[Babase] Re: Upmpi ready-ish

Lacey Maryott Roerish lroerish4 at gmail.com
Tue Dec 15 11:46:00 EST 2009


heres another weird situation.. I think this data set was made to be a rules
challenger!!!

1079 270 1.1 23/07/1999 APH AS SPY PREDATION:SPY HAD GRANT'S GAZELLE
INFANT,APH ASK FOR HELP TO GET KILL;YOY END UP WITH KILL P
1080 270 1.1 23/07/1999 APH ? YOY SUCC
1081 270 1.1 23/07/1999 YOY + APH
1083 270 1.1 23/07/1999 APH,YOY VS SPY

The issue is the last line having two actors... which is currently against
the rules.   usually, these lines are AS lines, so I just split them into
two.  It DOES seem as though a YOY AS SPY would be warranted.. if it weren't
already implied by the YOY + APH.  We haven't been entering those AS's since
they are redundant with the + line...  but what do I do with this VS
business :-\

Lacey

On Tue, Dec 15, 2009 at 10:49 AM, Susan Alberts <alberts at duke.edu> wrote:

> On Dec 15, 2009, at 10:41 AM, Lacey Maryott Roerish wrote:
>
>  867     218     2.2     01/07/1999      LUI     AS      LOZ,LIZ
>>                       N
>>
>> I think the same thing goes here.  This is the whole MPI.  So it seems
>> like we should (for both of these), just have these end up on two lines that
>> have the same seqid  right?
>>
>
> This does not count as an MPI in my view. There is no third-party
> interaction. I think this is not an MPI.
>
> But in theory an MPI could begin like this. In this case again I think that
> we need to split this one line into two separate interactions.  Make sense?
>
>
> S
>
>
>> Meaning that we change the rule to allow 'AS' to have more than 1 actor or
>> actee? I'm not sure if Karl has built in a rule disallowing the first two
>> lines of an interaction to both have act be AS. Karl?
>>
>> Thx
>> Lacey
>>
>> On Tue, Dec 15, 2009 at 10:25 AM, Susan Alberts <alberts at duke.edu> wrote:
>> Ok thanks. Do the rules allow two AS's to begin the interaction? If so,
>> then we should have two AS's here. If not, then we probably need to change
>> the rule. Also, it seems that we should change the seq = 1 rule we talked
>> about before, so that two AS's in a row (as in this case) can have seq = 1.
>> Does this make sense?
>> S
>>
>>
>> On Dec 15, 2009, at 9:32 AM, Lacey Maryott Roerish wrote:
>>
>> 474     117     1.22    24/07/1999      DOX,VAT AS      VIA
>>                       N
>> 475     117     1.22    24/07/1999      VEI     +       VIA
>>
>> On Tue, Dec 15, 2009 at 9:13 AM, Susan Alberts <alberts at duke.edu> wrote:
>> It looks to me like it should be two AS's.
>>
>> If you send me the whole MPI I might be able to comment more fully.
>>
>> S
>>
>>
>> On Dec 15, 2009, at 9:08 AM, Lacey Maryott Roerish wrote:
>>
>> So I just came across an error regarding this error message.
>>
>> 474     117     1.22    24/07/1999      DOX,VAT AS      VIA
>>                       N
>>
>> Should this be changed to a VS?
>>
>> L
>>
>> On Mon, Dec 14, 2009 at 9:20 PM, Susan Alberts <alberts at duke.edu> wrote:
>>
>>
>> I think we want the original: "two rows can't both have seq = 1
>> unless they are both "versus" interactions" unless you have
>> some reason to want a change.
>>
>> Lacey and I have worked it out.
>>
>> OK
>>
>>
>> S
>>
>>
>>
>>
>>
>> Karl <kop at meme.com>
>> Free Software:  "You don't pay back, you pay forward."
>>            -- Robert A. Heinlein
>>
>>
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>> ------------------------------------------------------------
>> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC
>> 27708. Phone 919-660-7272, FAX 919-660-7293
>>
>>
>>
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>>
>>
>> --
>> - -
>> Lacey K. Maryott Roerish
>> Alberts Lab
>> Department of Biology
>> Duke University
>> ph: 919-660-7306
>> fax: 919-660-7293
>> Lacey.Maryott at duke.edu
>> _______________________________________________
>> Babase mailing list
>> Babase at www.eco.princeton.edu
>> http://www.eco.princeton.edu/mailman/listinfo/babase
>>
>> ------------------------------------------------------------
>> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC
>> 27708. Phone 919-660-7272, FAX 919-660-7293
>>
>>
>>
>> _______________________________________________
>> Babase mailing list
>> Babase at www.eco.princeton.edu
>> http://www.eco.princeton.edu/mailman/listinfo/babase
>>
>>
>>
>> --
>> - -
>> Lacey K. Maryott Roerish
>> Alberts Lab
>> Department of Biology
>> Duke University
>> ph: 919-660-7306
>> fax: 919-660-7293
>> Lacey.Maryott at duke.edu
>> _______________________________________________
>> Babase mailing list
>> Babase at www.eco.princeton.edu
>> http://www.eco.princeton.edu/mailman/listinfo/babase
>>
>> ------------------------------------------------------------
>> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC
>> 27708. Phone 919-660-7272, FAX 919-660-7293
>>
>>
>>
>> _______________________________________________
>> Babase mailing list
>> Babase at www.eco.princeton.edu
>> http://www.eco.princeton.edu/mailman/listinfo/babase
>>
>>
>>
>> --
>> - -
>> Lacey K. Maryott Roerish
>> Alberts Lab
>> Department of Biology
>> Duke University
>> ph: 919-660-7306
>> fax: 919-660-7293
>> Lacey.Maryott at duke.edu
>> _______________________________________________
>> Babase mailing list
>> Babase at www.eco.princeton.edu
>> http://www.eco.princeton.edu/mailman/listinfo/babase
>>
>
> ------------------------------------------------------------
> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC
> 27708. Phone 919-660-7272, FAX 919-660-7293
>
>
>
> _______________________________________________
> Babase mailing list
> Babase at www.eco.princeton.edu
> http://www.eco.princeton.edu/mailman/listinfo/babase
>



-- 
- -
Lacey K. Maryott Roerish
Alberts Lab
Department of Biology
Duke University
ph: 919-660-7306
fax: 919-660-7293
Lacey.Maryott at duke.edu
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