's jo-lo?
jrichter: I'm going to try to do a rapid diagnose/fix on this term addition problem. I'll be back.
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gwg: how many more are expected to join this sesh?
midori: at least one!
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4:55 PM
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hjd: ok, have put back beta 14
jenclark: I can't get beta 14 or 15 to start on windows from the source version but I can get the windows installer version to start. It can't add terms though
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jenclark: doea anybody else have gizmo working? I was getting those forresty noises earlier but now I just get silence.
karenepilcher: i have silence too
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tberardini: vnc
hjd: I just get beemps and whistles
midori: beeps and shuffling noises for me
karenepilcher: can barely hear you
midori: yes!
5:00 PM
hjd: ok, I can hear people now
midori: I did for a minute, but beeps again now ...
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midori: that's not you beeping?
karenepilcher: i can hear you
hjd: I just heard alex, but it's echoing
pfey: I hear you John, but fainter than yesterday
hjd: I can't hear john at all
pfey: or was that Alex?
midori: I've heard John a couple of times, but not just this minute
pfey: I have no idea
pfey: and now it's just beeping
jenclark: I can hear shuffling now too
midori: the beeps are a lot louder than anything else
jenclark: yes
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jrichter: John shouldn't be heard at all.
jrichter: There's someone else out there with their mike unmuted, I think.
hjd: huh?
pfey: ok, I hear nothing but beeps
midori: now I hear nothing at all
jrichter: It's going to be a few minutes for me; I'm having some network trouble over here.
midori: oh wait, a quiet rustling ...
Alex_MGI: I've been keeping my mic muted except when speaking.
midori: are we having fun yet?
karenepilcher thinks so
jenclark: I'm finding that pizza helps a lot
tberardini: I hear you!!!!
jenclark: I heard someone too
J-Lo: I'd like some pizza
pfey: me too
hjd: I have crackers and cheese...
pfey: yes
midori: yes, me too ... and then it beeped again!!!
tberardini: Yes, I can!
5:05 PM
J-Lo: yep, we can hear you
jenclark: yes I can understand what you're saying
pfey: but you are not very loud today
jenclark: you're loud for me
hjd: John, any fixes ????
Alex_MGI: Try turning up the volume in the Gizmo Project preferences.
hjd: that "pop" is getting on my nerves 8-)
tberardini: It's a nice way to wake up.
midori: I want the beeps to stop.
gwg: I want the voices to stop!
midori: I hear they have pills for that nowadays ...
tberardini: The voices in your head?
J-Lo: lol!
hjd: Voices! aha! I knew it!
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hjd: The beekps and the earphones make me think of a hearing exam
midori: wha'?
tberardini: Suparna is here too, just can't seem to get the IRC thing to work on her machine.
gwg: is that an old person thing?
dsfashena: beeps and pops only at my end, no voices at all
pfey: I have to disconnect and connect on IRC all the time - not so yesterday
tberardini: We're torturing the rest of our room with the sounds.  Don't have enough earphones and Suparna is Typhoid Mary with a bad cold.
dsfashena: I heard that!  Woo-hoo.
5:10 PM
hjd: don't drop the mic! please!
carol: I hear everybody loud and with only a bit of interference.
tberardini: I don't hear anything.
jenclark: I don't hear anything
jenclark: oh wait, hooves
midori: is that what that is???
J-Lo: that's horrible
pfey: oh oh strange noises..
Alex_MGI: That doesn't sound good!
dsfashena: Phillip Glass musicL
tberardini: The Four Horsemen of the Apocalypse, pehaps?
gwg: It's the new Madonna single played backwards
Alex_MGI: Perhaps just played forwards.
J-Lo: i didn't notice any secret messages in it
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gwg: funny - I could have sworn it was saying "Obsolete the whole function ontology!"
jenclark: that's what I heard too
midori: hold music - yay
jenclark: pianos now
J-Lo: i'll get right to it then
hjd: it that the GO theme song?
J-Lo: stop with the muzac
tberardini: Do you really hear something?  Cause I've got nothing.
jenclark: is there a button for 'reinstate whole ontology'?
jenclark: try hanging up and redialling
tberardini: aha!  muzak!
tberardini: ...and beeps.
jenclark: nobody hears me on gizmo
dsfashena: muzak, then silence.  Normally a good thing. Still silence.
jenclark: still muzak for me
tberardini: lots of beeps, then music
Alex_MGI: Muzak for me too still.
J-Lo: please make that music stop
midori: I've got music AND beeps ... 
pascale: jen I heard you for a minute, when you said "I have a mic too". Now I dont hear anything anymore
jrichter: Okay, everyone. Let's hang up.
hjd: or at least let's have the Stones!
pascale: that was a great seminar!! 
5:15 PM
jenclark: I didn't actually say that, I think it was someone else
jenclark: or the voices
pascale: oh ok
tberardini: hung up, sir.
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dsfashena: totally novel feeling, Wanting to hear muzak...
J-Lo: i've hung up too
jenclark: me too
jrichter: Is anyone still on besides me?
gwg: Madonna's all hung up too, isn't she?
midori: not me
hjd: on where?
Alex_MGI: The muzak disappeared for a second and then came back.
dsfashena: Hanging up and redialing restored muzak for me.
hjd: ah; the musak stopped
J-Lo: hang up Alex
jrichter: Hang up, and don't log back on.
hjd: no, it's back again
jrichter: We need to reset this call.
tberardini: hang up, Harold.
jrichter: If you can hear muzak, you're still logged on.
jrichter: Okay, it's gone now.
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midori: ... and that's the least of your worries.
Alex_MGI: I've been off for a minute.
jrichter: Wait for a moment...
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jrichter: Now, I'd like just the Cambridge gals to log back in to Gizmo.
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J-Lo: done
gwg: yessir!
jenclark: musak
jrichter: Aha! One of you is creating the muzak.
midori: muzak.
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jrichter: It started when you logged on.
midori: ok, I'm hanging up.
jenclark: shall we log on one at a time?
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jrichter: When midori hung up, the muzak stopped...
midori: how utterly mortifying.
jrichter: Midori, is your "hold" button down? We may be hearing your hold music.
gwg: LOL!
midori: hmm. will have to call in ... when I'm hung up, everything's greyed out.
jrichter: Go for it.
5:20 PM
midori: I'm not hearing anything ...
midori: ... except the occasional beep
jenclark: who next?
midori: ... and the hold button's not down
midori: I'm still on 
Alex_MGI: I'm on the phone now.  I'll say something.
midori: deard you
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midori: ... I mean, heard you
jrichter: Okay. New plan. I believe our conference room may have gone insane.
kchris: I'm on now too, also not hearing anything except the occasional beep.
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jrichter: Everyone hang up from Gizmo.
midori: done
karenepilcher: ok
J-Lo: yep
hjd: done
kchris: OK
dsfashena: done
Alex_MGI: gone
jenclark: me too
jrichter: Then, just the Cambridge gals should dial into 1-222-626-3349
jenclark: now?
jrichter: The same number as before, but plus one.
Alex_MGI: '9' not '8' at the end.
J-Lo: i'm in
gwg: I changed my hold music to 'Metal', so if you hear some rockin', it's my hold muzak
jrichter: Can anyone hear me?
gwg: nope!
J-Lo: no
jenclark: I heard a beep
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midori: called in, and hear nothing.
midori: now the beeps are back
jenclark: hearing jane
gwg: can hear Jane...
jenclark: yes
gwg: yup!
J-Lo: yep
midori: ... and no classical music?
jenclark: nope
midori: good!
J-Lo: that god
jrichter: Everyone else can join gizmo now.
jrichter: Make sure to mute right away.
dsfashena: using the '9'-number ?
pascale: and we dial "9", not "8"?
jrichter: Using the 9 number.
tberardini: I'm in and don't hear anyone, except for beeps.
jenclark: that's good. Me too
5:25 PM
kchris: same here, only beeps
gwg: John, will you sing for us so we know you're there?
hjd: someone say something
J-Lo: yes
midori: yes
pascale: yes!! 
pfey: yes
dsfashena: yes
hjd: yes, can hear alex
tberardini: Yes, Hurdil!
jenclark: yes
carol: yes!
hjd: hurdil is not hear today; his evil twin hjd is 
tberardini: who was that?
gwg: lol!
carol: Is anybody talking now?
karenepilcher: still no musak...are we cured yet?
jrichter: I've been dropped from gizmo. I'll be back in a sec.
Alex_MGI: All quiet on the western front.
tberardini: Beep.
midori: all beeping on this front!
jenclark: is the hold button meant to have two bars like a pause button?
kchris: Pop!
midori: mine does
karenepilcher: yes
Alex_MGI: yes
jenclark: good
tberardini: Are you guys on Macs?  I don't see any 'hold' (or any other) button.
pfey: we Mac people don't need that
jenclark: i'm on windows xp
tberardini: There's just a pulldown menu that I can select mute from.
pascale: here the "pause" button (PC) is actually "hold"
dsfashena: my Mac has a 'hold' button on Gizmo.
5:30 PM
karenepilcher: in xp there is a hold (pause-like button).  the mute is a mini speaker with a line through it
pascale: the mute is a crossed out speaker icon
tberardini: aha!  had to click on something to show those buttons.
jenclark: help! musak!
kchris: I still hear nothing.
karenepilcher: yes...view -> call drawer
karenepilcher: pulls up hold and mute options
midori: nothing
dsfashena: nada. rien.
midori: (Which doesn't bother me so much if the alternative is muzak)
jenclark: did nobody else get that brief blast of funk?
karenepilcher: hmmmaybe
kchris: Not I
dsfashena: no funk here, alas
midori: funkless.
tberardini: I just clicked on the MapIt button but it only shows us and Wormbase.
tberardini: no funk here either
jenclark: it was different musak from last time
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hjd: I'm going to need to leave in about a half hour 8-(
midori: hanging up and calling again has restored beeps but no music of any genre
kchris: for me as well
Alex_MGI: I'll give you a transcript 
jenclark: it was only very brief and was when people were playing with mute and hold buttons
tberardini: I hear the hooves!
jenclark: i hear tapping keys now
tberardini: Me too.
dsfashena: my MapIt shows ZFIN (Eugene, OR) and San Diego only
carol: Mine too.
midori: mine shows Cambridge and probably WormBase .. looks like SoCal, anyway
midori: it's John!
tberardini: John!!!  It's you!
kchris: woo hoo!
carol: Hearing you!
J-Lo: certainly can
pfey: yesssss
hjd: yess
karenepilcher: yep
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tberardini: Yes.
jenclark: yes
kchris: yep
pfey: sure
karenepilcher: yes
J-Lo: yes
carol: Yes!
hjd: yes, with echo
midori: yes
Alex_MGI: yes
Alex_MGI: yes
midori: a bit ...
karenepilcher: si
jenclark: not much
kchris: a little
pascale: a bit
tberardini: slight echo
pfey: not much
J-Lo: a bit
dsfashena: yes - echo-ey here
pascale: no
tberardini: worse
jenclark: no
hjd: no
5:35 PM
midori: didn't make much difference
pfey: it's pretty good for me
Alex_MGI: no, but it's tolerable.
carol: It's okay over here.
kchris: It's OK for me
jenclark: it's fine really
dsfashena: It's a feature !
gwg: it's OK, we know you live in a cave
tberardini: can deal with it
hjd: it's not so bad
pfey: right
Alex_MGI: It's like you're lecturing to a large room.
midori: live on the edge
tberardini: let's go
pfey: big auditorium
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jenclark: i hear someone who isn't john
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jenclark: rama is your microphone muted?
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Alex_MGI: Now I can't hear John.
5:40 PM
hjd: vnc just quit, but I can't log in again; 
midori: silence from gizmo
tberardini: same here
hjd: firefox can't eastablis connection to frizzled.lbl.gov
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hjd: ok, back
jenclark: I hear typing but vnc quit
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jenclark: vnc back
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tberardini: I can't get in
midori: neither can I
jenclark: could you just talk us through the moves and we do stuff on our own oboedit?
hjd: i'm in but the window is very fragmented .. opps: gone again
jenclark: me too
kchris: I think I'm still in, but it's updated so slowly, there's really nothing to see
tberardini: OK. I'm back in.
midori: I saw it for a second, but now it says 'Network error: remote side closed connection'
MelissaH: Hi, I had to turn off my virus scan to get on.
Alex_MGI: John just loaded an ontology.
jenclark: I'm happy to just follow along
kchris: I just got bumped off again
tberardini: ok
dsfashena: white noise only here...
5:45 PM
jenclark: i lost you on gizmo
jrichter: Are we having audio problems?
jenclark: back now
tberardini: I still hear you.
Alex_MGI: Gizmo keeps dropping the audio for me, so I hang up and call back in.
kchris: I hear you great
pfey: yes
midori: I can hear you now, but I did have to hang up atd call again.
jenclark: I redialled
hjd: can hear you; vnc is really breaking up tho
midori: lost vnc ...
tberardini: lost audio
jenclark: redial, that should help
tberardini: hung up and called again, ok
MelissaH: I lostVNC too.
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jrichter: VNC is dead. We're just going to follow along.
tberardini: are you there john?
jrichter: It seems that it can't handle this many users.
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jenclark: I hear typing
jenclark: also john
jrichter: So I'm going to try to do irc and speak at the same time.
jrichter: Or roughly the same time.
jrichter: So follow along with what you can see.
jrichter: Or hear.
jrichter: <cough>
jrichter: The first thing we're going to look at is the button panel along the bottom of the term editor panel.
jrichter: Let's start with the split panel buttons.
jrichter: You should see a couple of buttons that look like a grey divider,
jrichter: but they've got little red arrows coming out of them.
jrichter: If you click the one where the divider vertically, it will vertically split your editor pane.
jrichter: Go ahead and try that.
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jrichter: Sometimes the split is way over to the side.
jrichter: More usefully, there's the horizontal splitter next to it.
jrichter: If you click that, your panel will divide with a horizontal divider.
jrichter: Go ahead and try that.
jrichter: And let me know if you have any problems.
5:50 PM
kchris: How do I get rid of a panel if I don't wnat it?
tberardini: The mouse over text says vertical split for the horizontal icon and horizontal split for the vertical icon.
jrichter: The good thing about this is that, you don't have to change your layout to get split panes in OBO-Edit anymore.
tberardini: I'm using beta14.
jrichter: Yeah, the mouseover text is better than what I just said, actually.
tberardini: ah.
jrichter: If you want to get rid of a panel...
jrichter: you have two options.
jrichter: You can click the button with the four green arrows, facing in.
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jrichter: And that will collapse the last divider.
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jrichter: Another way you can do it is just to right click the divider itself.
jrichter: That only works if the divider was created with these buttons.
jrichter: If the divider was specified in the layout, you can't get rid of it that way.
kchris: what's the mac equivalent of right click?
jrichter: Ctrl+click on a mac.
jrichter: Does that make sense?
midori: nope, splat-click ... er, I mean apple-click
jrichter: Oh, yeah.
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kchris: yep, apple-click works
jrichter: Normally on macs, ctrl+click means right-click. But I've changed OBO-Edit so that it's command-click for right click.
gwg: cunning!
jrichter: I did that because control click has special meaning to java, and it was creating problems in DAG-Edit.
jrichter: Moving on...
jrichter: The next button is the lock button.
jrichter: The lock button makes it so that the screen won't scroll.
jrichter: To demonstrate, expand a bunch of terms so that the screen is really long.
jrichter: Then go somewhere in the middle and click something.
jrichter: Click the lock button to lock the screen in place.
jrichter: The screen won't scroll away from the thing you've locked.
tberardini: The color changed. Is it supposed to do that?
5:55 PM
jrichter: The color is supposed to change to indicate that the panel is locked.
jrichter: Only the panel that you've locked has disabled scrolling.
jrichter: So this can be useful when you've got a bunch of panels open.
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jrichter: You can lock the screen on something you want to move
jenclark: can we make the grey background a bit lighter?
jrichter: and you can be sure it's not going to scroll away and disappear when you search, for example.
jenclark: it's a bit hard to read
jrichter: Yeah, I can change that in the next version.
jenclark: thanks 
jrichter: Let me put that on the todo list now.
jrichter: Quick question: is there anybody who is using IRC to understand what I'm saying?
jenclark: on and off
tberardini: no
hjd: yes, but gizmo is working ok also
dsfashena: no
J-Lo: no
karenepilcher: it's good if you miss something, though, you can refer back
kchris: yea, occasionally when my Gizmo gets dropped
gwg: de temps en temps
jrichter: Okay, I'll keep IRC going.
Alex_MGI: Gizmo keeps dropping out for me.
midori: I'm using it to catchup when Gizmo craps out ...
jenclark: I'd be fine with just gizmo
jenclark: me too
Anon544: Using both..
gwg: John, could you put tool tips on those little icons?
midori: ... I dial back in immediately but usually miss a sentence or two in the time it takes
tberardini: There are tool tips.
jrichter: gwg there should be tooltips already.
jenclark: I have them
gwg: I have 'em now
gwg: ahem
kchris: tooltips being the mouseovers?
gwg: ya-huh
jrichter: Yeah, little mouseover messages are called tooltips.
jrichter: Anyway, let's unlock the screen and move on.
jrichter: Unlock the screen using the lock button again.
jrichter: The next button over looks like two swirly arrows.
jrichter: That's the reload button.
jrichter: Normally, you should never have to use it.
jrichter: But occassionally there'll be a bug where the screen doesn't redraw correctly.
J-Lo: does ctrl-W still work too?
midori: I've met that bug.
jrichter: You can use that button to get a correct screen redraw.
jrichter: I didn't know Ctrl+W ever did anything.
J-Lo: lol! it used to...
jrichter: The next button is the filter/render button.
6:00 PM
jrichter: In DAG-Edit, it was in the bottom right corner of the term editor panel.
jrichter: We'll skip it for now and talk about it when we do filters.
jrichter: The last button is the mysterious root selection algorithm button.
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jrichter: There are two algorithms.
jrichter: The second one, STRICT, will only show roots that are defined as roots in the ontology.
jrichter: The STRICT algorithm prevents terms that are orphaned by filtering from showing up as roots.
kchris: does that mean that they won't show up at all?
hjd: bye
gwg: does defined as root in the ontology == no parent terms?
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jrichter: Yup, that's right Amelia.
tberardini: Can you show an example?
tberardini: Ok.
jrichter: We'll show some examples when we do filtering.
jrichter: I'll describe one now though.
gwg: just like the term "biological process", which has no is_a or part_of parents
jenclark: how?
jrichter: Let's say you do a filter that only shows isa links.
jrichter: Right gwg.
jrichter: If you do an isa only filter, a lot of terms can't be shown.
jenclark: how do you do that filter?
jrichter: Because there's no path to them.
jrichter: Patience, Jen, we'll do that in a little bit.
jrichter: Anyway, if you're using strict filtering, the terms you can't get to because they're filtered out will just not show up.
jrichter: If you use the greedy algorithm, they'll appear as roots.
jrichter: And we'll revisit this with filtering.
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jrichter: We haven't looked at the button all the way to the left.
jrichter: That's the primary selector button.
jrichter: That button decided which term editor panel is the primary selector panel.
jrichter: The primary selector panel controls what the global selection is.
6:05 PM
jrichter: If you've got a split panel, for example, and you select something in the bottom panel, it doesn't become the primary selection.
jrichter: Try that now. Split your panel (if it isn't split already) and select something in the bottom panel.
tberardini: It's a lighter purple than the term selected in the upper panel.
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jrichter: Yeah, it's lighter purple to show that it's not the primary selection.
tberardini: aha.
jrichter: If you click the primary selector button on the bottom, the selection on the bottom will become the primary selection.
jrichter: Try it.
jrichter: This is useful for working with different sections in the ontology in different panels.
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jrichter: When you do a search or render by clicking the search or render button (as opposed to another way we'll discuss later), the search or render happens in the primary selector panel.
jrichter: Any questions about those buttons?
jrichter: Oh, I thought of one more thing.
jrichter: There's a little button with a minus sign on it in the bottom right of the term editor panel, above the button panel.
jrichter: Click that to hide the button panel.
tberardini: I can't hear you anymore and I hung up and called back three times.
Alex_MGI: same here
midori: same here ...
J-Lo: I'm interested in the root selector thing, but I'll wait until we do filters
midori: lots of beeps
MelissaH: me too
midori: yes
6:10 PM
dsfashena: yup
pascale: same here- I can hear a few seconds and then it goes away. Maybe there are too many people? 
jenclark: yes
tberardini: you're back!
Alex_MGI: yes
kchris: yep
MelissaH: yes
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jrichter: Anyway, any questions about those buttons?
jrichter: Besides the root selector or filter buttons.
jrichter: Cause we'll do those later.
jrichter: Okay, then lets to move on to editing.
jrichter: If you look at the user's guide on editing, you'll see a lot of references to targets and sources when editing.
jrichter: There are a lot of ways to achieve an edit in OBO-Edit. They all work the same way, as long as you realize how targets and sources work.
jrichter: To demonstrate, let's start with a term move.
jrichter: Choose a term from anywhere in the ontology, and drop it somewhere else.
jrichter: The term (or terms) that you moved are the source terms.
jrichter: The place you dropped it, is the target term.
jrichter: When you dropped that term, a popup menu showed up.
midori: 14's ok
jrichter: There's another way to do that edit.
tberardini: I see the pop up in 14.
jrichter: The popup works in every version, but the actual move doesn't
MelissaH: if you don't choose anything from the menu, then does nothing happen?
jrichter: Yeah, if you choose nothing, nothing happens.
jenclark: move doesn't work in b15
MelissaH: lost your voice
jrichter: The other way to do an edit like that is to select the source terms, and then right-click the target term.
6:15 PM
MelissaH: yep
pfey: you are back
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jrichter: When you right-click, you'll see the exact same menu that would have popped up when you dropped them term.
jrichter: Rama, are you having connection problems?
tberardini: Rama is just trouble.
rama: yes, I did. I just got in fine. thanks
jrichter: Okay, good.
jrichter: Anyway, the important thing to remember is that right-clicking is targeted, like drag and drop.
jrichter: This can be really useful if you need to move/merge/copy terms that are really far apart.
jrichter: You don't have to drag a term a long way, you can just right-click where you want it to go.
jrichter: Give that a try, and see if it works.
midori: yep
tberardini: Wonderful!
kchris: cool, that's really nice!
Anon544: Very useful!
jenclark: the idea is great. It doesn't actually work in b15 but the idea is good.
MelissaH: awesome.
tberardini: lost your voice again, John.
jrichter: If anyone's using beta15, go ahead and get beta14 for this demo.
midori: anyone else lose gizmo?
jrichter: I'm downloading it right onw.
MelissaH: me too
Alex_MGI: can't hear you
jrichter: Gizmo just died for me.
jrichter: I'm logging back on.
dsfashena: nice feature!
jrichter: I'll proceed using only IRC for the moment.
jrichter: There's another way to define targets and sources.
jenclark: wasn't there a problem with the windows installer on b14?
MelissaH: I installed windows b14 ok
jrichter: I think the windows installer should be okay on beta14.
6:20 PM
jrichter: It was the mac installer that was screwed.
jrichter: Anyway,
jrichter: there's another way to define targets and sources.
J-Lo: beta 12 didn't work on windows - beta14 fine
jenclark: i lost you on gizmo
J-Lo: i meant beta 13 didn't work on windows 
tberardini: Are we just on IRC now?
pfey: seems like it
Anon544: Seems like it.
jrichter: Gizmo should be back in a second.
jenclark: yes
dsfashena: yup.
tberardini: hear you
kchris: yep
J-Lo: yep
Alex_MGI: yes
jrichter: Great.
jrichter: Anyway,
jrichter: When you select a bunch of terms at once, you'll  notice that one is colored darker than the other.
midori: those options are greyed out when I select two terms ...
jrichter: If you select a targeted operation like move/merge/copy from the edit menu, the darker colored one is the target term.
jrichter: The others are the sources.
J-Lo: sorry - can you define source and target again please?
jrichter: It may be, that recent versions of OBO-Edit have this disabled, because it's a little confusing.
jenclark: i have it
jrichter: For J-Lo, sources and targets mean different things for different operations.
karenepilcher: the color difference is subtle for me
jrichter: For copy, the sources are the terms that you're copying, and the target is the place you're copying them to.
J-Lo: okay
6:25 PM
jrichter: When you look at the docs, the sources and targets are listed for each operation.
jrichter: Open up the help menu now, so we can look at this.
midori: wait - it's only the Edit menu that's greyed out ... the editing operations are 'live' via right-click
jrichter: That's good news, midori.
MelissaH: I have two terms selected, and a right click on either gives greyed move, merge, etc.
jrichter: Anyway, if you've got the user's guide open, look at the section called structural editing, under editing.
jrichter: And click the Moving section.
jrichter: You'll notice that it shows how you can achieve the operation under gesture types, what hot keys work, whether a target term is required, and what kind of sources are needed.
jrichter: Some operations don't need a target at all.
jrichter: For example, select the "Deleting" section.
jrichter: Deleting operates only on the sources, so when you right click and choose delete, it doesn't matter where you right click.
jrichter: The target is just ignored.
jrichter: So let's look at drag and drop some more.
jrichter: If you just drag and drop a term, you always see the operations menu when you drop.
jrichter: But usually you'll know what you want to do before you drop.
jrichter: You can use hotkeys to specify the drag and drop operation so you can skip the popup operation menu.
6:30 PM
jrichter: So pick up a term and drag it, but don't drop it.
jrichter: You'll notice that the title bar of the dragged terms says "Dragging terms..."
jrichter: Now hold the X key on your keyboard.
jrichter: The title should change to "Move..."
J-Lo: fancy!
jrichter: If you drop that term somewhere, you'll automatically do the move.
jrichter: It'll still popup the type selection menu, but that's one less step.
jrichter: If you hold down shift+X while you drag, it'll say something else.
gwg: if the 'term filter' window has the focus when you're doing the d-n-d, you get a term filter text box full of Xs
jrichter: Good point, gwg.
gwg: is that a 'feature', tho?
jrichter: I'll fix that.
jenclark: i lost you on gizmo
Alex_MGI: Are you still connected on Gizmo?
tberardini: lost you on gizmo too
dsfashena: soundless despite 2 redials
pfey: can't hear youcancan't hearcan't hearyes
midori: not just me then ...
jrichter: The problem on Gizmo is me.
tberardini: No one can hear John scream.
jrichter: My router keeps choking.
MelissaH: mine changes from move to move(original type)with the shift.
jrichter: Yeah, when you hold down shift it says "Move (original type)"
kchris: Gizmo drops the sound for me every 5 minutes, though it still shows the call as going
jrichter: When you drop, no menu appears at all.
jenclark: yes that's right. I think it just means that you get the same relationship as the original parent
tberardini: Yup, did that for me.  Very nice shortcut.
jenclark: yay
pfey: yes
dsfashena: yes
jrichter: There are couple of operations that have drag and drop shortcuts.
6:35 PM
jrichter: Move is X
jrichter: Copy is C
jrichter: Merge is M
jrichter: Change relationship type is T
jrichter: Lets look at that last one.
jrichter: You can change relationship types via drag and drop.
MelissaH: sorry, just got you back, where do I get the part of from?
tberardini: How do you select the part of bit only?  I'm gettng the whole term.
jrichter: Drag the "part_of" relationship onto "cell envelope -is_a-> envelope"
tberardini: Oh, there.
jrichter: Oh, select the part_of relationship from the Properties section of your ontology.
jenclark: eh?
MelissaH: where?
jenclark: ah!
jrichter: There's a section of every ontology, called Properties.
jenclark: got it
jrichter: It's blue.
MelissaH: me too
jrichter: All your relationship types live there.
tberardini: Isn't it just easier to do the right click and change relship type?
jrichter: Anyway, you can drag those right onto relationships to change their types.
jrichter: It's probably easier to use right-click in most cases.
jrichter: If you had an ontology with a lot of relationship types, you might be better off doing it this way.
jrichter: Anyway, the idea is that drag and drop does a lot of things.
jrichter: I'm not going to go over every editing operation, because they're in the manual, but I do want to discuss cloning and rerooting.
6:40 PM
jrichter: Cloning makes an exact copy of a term, with all the same parents, children, and other attributes, but a slightly different name and different id.
jrichter: Select a term you want to clone.
jrichter: Right click and select "Clone" from the right click menu.
jrichter: If you select your clone, you'll see it's just the same as the parent.
jrichter: This can be useful if you want to do a split.
jrichter: Particularly if you want to do an N-way split.
gwg: that's magnificent, John!
jrichter: There seem to be a slight bug, because the namespace isn't being preserved.
jrichter: I'll put that on my to-do list now.
jrichter: This kind of thing is really easy for me to add to OBO-Edit, so if you have suggestions for new operations, please let me know.
jrichter: Another thing I want to talk about is re-rooting.
jrichter: Sometimes you may want to make a root out of a term that is currently a child of another term.
rama: okay, nothing happened when I selected clone
jrichter: Rama, are you using beta15?
pfey: it takes a little bit
rama: yes
J-Lo: lost yr vocals John
jrichter: beta15 has broken link creation behavior.
pfey: me too
pfey: lost John
Alex_MGI: me too
rama: okay. 
tberardini: linking works in beta14
6:45 PM
pfey: what's going on?
midori: gizmo is beeping a lot
tberardini: radio silence here
jrichter: Rama - go ahead and install beta14 for these demos.
jrichter: Everyone else - I'm rebooting my router, we'll have voice back in a moment.
jrichter: Anyway, back to the re-root command.
jenclark: I still don't hear you
rama: yes, i am installing it now
jrichter: Gizmo is hosed for a moment. Proceeding with text...
6:50 PM
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rama: I installed beta 14, i right clicked on a term and picked Clone. i still don't see the clone. Obviously i am missing something
jenclark: the name says' 'CLONE'
J-Lo: it's called CLONE OF and then the term name...
jrichter: The new term name should be "CLONE OF <original term>"
tberardini: Highlight the term first, then right click and select clone.
Anon544: the cloen appears under the same parent, and the name is preface by "clone of"  It's in alphabetical order.
jrichter has quit the server saying: Quit:  Leaving
tberardini: Is it lunchtime?
jenclark: always
MelissaH: For me too. I just ate mine.
rama: I am really missing something. I don't see a CLONE OF option. I only see Clone. Sorry for being slow
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jenclark: it's just called clone in the menu
midori: clone is the option ... the resultshould be a new term with CLONE OF in front of the term name
6:55 PM
MelissaH: Maybe pick something with only a few children, maybe its far away from your choice.
dsfashena: is all this cloning still legal ?
rama: got it. sorry.
midori: we should be fine on this side of the pond
kchris: pick something with only a few siblings, or pick something that starts with a letter close to C, since the clone will be in the c's
jenclark: you are
MelissaH: loud and clear
jrichter: We seem fine with cloning.
jenclark: yes
rama: yes, yes.
MelissaH: BTW, what about having an option to not alphabetize?  There is anatomy inherent in the order.
jrichter: Open up cellular component and select "cellular component unknown"
jrichter: Whoa! Wait a sec!
jrichter: There shouldn't be any information encoded in your term order.
MelissaH: Why not?
jrichter: Term names shouldn't encode any information.
jrichter: If there's ordering, it needs to be communicated via a relationship type.
MelissaH: Our anatomy advisors really want that feature, maybe need a new relationship type?
jrichter: Like structure_a --becomes--> structure_b
MelissaH: is anterior to?
jrichter: Perfect.
jrichter: Yeah, is_anterior_to is exactly the kind of thing you want.
tberardini: PO (plant ontology) developmental stage ontology has ordering of the dev. stages but they imposed it using artificial numbers at the beginnings of their terms. Ugly but that's the way they got ordered stages displayed.
jrichter: Again, that's fine for people, but reasoners won't be able to use that information.
MelissaH: doesn't work for roman numerals...
tberardini: How would one encode that type of info in a relationship type then?
7:00 PM
gwg: A is_followed_by B
jrichter: Well, if you're describing spacial relationships, is_anterior_to is perfect.
tberardini: Temporal relationships though.
jenclark: relationship type: precedes?
MelissaH: You can use develops_from for stages
jrichter: Or, like Amelia said, is_followed_by or develops_from
jrichter: A lot of groups are using develops_from already.
jrichter: Okay, moving on to rerooting again...
jrichter: Select one of the unknown nodes, like cellular_component_unknown
jrichter: Right click and choose reroot from the menu.
jrichter: You'll see that it has become a new root.
jrichter: Reroot only works on terms that have a single parent.
jrichter: Reroot deletes the selected parent relationship, but doesn't obsolete the orphaned term.
jrichter: Instead, the orphaned term becomes a root.
jrichter: This is most useful in young ontologies where the roots haven't been fully nailed down yet.
Alex_MGI: Can this be used to store terms for later use?
jrichter: What do you mean, Alex?
pfey: you sound like very far away John
tberardini: I think that was Alex.
jenclark: I heard him
midori: shoot, I missed that ... Alex was very very quiet
jrichter: I can't hear spoken questions; I have my volume turned off to reduce echo.
jrichter: Please type your reply, Alex.
tberardini: I think Alex is frantically typing.
jrichter: Welcome to my world.
jrichter: Have you ever tried to type and speak at the same time.
pfey: someone is
jrichter: Maddening!
7:05 PM
jenclark: you need an assistant
jenclark: alex says he is typing
jrichter: Cool.
Alex_MGI: Okay, what if you had a small hierarchy of terms and you realized it was in the wrong place.  Could you 'store' the term hierarchy as a root for use later, under some other term?
jrichter: Absolutely.
Alex_MGI: Good.
jrichter: Ideally, you would reroot them, and then save them to a seperate file.
tberardini: Gizmo be gone.
MelissaH: for me too.
jrichter: We'll talk about how to do that when we get to filtered saves later in the day.
midori: same here
pfey: yep
Alex_MGI: It's too bad I talk faster than I type.
Alex_MGI: No more questions at the moment, though.
jrichter: I'll try to fix Gizmo during lunch, but it's wasting a lot of time to keep rebooting the problem router.
jrichter: For now, we'll just do text.
Anon544: sounds good.
midori: ok; a respite from the #*&^&#^(&^@*^#P BEEPING!!!
midori: (ok, calm now)
MelissaH: yeah!
jrichter: Let's move on to Namespaces.
jrichter: Strike that, let's do categories first.
jrichter: To add or remove a category, you use the Category Manager Plugin. Go ahead and open it now.
jrichter: (Under the Plugins menu)
jrichter: To add a new category, hit the add button. On the right, type in the new category information.
jrichter: Particularly important is that Category Name (that should probably be called "Category ID")
7:10 PM
jrichter: The Category Name is the id that you'll use to refer to the category in the filtering dialogs.
jrichter: The category description is what you'll see in the text editor window when you select a term.
jrichter: Let's create a new category with the name "boring" and description "Boring Terms"
jrichter: Click the save changes button to make your changes permanent, and then close the window.
jrichter: Now, select a term and click the "Categories" tab in the text editor panel.
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tberardini: I clicked on save changes and the changes went away, didn't get saved.
tberardini: beta14
jrichter: Huh.
midori: maybe Jane's method will work
jrichter: What's Jane's method?
dsfashena: my new category also vanished (b14)
tberardini: The changes were there for a split second, then reverted to the default.
jenclark: mine stayed
MelissaH: mine is fine
J-Lo: just keep clicking save until it works
karenepilcher: me too, it's ok
midori: hit save over and over again until the bloody thing finally caves in and retains your info
Anon544: mine stayed.
kchris: mine stayed too, using 14
jrichter: That doesn't happen on mine.
tberardini: but I have to keep changing the info over and over because it goes away when I click save!
jrichter: Are you sure that your changes are being lost? When you hit save, your new category becomes unselected.
jrichter: But it shouldn't disappear.
midori: it's analogous to the Great Dbxref Library Bug
tberardini: It's gone, baby, gone.
midori: (item 1420771 in the SF bug tracker)
jrichter: What OS are you using?
tberardini: Windows XP
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dsfashena: 2nd attempt succeeded.  b14 mac os x
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pfey: doesn't stick for me either
pfey: beta 14
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jrichter: Strange. This doesn't happen at all on my machine.
pfey: OS 10.4.4
7:15 PM
tberardini: Hmmm.  I started all over again and now it worked and added another new category.  Go figure.
J-Lo: i think it's part of the Great Dbxref Library Bug - the Global filter save doesn't work either...
midori: I've got 10.4.4 too, but mine worked.
kchris: also using b14, Mac OS X, and it worked fine, now I just need to learn how to apply the category
Alex_MGI: At first it appeared to save it, but then the new category disappeared, but now I got to work on a third try.  OS 10.3.9 mac.
jrichter: There must be some kind of timing problem on non-Linux systems.
jenclark: it works on my xp with b14
Alex_MGI: Also b14.
jrichter: I'll revisit this bug this evening.
tberardini: It's something.  ANyway, looks like we can move on.
jrichter: Has everyone gotten a new category to stick.
jrichter: ?
jenclark: yes
rama: yes
tberardini: yes
kchris: yes
MelissaH: yes
carol: yes
dsfashena: yup
pfey: well, I tried to save 'Super_Boring but no luck with this either
pfey: no
Alex_MGI: yes
pfey: well
pfey: it is 'NEWCAT
J-Lo: no
jrichter: If you're having trouble, pretend that it worked, and just use an existing category for the next step...
jrichter: Select some term and click the "Categories" tab in the text editor panel.
jrichter: You can assign a term to a category by clicking the checkbox next to the category name, and then clicking the commit button.
tberardini: Got it.
jrichter: Now let's move on to namespaces, that work similarly.
jrichter: (And, I suspect, have similar interface bugs for non-Linux users)
jrichter: First of all, namespaces are misunderstood creatures.
midori: much like curators ...
dsfashena: and leeches
7:20 PM
gwg: and sociopaths
jrichter: In OBO, a namespace is a really just a special kind of term category.
Alex_MGI: Namespaces are better paid, however.
tberardini: and amelia
gwg: thank you Tanya! Someone who understands... finally 
jrichter: Let's focus, children. Otherwise we'll have quiet time.
jrichter: Anyway,
jrichter: Namespaces are used to organize where
jrichter: a term belongs.
jrichter: That is, a namespace indicates which ontology a term (or relationship) belongs to.
MelissaH: Kinda like which root, as per the GO example?
jrichter: I should have said, which LOGICAL ontology a term belongs to.
jrichter: Yes, Melissa, but it gets fuzzy.
jrichter: For example, let's say we've decided to make cross products between GO and the mouse anatomy.
jrichter: Where does "mouse heart development" belong? Where do the links between "mouse heart development" and "development" belong.
jrichter: ?
jrichter: This becomes really important when you've got a whole bunch of ontologies loaded, and you need to save some terms in one file, some other terms in another file, and yet other terms in a third file.
jrichter: Namespaces allow you to say exactly which logical ontology terms and links belong to, and that information can be used to direct different terms and links to different files when you save.
jrichter: We'll look at some examples when we get to filtered saves this afternoon.
jrichter: To create a new namespace, open the Namespace Manager Plugin.
jrichter: Namespaces only have one attribute: id.
pascale: are you going to talk about IDs? I'd like to know what IDs I should use if I make cross products
7:25 PM
jrichter: Yeah, we'll talk about id generation this afternoon also.
pascale: ok thanks
jrichter: You get to make up whatever id you want for a namespace though.
jrichter: Let's try "cross_products" for our new namespace.
jrichter: (Hopefully it will work)
tberardini: Worked here.
midori: worked for me
Alex_MGI: worked here too
kchris: here too
MelissaH: me too
rama: yup
jenclark: and me
carol: yes
jrichter: (It worked for me too, but I think I just got a hint about what's wrong with the category manager from the way it saved)
dsfashena: me too
jrichter: Okay, now select a term to assign to the new namespace.
midori: the prlot thickens
pfey: worked even for me
jrichter: When you click the Namespace dropdown in the Term Text Editor, your new namespace will appear.
pfey: oh no, it didn't stay.. the same bug
jrichter: (pfey - I'll work on this during lunch. Hopefully it won't be too hard to fix)
jenclark: i have this bug though i didn't have the other
MelissaH: mine appeared ok
dsfashena: lack of persistence here as well
ranjana: I see mine in the drop-down
jrichter: Excellent.
kchris: mine are showing up in the dropdown, in b14
pfey: now it did stick..
tberardini: ok here too
jrichter: If you had a bug saving, just try selecting an existing namespace from the dropdown.
rama: okay, showed up in the drop down, in beta 14
jrichter: It's also possible to select a namespace for a link.
jrichter: To do this, open the Parent Plugin.
jrichter: It will show you a list of all the parents of the selected term.
J-Lo: yeah - doesn't save existing namespaces either...
7:30 PM
jrichter: You have to hit commit to save a namespace change to a term.
jrichter: In general, anything you do in the term text editor doesn't stick until you hit the commit button.
midori: ok, I did hit commit, and it changed back to the original namespace!
tberardini: In the Parent Plugin, I don't see the namespaces of the terms, though they have them.
dsfashena: same problem here - odd - it has worked o.k. before.
jrichter: Yikes, midori. You're right!
jrichter: It's a bug.
gwg: what is supposed to happen?
jenclark: it worked for me! Yay!
jrichter: I'll look into it.
jrichter: Anyway, about the parent plugin.
Alex_MGI: Changed it back for me on at least two tries.
MelissaH: my terms don't seem to have a namespace assigned in the parent plugin, but do in the term editor. mine doesn't commit either.
jrichter: In the parent plugin, the namespace dropdown will always say "no namespace", even if the parent term has a namespace.
midori: same here - changed back whether I tried to change TO te new 'cross_products' namespace or to one of the other existing ones
jrichter: That's because this is the namespace of the LINK between the child and parent, not the parent term.
MelissaH: gotcha
rama: wait, please
jenclark: mine can have different namespaces
jrichter: There's a bug in the term text editor namespace assignment code. It just doesn't seem to be working.
rama: I picked a term, opened the parent plug in and then I just hit commit on the text editor?
jrichter: Rama, here's how it works -
jrichter: To change a TERM namespace, choose a new namespace in the dropdown box in the term text editor, and hit commit.
jrichter: (It won't do anything right now, because there's a bug. But that's how it's supposed to work)
jrichter: To change the namespace of a LINK, just pick a new namespace from the namespace dropdown in the parent plugin.
rama: keep going. i am following
jrichter: It commits automatically.
jrichter: Does anyone have any questions about that? Particularly the distinction between term and link namespaces?
7:35 PM
jenclark: yes
jrichter: ...?
kchris: This works for me, but I don't understand what the point of giving the link a namespace is.
midori: OK, that part works for me (i.e. I can assign a namespace in the parent plugin).
rama: I did not get the Link part
jenclark: how can a link have a namespace?
jrichter: Consider:
midori: Now, when and why will I want to do that in real life?
jrichter: I believe you will, midori.
MelissaH: would that be the third "mapping" file between two ontologies?
jrichter: Let's consider an example:
jrichter: What if we wanted "heart development" to have a link to the term "heart" in some generic anatomy ontology.
jrichter: ?
jrichter: We don't want that link to show up in the regular go file; people will want to know why there's a dangling link in the ontology.
jrichter: We also don't want that link to show up in our generic ontology for the same reason.
MelissaH: a third mapping file?
jrichter: Exactly. We want to create a third file called "go_anatomy_ontology_links.obo"
MelissaH: and that would be a namespace, correct?
midori: gotcha
jrichter: We create a special namespace for those links, and we save that namespace into a third file at the end of the day.
jrichter: Note that there are other ways to do this; namespace are just the most straightforward way.
jenclark: what do you mean 'that would be a namespace'?
jrichter: You can do something similar with tricky link filters.
MelissaH: or different ID prefixes
jrichter: I think Melissa means that you would use a special namespace to designate those links that belong in a third file.
MelissaH: yes
jrichter: A special ID prefix wouldn't do anything for us because there aren't any new terms - only new links.
7:40 PM
jenclark: so it's a file with terms in it but they're not linked within that file, just out to other files?
jrichter: The third file wouldn't contain any terms even. It would only contain links between terms.
jrichter: The stanzas would look like this:
jrichter: [Term]
jrichter: id: GO007507
MelissaH: and couldn't be run without the other two, right?
jenclark: yes I see
jrichter: relationship: works_on_structure GENERIC_HEART_ID
jrichter: Melissa is right.
jrichter: If you tried to load the file by itself, there would be an error.
jrichter: However, you could add import: directives to the top of the file to force the other files to be loaded automatically.
jrichter: Moving on...
jrichter: There's one last "Manager" plugin I want to look at.
jrichter: Open up the Synonym Category Manager Plugin (and be prepared for the same bugs as before)
jrichter: If you're using the GO, this will be blank.
jrichter: Click "Add" to add a new synonym category.
jrichter: Type UK_SPELLING for the category id.
jrichter: And "Incorrect British Spelling" as the description
J-Lo: oi!
jrichter: Choose "Exact Synonym" from the scope drop down.
tberardini: So far, so good.
jrichter: Then grit your teeth, pray, and click "Save Changes"
7:45 PM
tberardini: Success!
jrichter: If it doesn't work, keep trying until it does.
jenclark: worked
kchris: me too
rama: yup!
MelissaH: me too
Alex_MGI: yes
midori: worked
carol: yes
J-Lo: yes, saves for me
jrichter: The point of Synonym Categories is to designate special types of synonyms.
jrichter: So this synonym category would be used to record the UK Spelling for a term.
jrichter: So select the term "biological_process"
jrichter: and click the synonyms tab.
jrichter: Click the "Add" button to add a new synonym
jrichter: As we know, the correct British spelling of "biological_process" is "Her majesty's biological_process"
jrichter: So type that in as the synonym text.
jrichter: Choose "UK_SPELLING" from the synonym type dropdown.
jrichter: Sorry "Incorrect British Spelling"
jrichter: You'll notice that the synonym scope box was grayed out.
jenclark: funky!
jrichter: That's because we specified a scope for our synonym category, so it was chosen automatically.
jrichter: As usual, hit the commit button if you want to save the changes.
jrichter: This feature can be used to specify different languages, spelling conventions, or to indicate a special standardized name for something.
jrichter: Chebi uses a special synonym category for long standard chemical names.
tberardini: does one have to select a synonym type for a synonym?  What about a synonym scope?
7:50 PM
jrichter: You don't need a synonym type, but you do need a synonym scope.
tberardini: OK.
jrichter: If you don't choose a scope, "related synonym:
jrichter: is chosen by default.
jrichter: Any other questions about namespace, categories or synonym categories before we move on?
midori: nope
jrichter: (Lunch/dinner/hour long bathroom break in 10 minutes)
jrichter: Okay, last thing...
jrichter: Assigning replacements for obsolete terms.
jrichter: First, expand the "Obsolete" section of the ontology.
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jrichter: Let's say that the first item in the list can always be replaced with "protein complex"
jrichter: (I know this is wrong)
jrichter: Select "protein complex" and drag it onto that first obsolete term.
jrichter: You'll see a menu.
jrichter: "Add consider term" means "Add a term that humans should consider to replace this one"
jrichter: You can have as many "add consider terms" as you want.
jrichter: "Set replacement" means "This term can always be used to replace this obsolete term. A human doesn't even have to look at it."
jrichter: Go ahead and pick one of the menu options.
tberardini: It added protein complex and all of its children, is that what's supposed to happen?
jrichter: That's just a trick of the interface.
7:55 PM
jrichter: protein complex is the only one that was really added.
J-Lo: by clicking on the obsolete term, there's no way of telling in OBO-Edit what its replacement terms are?
MelissaH: under the +
jrichter: You can expand the obsolete term to see its replacements
J-Lo: oh i see
rama: I added protein complex and now i see the same obsolete term under the +
jrichter: I'll put it on my to do list to hide the children of the replacement terms.
tberardini: Yes, that would be less confusing.  Thanks.
jrichter: Rama - hit undo.
rama: did it
MelissaH: Presumably one would never be able to have relationship replaced_by or consider anywhere but in obsolete terms?
midori: correct
jrichter: Rama - Drag "protein complex" onto the obsolete term and release.
jrichter: The obsolete term should have a plus next to it. Click the plus to see the replacement terms.
jrichter: Melissa - replaced_by isn't even a real relationship type.
jrichter: It's just a way of showing those replacements in the interface.
MelissaH: ok
jrichter: You'll notice that consider and replaced_by don't appear in the properties section.
kchris: How do these show up in the OBO file?
jrichter: There's a special line that says replaced_by: or consider:
kchris: cool
jrichter: This is a better than putting that info in the comments, because its more easily parseable.
tberardini: very nice
rama: cool
jrichter: Select the replacement term under the obsolete term and right-click.
J-Lo: we should start using this really
midori: It appears that one can only add one term with the 'set replacement' opition - is taht true?
jrichter: Near the bottom of the first section, you'll see the options "Remove replacement term" and "Remove consider term"
jrichter: Yes, midori.
jrichter: That's because there can only be one term for automatic replacement.
midori: That won't work for GO (can't comment on other ontologies).
8:00 PM
tberardini: You can also have a consider term and a replacement term.  Should it only allow a replacement term alone and not in conjunction with a consider term?
jrichter: Otherwise, you need a human to look at it, and you're dealing with a "consider" term.
jrichter: You should only be allowed to have consider terms or a single replacement term.
jrichter: If it's allowing both that's a bug.'
tberardini: I mean, you can have a consider and a replace together in beta14.
MelissaH: i have both
jrichter: Yeah, that's bad. On to this list it goes.
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jrichter: That should be easy enough to fix.
gwg: you can have terms where there are two or more direct 'replace' terms
jrichter: How?
jrichter: How could you know which one to use?
gwg: you would use both
midori: Not true! 'Use' (i.e. replacement) versus 'consider' has to do with whether a term can safely be applied in all cases, and that doesn't depend on whether there's one or more. We have some obsolete terms for which we're quite confident that two terms can both be applied to the gene products in question.
kchris: but if there are two or more direct replace terms, then don't you need a human to consider which one to choose anyway? making them effectively consider terms
jrichter: I'm with kchris.
gwg: I'm with Midori
midori: Not true! I'll type up the explanation over the break.
jrichter: Okay, Midori.
midori: oops, sorry fo rthe duplication there ...
kchris: It hadn't occurred to me that you could have more than one always correct replacements, if that's true, then seems fine
Alex_MGI: John,
jrichter: But if we allow more than one replacement, that should mean that a computer can go through a gene product file, and every time it sees the obsolete term, replace that line with BOTH replacement terms. Is that right?
jrichter: Yes, Alex?
midori: yes
Alex_MGI: I can't get the replace term option on the pop up menu after doing the first one.
jrichter: Which version are you using, Alex?
Alex_MGI: b14
midori: Anyway, we may also have obs terms for which we're sure one term can be used, but another must be looked at. So it's not a bug to allow a 'set replacement' and 'consider term'.
jrichter: I think we're having a semantics disconnect here.
8:05 PM
jrichter: In OBO format, replaced_by just means - "In every case where the obsolete occurs, blindly use this replacement"
midori: (OK, I think I've said everything now, so there isn't anything to leave after all.)
kchris: We might want to use the replace only for cases where the replace not just 'can be used', but always should be used
jrichter: "consider" means "There are a couple of terms to look at, so a human needs to be involved"
jrichter: [Anyone who isn't interested in this conversation should feel free to go to lunch]
jenclark: when do we come back?
midori: 'consider' means a human must look, regardless of how many. lots of terms say 'consider this [one] term.
jrichter: 1pm PST (it's now 126 PST)
jrichter: That's fine, you can have "consider" this one term.
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pascale: John, are you able to save the chat and post it somewhere after the seminar ? (or email it)
jrichter: replaced_by just has a special meaning for obsolete resolvers.
jrichter: Yes, pascale, but I only have the chat as of my last disconnect. The previous archives are gone.
pascale: that's better than nothing
dsfashena: Maybe the NSA has recorded it.  Let's ask them.
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kchris: I should have the whole thing, I haven't been disconnected from the chat, and I just saved it to a file, I think, I'll check the file
jrichter: Thanks, Karen.
pascale: I cant copy the chat from this window here
midori: I have everything since 4:35 PM GMT/8:35 AM PST
Alex_MGI: I have a record from before the official start.
pascale: great! 
jrichter: Everyone who has a chat archive should save it and email it to me.
jrichter: I've also put my IRC client in logging mode, so I should now have an uninterrupted log no matter what happens.
kchris: Yea, I have from before 9:20 am and I just checked the file.
8:10 PM
jrichter: Midori - should we take the replacement conversation to the working group email list?
jrichter: ?
rama: sure (to the working group mailing list)
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hurdil: hurdil has overcome his evil twin
Alex_MGI: I think they're all on break now.
jrichter: Hmm... am I to assume that hurdil has the power of flight?
jrichter: Unlike Harold, who just has minor sprinting capabilities?
jrichter: (Thanks Alex)
hurdil: he sees all
midori: ok
jrichter: Okay hurdil & co. I'm going to lunch. See you in 45 minutes.
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8:15 PM
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8:45 PM
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8:55 PM
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jrichter_: Hey, folks.
Alex_MGI: Still here.
midori: I'm back
midori: although the cat has taken my chair
kchris: I'm  here too
9:00 PM
jenclark: that must have been a nice warm chair
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tberardini: Suparna and I are back too.
jrichter_: I think I've solved some of our gizmo problems, so try to log back in...
midori: I hear you ..
tberardini: I hear you too
jenclark: me too
MelissaH: Ihear you too
karenepilcher: hello
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hurdil: i just connected with Gizmo
hurdil: I heard the comment about the beeping
pfey: yes loud and clear
hurdil: I guess we should use the Roadrunner as our mascot
midori: arg - mine's gone silent again
kchris: are you still talking? I heard you when I first logged in, but now I don't hear anything.
MelissaH: mine too
jenclark: i hear you
kchris: OK, loud and clear
midori: ok, heard you then
MelissaH: hear you now
9:05 PM
jenclark: amelia, are you there?
tberardini: What's with the beeping and popping again?
tberardini: Thanks.
Alex_MGI: My gizmo dropped out a short time ago.
J-Lo: i'm back
pfey: I think we all fall off now and then..
karenepilcher: the beeping and popping IS logging on and off...i think everyone has it!
hurdil: the echo I was hearring before is totally gone now. Sound is very crisp
midori: I certainly do
kchris: you can edit your preferences to choose no sound for those events
jenclark: yes much better
karenepilcher: great!!!
kchris: I just got those beeps too, so whatever I turned off didn't eliminate those sounds
MelissaH: are you looking under options?
midori: I've turned all the sounds off ...
MelissaH: how?
hurdil: I just turned off all sounds but still get the pops
MelissaH: found it
9:10 PM
Alex_MGI: John, are you typing things?
midori: or talking?
rama: or eating?
Alex_MGI: Is anyone getting what John is typing?
tberardini: no
jenclark: yes
midori: Sorry, I must have missed part of that.
kchris: I don't see any typing from John either
MelissaH: no
jenclark: he is telling us stuff now
J-Lo: he can't hear you Alex
midori: No typing from John here...
jenclark: can you not hear him?
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tberardini: what box?
rama: i don't see anything either
midori: I lost him via Gizmo but have that back ... but I'm not getting his typing, and I missed the beginning of whatever we're doing with search/filterinng
tberardini: oh, click the term filter tab
MelissaH: me too
kchris: I just emailed John to try to tell him to log back into IRC
midori: thanks
MelissaH: when I unmute no one hears me.
9:15 PM
Alex_MGI: John has the volume turned down on his computer.
tberardini: does anyone know john's gizmo handle?
jenclark: johnrichter
tberardini: you can IM him in gizmo.  I don't think he knows he's lost us.
kchris: jrichter or jrichter_ are the ones logged off below
kchris: I mean above
tberardini: HELP!
jenclark: it's okay he's just doing the search facility
jenclark: can you hear him?
tberardini: yes but I got lost way back somewhere
kchris: yea, but it's 
Alex_MGI: I can hear him fine, even his typing.
midori: not OK -- I'm WAY behind what he's doing, but I'm fairly sure he's covering things I haven't done.
jenclark: harold can you phone john's mobile?
MelissaH: he doesn't answer his personal Gizmo
midori: Yes, same as Tanya - I can hear him now, but I don't know what he's doing because I missed stuff earlier.
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tberardini: I tried that too, no dice
karenepilcher: in gizmo his name is johnrichter
gwg: I'll put on my mute music, see if he notices that
Alex_MGI: Is he just playing a recording?
jenclark: in the advanced search click term filatering and keyword filtering
MelissaH: great music choice
J-Lo: lol!
jenclark: no he wont, he can't hear
gwg: he didn't notice, did he? Arses!
9:20 PM
karenepilcher: he is unaffected by musak
tberardini: is anyone calling his cell?
carol: Now I just hear static, no musak anymore.
Alex_MGI: Does anyone know the number?
midori: I don't have his cell number...
jenclark: harold does
kchris: yes, tons of them. We've all lost you from IRC!!!
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tberardini: NOOOOOOOOOOO!
tberardini: DOn't move on.
hurdil: 303-519-4760
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tberardini: Call him Harold, call him and save us!
jenclark: he's started a new chapter. start listening!
jenclark: only select term filter in the advanced option
jenclark: then click on the term filter tab
MelissaH: I heard his cell ringing
midori: Gizmo crapped out again!! Curses!!!!
gwg: it cuts out after 5 minutes :\ 
tberardini: gizmo gone from here too.
tberardini: I hear music.
midori: He's gonna have to start over (apologies to those who caught the whole thing)
jenclark: me too
hurdil: i left him a voice message; 
tberardini: now, nothing.  Suparna just left a message on his cell phone, he didn't answer.
Alex_MGI: Maybe he'll respond to an SMS.
jenclark: yes
hurdil: I can hear you 
9:25 PM
Alex_MGI: Oh we've been talking.
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midori: hahahahahaha!!!
MelissaH: we see you now
midori: no
tberardini: yes, I got the copy parent/child.
midori: best thing
jrichter: There's on more operation I want to look at before we get into filtering.
tberardini: But it was by audio, not by text.
midori: lucky you - I missed it!
jrichter: That's the copy parent, copy child operation.
jrichter: When you drop a term onto another term, you'll see two options, add child term and add parent term.
jrichter: Add child term adds the SOURCE term as the child of the TARGET.
midori: (I heard things, but couldn't follow - was too lost already)
jenclark: i don't hear you now and i have redialled
jrichter: Add parent term adds the source term as the parent of the target.
jrichter: Any questions about add child term vs add parent term?
tberardini: No.
kchris: made sense to me
jenclark: fine
jrichter: Let's move on to filtering
jenclark: are you talking?
jrichter: While I'm restarting Gizmo, let's proceed with text
jrichter: Click the advanced options tab in your search panel.
jrichter: Turn off everything but term filtering and keyword filtering.
jrichter: Then click back on the term filter panel.
jrichter: You'll just see one big box. That's the keyword search box.
jrichter: It works like google.
jrichter: Let's search for kinase.
jrichter: Type kinase into the box and hit the search button.
jrichter: You get a bunch of results, not all of which have kinase in the name.
jrichter: The keyword search searches all the text fields, not just the name, to find the results.
9:30 PM
jrichter: Let's look at some features of the search results page.
jrichter: (everyone still seeing me on IRC?)
kchris: yes
MelissaH: yep
jenclark: yes
carol: yes
tberardini: yes, can hear you on gizmo too.
jrichter: You can name your search results.
jrichter: To name a search result set, type a new name into the "Results label" box and hit enter.
jrichter: The tab at the top will be assigned the new label.
tberardini: How do you get rid of older searches?
jenclark: are you talking?
jenclark: okay I redialled
tberardini: got it
tberardini: works great!
jrichter: Click the circle with a red line through it to get rid of search results.
jrichter: To detach search results from the panel, click the button to the right of the results label.
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jrichter: The panel will become a detached window.
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pfey: this is nice!
pfey: missed that
MelissaH: me too
jrichter: Click the little window button to the right of the search results window to detach the panel.
jrichter: search results label, not window
jrichter: It becomes its own window.
MelissaH: got it
jrichter: When it's a window, you can click the tab button to reattach the window to the panel.
jrichter: When you click a line in the results panel, the term is automatically selected.
jrichter: You can turn that behavior off by clicking the autoselect checkbox.
jrichter: Then you can click things at will, and they aren't selected.
jrichter: You can select a bunch of search results using a shift-select
9:35 PM
jrichter: Go ahead and select a bunch of things, and click the "select terms" button.
tberardini: What should happen?
rama: I am kind of stuck. How do I refresh or clear?
jrichter: A list of all the terms you've selected should appear to the left of the text editor panel.
jrichter: What do you mean, Rama?
tberardini: Yes, a list of all the terms appears but it does that without my clicking on Select terms.
jrichter: The select terms button is only useful if you've turned off autoselect.
tberardini: Aha!
jrichter: Then you use the select terms button to select what you've picked out of the list.
jrichter: While we've got a bunch of things selected...
jrichter: There's the list of terms to the left of your text editor panel
jrichter: Clicking something in that list causes it to be selected in the text editor panel.
jrichter: It also causes that term to appear in the DAG View.
jrichter: You can make all the terms you've selected appear in the DAG view by clicking the "allow multi select" checkbox under the dag viewer.
midori: cool - I've been wondering what that button does
jrichter: It creates a compound DAG View of everything you've got selected.
jrichter: Any questions about any of this, before we move on to more complex filtering?
tberardini: No.
jenclark: no
jrichter: One more thing about searching (and filtering and rendering)...
9:40 PM
jrichter: Just clicking the buttons causes the search or filter or render to occur in the primary selector window...
jrichter: You can target a search or filter or render to a particular term editor panel by dragging the search or filter or render button to the target panel.
jrichter: When you do that for a search, for example, when you click a search result it becomes selected in the targeted panel.
jenclark: I know what you mean about that but it doesn't seem to be working in my copy.
jrichter: This can be useful if you've got a bunch of panels open, and you want to target a search into a non-active panel.
tberardini: can we work an example?
jrichter: For example, if the kinase search is still up...
midori: Looks like it just worked for me.
J-Lo: can you drop the search on to just a specific node?
jrichter: Click and drag on the word "search" in the search button, and a little magnifying glass would appear. Drop that magnifying glass on a term editor panel to target the search.
jrichter: You can't do that right now, Jane, but it's a good idea.
J-Lo: 'kay
jrichter: You could search children that way...
jenclark: that's definately not working for me in b14 in xp
tberardini: which one is the term editor panel again?
Alex_MGI: I can't say if it's working or not, since I am not sure of the desired result.
jrichter: The term editor panel is the one on the left with the graph of the ontology in it.
tberardini: I keep seeing the same results show up, i.e. results for kinase instead of the search for the new term (different one) that I dropped it on.
Alex_MGI: I see it now.
9:45 PM
jrichter: You'll know it's working if you've got two panels open, and you drag your search to the non active panel, the results will be selected in the non-active panel when you click them.
tberardini: Oh. so how's this drag and drop supposed to help then?
jrichter: tbernardini - the search will look for whatever you've typed in the search box, not the term you dropped it on.
jrichter: The drag and drop indicates which term editor panel will be receive the selection when you click a search result.
jrichter: Let me rephrase that...
midori: it's all about which window you want the terms highlighted in, right?
jrichter: The drag and drop just says, make the selection happen in this particular term editor panel when I click a search result.
jrichter: RIGHT! Midori is right.
tberardini: sorry, still confused
jenclark: ah!
MelissaH: I understand now!
midori feels clever
jrichter: Thank you Midori for clarifying.
jrichter pats Midori's virtual head
jrichter: Moving on...
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jrichter: Unclick keyword filtering in the advanced options tab, and then click back on the term filter tab.
jrichter: Things look different, but the equivalent of the keyword search you just did has been loaded up.
jrichter: Lets go through the different pieces of this search control.
jrichter: The NOT box inverts the search.
kchris: Sorry John, where's the NOT box?
jrichter: The not box should be in the top left corner of the term search panel.
jrichter: From left to right, you should see something like [NOT] [Self] [Keyword] [contains] and then underneath your search string.
9:50 PM
jrichter: Let's look at the second dropdown, the one that contains the word Keyword right now.
kchris: sorry, I'm completely lost, where are the dropdowns
pfey: it has 'synonym' twice - not that it matters
jrichter: Karen, did you turn off keyword filtering in the advanced options tab?
kchris: I missed that, there was some talking in this room. Turn off keyword filtering. OK. doin gthat.
rama: got it!
midori: mine only has synonym once ...
kchris: mine too
MelissaH: I have two
tberardini: I have two too!
Alex_MGI: mine has it twice, b14
kchris: sorry, mine, like John's has synonym twice in the order that he spoke it 
hurdil: yes, I have it twice also
midori: oh that - OK, didn't see both at once cos of where it was scrolled
jrichter: This box contains the property you are searching on. Remember that Category searches Category ID, not category description.
jrichter: and the box to the right indicates which comparison you want to do.
hurdil: future version: be able to set a default way of searching; like, on name only, etc.
jrichter: If you're searching on a property that gives a text result, the possible comparisons are contains, starts with, ends with, equals.
hurdil: I remembers what I searched on, but not the type of search
jrichter: Harold - it should be retaining information about the last kind of search you did.
midori: I'm not sure it's been retaining all of my settings, but will have to pay closer attention.
jrichter: Different search properties return different kinds of results. Select "Parent count" from the properties list.
tberardini: where's the parent count?
9:55 PM
jrichter: It's near the end of the list.
jrichter: You may have to scroll to get to it.
tberardini: Found it at the bottom!
MelissaH: thats really cool
jrichter: The available comparisons are numerical.
tberardini: cool
jrichter: Search for "Parent count" > 4
jrichter: You'll get 14 results.
midori: I get 13 ...
pfey: me too - 13
jrichter: Maybe we're working with different versions of the ontology.
MelissaH: 13
jrichter: I probably have an old version of the data.
midori: could be - mine's fresh from this afternoon 
jenclark: might it be good to have 'ancestor count' too?
jrichter: It would be pretty easy to add an ancestor count.
jrichter: Do you want to program that, Jen?
jenclark: yes please 
jrichter: Choose "Is property" from the property list
jrichter: You'll notice that the comparison box and the text box disappear.
jrichter: If you do the search, it will return only the properties in the ontology.
jrichter: Now for that first box, the ancestor/self/descendant box.
midori: ok, I get GO007507
jrichter: Do the following search: [Self] [Name] [equals] "heart development"
jrichter: Okay, now do this search: [Ancestor] [Name] [equals] "heart development"
jrichter: It will take a lot longer
10:00 PM
jrichter: This time, I get 18 results.
jrichter: It has found everything that has an ancestor whose name equals "heart development"
jenclark: does anybody hear john?
tberardini: you appear to be gone from gizmo, john.
J-Lo: John you've gone
MelissaH: no
midori: gizmo silence (except for many beeps)
jrichter: Gizmo dropped me, I'll be back
midori: on the plus side, I did get those 18 results ...
jrichter: You'll notice that heart development itself is not in the list.
hurdil: schwartzenegger
J-Lo: mine still hasn't finished searching!
kchris: yep
jenclark: yes
MelissaH: yep
J-Lo: yes
rama: got 18 results
pfey: mine is very slow too
midori: from the 'wrong question to ask' file ...
tberardini: We don't see the 'heart development' parent for all of these terms though.  Checking 'cardiac cell differentiation'.  Where is heart development.
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tberardini: Mine was pretty fast.  Windows XP, beta 14 about a two year old DELL.
jenclark: me too
pfey: mine is still not done..
J-Lo: so it's basically showing all the terms that are descendants of 'heart development'?
jrichter: "cardiac cell differentiation" -part_of-> "embryonic heart tube development" -is_a-> "heart development"
J-Lo: i see
tberardini: Oh, but you don't necessarily see 'heart development' in the DAG view.
jrichter: Yes, Jane. It's showing the descendants of 'heart development' because all the things that matched had the ancestor heart development.
midori: I see it in my dag view
jrichter: Some things are collapsed in the DAG View.
jrichter: Showing the whole DAG View can really slow down OBO-Edit.
tberardini: OK.  We understand now.
jrichter: Branches that have already been shown near the top are collapsed near the bottom.
10:05 PM
MelissaH: can you specify the search to do only ancestor searches with particular relationship types (like developsfrom?)
MelissaH: ok
jrichter: Melissa - We'll talk about something similar when we get to link searches.
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jrichter: But some searches cannot be done easily.
jrichter: Let's do that search again, but change Ancestor to Descendant.
pfey: my search didn't work
pfey: stupid Q
pfey: is NOT clicked?
jrichter: NOT is not clicked.
tberardini: I got 5 results.
MelissaH: I got 5
midori: got 5
jrichter: I got 5 also, and they're the ones you'd expect.
jrichter: Again, heart development isn't among them, because it isn't its own ancestor or descendant.
jrichter: The ancestor and descendant searches aren't so useful on their own, but they're really useful as part of a compound search.
jrichter: Click the "Advanced" tab and turn on "Rendering Controls"
jrichter: A new button should appear called render, and you have a new render options panel when you click back on Term filte.r
jrichter: filter.
jrichter: Change your search to [Self] [Name] [contains] "kinase"
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jrichter: Then click the Change Color checkbox.
jrichter: Then click render.
10:10 PM
pfey: it doesn't say 'render'
tberardini: Suparna says 'I like that!'
J-Lo: Jonh - when the render options are visible on my machine, they're obscuring the other pulldown menus
jrichter: If you scroll through the ontology, you'll see that all the terms that contain kinase are in read.
jrichter: red.
hurdil: this occurs before you even hit search
J-Lo: because there's not enough room
jrichter: Can you make your screen wider?
midori: aaaaaaaaa - mine got changed to gray! (worked otherwise, tho)
J-Lo: no - small screen
jrichter: Try shrinking the term editor panel.
jrichter: Petra - do you not have a render button? It should be under the search button.
pfey: ah ok
jrichter: You don't have to click the search button to do a render.
pfey: I have this other button in the render options that is blank
pfey: aha - worked now
jenclark: did we lose john on gizmo?
midori: I did
tberardini: I lost him.
Alex_MGI: I did
MelissaH: I lost the whole connection
midori: yep
carol: yes
tberardini: yes
hurdil: ya
kchris: In the render controls, even on a huge screen (20), the last option under the Render controls is only half showing
pfey: that's what I did earlier
MelissaH: Nice
jenclark: is the last 'make italic'?
tberardini: We're dying of laughter here.
jrichter: To change to another color (mine is red by default) click the little button next to the change color text box to pick the color.
pfey: yes, this top window with all the controls can we make that bigger?
rama: how many options are available under Render?
kchris: actually, I don't even see 'Make italic', for me "Make bold" is half way disappearing.
rama: I cannot see the ones below Change Size
jenclark: john are you playing a guitar?
kchris: My OBOEdit is almost full screen on a 20 inch monitor
10:15 PM
hurdil: Thee appears to be something below Change size,begining with a M
tberardini: I think we may have a squatter.
MelissaH: I have 4 options
carol: I have five options.
midori: Two things - I get the same layout problem as Karen, and I can't get anything to turn red!
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jenclark: who is dieirvonsatan?
tberardini: guitarist is gone
carol: yes!
midori: yes, and you're on
kchris: sounds good to me
jenclark: yes no guitarist now
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DiEirVonSataN: Sup
midori: ok, I'll deal with my layout off-vebinar
hurdil: no sound
midori: i mean webinar ....
midori: change color checked; it's red ...
kchris: The color changed just fine for me, a lovely shade of pink
tberardini: Changing colors did not work for me.
jenclark: we have three colours
jrichter: Midori, what's the search that you're using?
midori: oh wait, it finally worked this last time I tried
midori: search was [Self] [Name] [contains] chromosome
kchris: but I still can't see some of the render options and am not seeing any options to increase the height of the little window for term filtering
jrichter: Now everyone should have some terms in red...
jrichter: To get rid of your renders, click the render/filter button at the bottom of the term editor panel.
tberardini: OK, that made the color change work.
jrichter: Click the button and a little menu will appear that allows you to remove filters, all renderers, or a specific renderer.
midori: grrrrr - the color changed itself to grey again! (but terms did turn grey)
carol: don't see the render/filer button....
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10:20 PM
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tberardini: I think we finally bored Satan to death.
tberardini: or not
jrichter: Are we good with renderers now?
rama: yes
carol: no
jenclark: fine here
tberardini: we're good
kchris: my rendering disappeared as expected 
midori: what about things that match more than one search string?
hurdil: no, where is this remove button?
pfey: mmine doesn't..
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carol: Oh, I see it. It worked.
pfey: my render/filter menu is grey - not active
hurdil: ok, I see it
midori: testing 'remove specific renderer or filter' ... seems to work ... but made me wonder what the renderer should show
jrichter: Petra - if your render/filter menu is gray, there are now renderers active.
pfey: oh yes, never mind - was in the wrong panel..
jrichter: Midori - if a term matches more than one renderer, it will try to render them all.
pfey: cool
midori: ok ... not sure it succeeded with two colors 
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jrichter: That's why you should use different types of renderers if you have more than one active renderer at once.
midori: got it with one color and one font change!
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midori: won't digress any further
jrichter: Now let's look at filtering.
jrichter: Set up the following search [Self] [Category] [equals] "goslim_plant"
jrichter: And then click the filter button.
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10:25 PM
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jrichter: This dull, dull software tutorial room is becoming popular.
hurdil: ontology collapsed, and I cant expand it now
jenclark: I see 'behavior' is in plant slim
midori: mine collapsed too, but I can expand it
tberardini: open it up harold, it's just the slim terms now
jrichter: The ontology will collapse, but you should be able to expand the classes node.
Alex_MGI: lots of roots?
hurdil: no, classes won't open
J-Lo: can you talk a bit about the fewest path thing?
pfey: clicking on the Classes node doesn't work
midori: yes, me too
jenclark: I think I missed something
MelissaH: mine works ok
jrichter: If you can't expand your classes node using the little plus sign, check to make your search is spelled correctly.
MelissaH: GOslim_plant
midori: all lower case (worked for me)
tberardini: goslim_plant worked for me
pfey: yes 'goslim_plant'
J-Lo: if the term has multiple paths to root, will it show all possible terms?
jenclark: I'm fine
pfey: me
hurdil: still can't expand; I typed goslim_plant
pfey: doen't expand
J-Lo: sorry - that didn't make sense
jrichter: J-Lo - it will show all the paths that include matching terms.
DiEirVonSataN: :]
jrichter: If it isn't working, remove all filters and renderers and try again. Also, try just searching, and make sure you get around 108 results.
midori: is 84 close enough to 108?
pfey: yes
pfey: 108
tberardini: 109
hurdil: yes, I get 108 reslults for a search
jenclark: did we lose sound?
jenclark: no
pfey: wow doggy now
midori: I did lose sound but go tit back when I redialed.
MelissaH: I can expand but don't know what to look for
jrichter: When you expand the classes node, you'll see a lot of roots.
MelissaH: I see 4
hurdil: going through the terms, I can select one, and it expands, but I can't manually expand or collapse any
10:30 PM
jenclark: what do you mean by roots?
pfey: my classes node still doen't expand
jrichter: If you're still having trouble, you may need to restart OBO-Edit and try again. Sounds buggy.
jrichter: I see many, many roots when I do this filter.
jrichter: This is happening because the goslim_plant category isn't fully connected.
jrichter: There are some gaps.
kchris: Huh, the first time I did the filter for goslim_plant, it worked great, but I removed it and now I can't duplicate the filter...
jrichter: Because I'm using the greedy root detection algorithm, everything that has been orphaned by the filter shows up as a root.
tberardini: No difference.
midori: mine didn't change ...
jenclark: where do you set that again?
jrichter: If I switch to STRICT root detection, I get a much smaller number of roots in theory.
MelissaH: no difference
Alex_MGI: That pop up menu does not switch for me.
kchris: beta14 doesn't seem to be letting me select the strict root algorithm
jrichter: Mine isn't changing either, so there seems to be a bug.
tberardini: The little octopus icon beside the render icon.
tberardini: Clearly.
jrichter: It's not an octopus, it's tree roots.
MelissaH: mine just finally gave a whole bunch of roots
jenclark: ah!
J-Lo: John - in configuration manager, behaviour - what does that pull-down menu control?
jrichter: Okay, are there any questions about how that's supposed to work.
jrichter: ?
jenclark: no
kchris: no
tberardini: no
J-Lo: John - in configuration manager, behaviour - what does that pull-down menu control?
rama: no
MelissaH: I don't understand the basic difference between filtering and searching

MelissaH: does it just show only that portion of the ontology?
hurdil: restarting now allowed me to do the goslim_plant expansion
jrichter: ITSMIKEEH - I guarantee that that kind of spamming is not allowed on this server. Please desist or be banned.
10:35 PM
jrichter: Right, Melissa. It's only showing the terms that match.
MelissaH: ok got it
jrichter: Filtering hides non-matching terms in the term editor panel, searching shows a selectable list of matching results.
jrichter: Go to Advanced Options, and turn off everything but link filtering.
jrichter: Link filtering searches not for terms, but for relationships between terms.
jrichter: The link filter box looks just like the term filter box, but there's a new drop down on the top.
jrichter: That drop down lets you search for links based on the parent, child, type, or link itself.
jrichter: Let's search for [Type] [Self] [ID] [equals] "part_of"

hurdil: 3722
midori: 3729 results!
Alex_MGI: 3723
jrichter: You should get several thousand results.
pfey: 3722
jrichter: That shows every relationship that has the type part_of.
jrichter: You'll notice the search results look different.
jrichter: It shows the child, type, and parent of the matching links. A child, type, parent combination uniquely identifies any relationship in the ontology.
jrichter: When you click one of these, it selects that link in the ontology.
10:40 PM
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jrichter: When you click a term in the term search, you're not really sure what's going to get selected in the term panel, because the term might show up in a lot of different places.
jrichter: But when you click a link result, you know exactly what's going to get selected.
tberardini: Where do you click to see the result?
jrichter: Click anywhere on the line.
tberardini: What should happen, because nothing's happening here.
jrichter: Make sure your filters are turned off first.
jrichter: I should have said that before.
kchris: works fine for me, when I click things, the appropriate place is highlighted
jrichter: Remove all your filters.
tberardini: Yes, that made the difference.
jrichter: It can't select a hidden link.
rama: yup, works fine
jrichter: Let's go to advanced options and turn rendering back on.
jrichter: There's a different collection of rendering options.
hurdil: ooh
jrichter: Click the "change line type" choose "Wavy" and hit render.
jrichter: Link renderers change the way the link, not the term, is drawn.
jrichter: All the part_of relationships should now have a bent arrow.
jrichter: Is that working/
jrichter: ?
midori: yep
tberardini: yes
MelissaH: yes
kchris: yep
hurdil: cool
jrichter: Let's remove the renderers and try something else.
jrichter: Choose "Self" from the top dropdown box.
10:45 PM
rama: no, i don't see wavy lines and I am not even sure if it is still working on the rendering
jrichter: Rama - rendering should happen quickly.
jrichter: When you choose "Self", you'll notice that the properties drop down has fewer and different options than before.
jrichter: These are all options that pertain only to links, not to terms.
pfey: that's cool
jrichter: When doing a link search, you can do a search based on attributes of the link child, parent, or type, or on attributes of the link itself.
jrichter: You can also search link ancestors and descendants.
kchris: nope, go ahead
jrichter: Can we move on to compound filtering, or are there questions?
jenclark: we're fine here
jrichter: Okay. Go to advanced options, and first turn off everything but keyword filtering and term filtering.
MelissaH: mine already assumed compound filtering
10:50 PM
midori: mine too
pfey: same here
kchris: mine too, compound filtering was ticked simultaneously with unchecking keyword filtering
J-Lo: oh i see
MelissaH: did someone hear recording conversation?
jrichter: Type kinase and activity into the search box
jrichter: Now go back to advanced options, turn off keyword filtering, and turn on compound filtering
jrichter: That's good.
jrichter: When you go back to the term filter tab, you'll see that it's broken the keyword filter into a compound filter.
midori: I did ...
jrichter: Compound filters are structured like a tree.
kchris: yep
pfey: yep
jrichter: So, if we had a search for "kinase" and "activity", in the little box on the left you'll see a tree structured version of that expression...
jrichter: Like so:
jrichter: AND
jrichter: + kinase
jrichter: + activity
jrichter: So lets find every term that kinase but belongs to a go slim.
jrichter: Click the top expression in that treeview.
jrichter: And change it to [Self] [name] [contains] "kinase"
jrichter: And then lets the bottom to [Self] [Category] [contains] "slim"
hurdil: 2
jrichter: I get six results.
J-Lo: me too
jrichter: But I'm working with an older version.
Alex_MGI: 2 results
midori: 2
jenclark: 2
kchris: 2 as well
MelissaH: I get 2, but I had to delete the "AND" search
pfey: 2
jrichter: Harold's right, I screwed up.
jrichter: What do you mean you had to delete AND?
Alex_MGI: The interface would not show the drop down menus.
MelissaH: originally, we typed kinase and something else
MelissaH: activity
10:55 PM
MelissaH: ooppps
jrichter: Ahh... that was a misunderstanding. You don't need to type AND in the keyword view.
Alex_MGI: I went back to Advance Options and turned compound fitering off and then on again to restore the box.
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jenclark: is john's sounds gone?
MelissaH: I lost him too
midori: me too
tberardini: gone
Alex_MGI: I can't hear him.
kchris: me too
pfey: yes gone
jrichter: Lets find things whose name contains "kinase", belong to a slim, and contain the word "protein"
jrichter: (Fixing my audio now)
pfey: we can't hear you!
jrichter: (Still working on the audio)
Alex_MGI: Good time to stop perhaps.
jrichter: Almost done with this part--
MelissaH: How do you add a third search?
jrichter: Right click the top item in the compound search tree, the one that looks like a folder.
jrichter: Click "Add Filter"
jrichter: (Make sure to select that top item before right clicking)
MelissaH: got it
jrichter: Select the new filter aspect, and set it to [Self] [Name] [contains] "protein"
midori: 1 results [sic]
kchris: same her
jrichter: You should get 1 results
MelissaH: yep
hurdil: yup
tberardini: yeppers
jrichter: Okay, you don't have to do an AND search. You can do an OR search.
jrichter: To change our search to OR, select the top item in the tree.
jrichter: And pick "OR" from the dropdown menu.
Alex_MGI: 1591
jrichter: You should get thousands of results.
tberardini: 1593
11:00 PM
hurdil: 1589 
MelissaH: 1591
midori: what if I want name contains 'protein' or 'kinase', but AND is in a slim?
jrichter: One last thing to try.
kchris: does it make it OR everywhere?
jrichter: That's just what I was going to do!
jrichter: To do midori's search, change the search type back to AND.
jrichter: Then, right click and choose "Add Boolean Filter"
MelissaH: is john typing?
J-Lo: mine's gone all weird
tberardini: 14 too
kchris: not sure
jenclark: not quite
Alex_MGI: 301
11:05 PM
tberardini: there are four or five responses so far
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midori: not sure the 'add filter' step is playing nice ... gimme a minute ...
hurdil: 188, but some of the filter tree blank; I think I need to quit/restart
tberardini: the add filter step did add two but one of them was blank and didn't fill out until I'd edited in the boxes to the right
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kchris: I'm not sure where the filters are all supposed to be, I still have the original top filters, and also the ones I added, but I don't understand the logic of which ones are getting ANDed or ORed
J-Lo: mine's gone all weird - everything I put in has disappeared out of the tree box
Alex_MGI: Now I got 14 results.
jrichter: Okay, where did we leave off...
jrichter: Well done alex.
hurdil: 188
MelissaH: 114
midori: got 303
tberardini: I had 14 as wel
tberardini: well
jrichter: Here's what the tree should look like:
jrichter: AND
jrichter: category contains "slim"
jrichter: OR
jrichter: Name contains "kinase"
midori: oh grr, my AND and OR are backwards ... lemme fix 
jrichter: Name contains "protein"
midori: ok, 14!
J-Lo: mine has completely frozen - I can't select anything now
jrichter: (AND category_contains_slim (OR name_contains_kinase name_contains_protein))
jrichter: If you're frozen, you have to restart.
tberardini: My tree looks a little different:  Category contains "slim" AND Name contains "kinase" OR Name contain...
tberardini: That's the top  one, not just "AND"
jrichter: Tanya I'm how you're laying out your tree structure there...
jrichter: But it seems to be working because you're getting the right number of results.
tberardini: Maybe I can just send you a screen shot after we end.
kchris: Hmm, with the tree structure you describe, I'm getting 41 results
jrichter: Make sure that you're using [Name] [contains] rather than [Keyword] [contains]
11:10 PM
jrichter: This notation is called prefix notation.
tberardini: Suparna: What's the difference between Keyword and Name?
tberardini: OK.  Thanks.
jrichter: Keyword searches all the fields, not just the name.
kchris: yea, that does it, I had keyword searches, with name searches, I get 14
jrichter: I don't know if this will help, but if the compound search tree did math equations...
jrichter: (1 + (5 - 4))
jrichter: +
jrichter: 1
jrichter: -
jrichter: 5
jrichter: 4
jrichter: That's the way prefix notation logic works too.
jenclark: no
midori: thanks!!!
tberardini: Tomorrow at 1 pm PST?
kchris: just
jenclark: great 
jrichter: Yes, Karen?
pfey: Thanks a lot!
kchris: sorry, was trying to erase, hit return instead. might not be able to make it tomorrow (child is sick) but today was great, really helpful
jrichter: Make sure to review filtering for tomorrow when we talk about complex saves.
tberardini: Goodnight GO girls!
jrichter: Thanks, everyone. See you tomorrow.
gwg: cheers John-boy!
karenepilcher: bye!
Alex_MGI: thanks
tberardini: Thanks John.
hurdil: I restarted the whole thing and got 14 now
MelissaH: Thanks to you too!
pfey: Thank YOU!!
midori: bye 
jenclark: are we going from 1-3 tomorrow?
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jrichter: Make sure to save your transcripts, if you have one.
carol: bye
jrichter: Tomorrow is 1-3, or later.
rama: can we review the last part from today- compound filtering again. I did not get any of it.