[Babase] AMOK/Billy Questions

Lacey Maryott lacey.maryott at duke.edu
Tue Dec 30 09:28:19 EST 2008


I'm working on this now, and realizing I'm not sure we necessarily came 
to solid decisions on some of these things

Susan Alberts wrote:
> Thanks for the reply Karl, see below.
>
> Karl and I talked on the phone about the problem that we think AMO = 
> BIL. He said, basically, that if we think they are the same individual 
> then we should just have one row. If we think they might be different 
> individuals then we should not try to have the same row for them. This 
> makes sense.
>
> Problem is, "sure" is a tricky word. We are as sure as one can be with 
> genetics that BET and NAC are his parents. We are not 100% sure that 
> he is the same individual as BIL. These are different things. He is 
> probably, but not certainly, the same as BIL. So, for instance, we 
> might feel comfortable saying that all of BIL's group-level attributes 
> (density and group composition at BIL's birth, for instance) apply to 
> AMO, and we might be happy with some individual-level attributes too, 
> such as birthdate. We might not really want to use BIL's parity 
> though, for AMO, depending on how sure we were about AMO = BIL.
Should I or Shouldn't I use BIL's parity for AMO?  If not, what should I 
use, or should I leave it null (I don't know if there is a validation 
rule against having a mom but no parity or not)
>
> GIven that we are sort of waffly on the "sure" part, I like Karl's 
> suggestion:
>
>>> ......
>
>>> I could see a table called something like
>> ALTERNATE_SNAMES.  It'd have, say, 5 rows:
>>
>> Asnameid  Integer used for a row id.
>> Sname   The real sname of the individual
>> Nick   The alternate sname of the individual
>> Date   The date the alternate sname was assigned
>> Notes  (text)  As much comment as you'd like about why the
>>        alternate sname exists.
>>
>> That way when you've got data outside Babase with the "bad" sname
>> in it you can still work with the data and link it to the "good"
>> sname.
>>
>> "Inside" babase I'd still prefer that 1 baboon means 1 row in
>> BIOGRAPH.  IMO moving away from that is going to cause real
>> headaches.
So after updating Amok with birth, btatus, pid(what value?), and matgrp, 
I should go ahead and create this table in Babase pending, correct?


Something else we haven't addressed is how the PID decision will affect 
the pregs table... If we delete BIL, we lose information linked that 
that PID in pregs. This may or may not be ok depending on whether or not 
we would be confident in using that data for AMO anyway...

Thoughts?
>>
>
>
> Jeanne, thoughts? Others?
>
> Susan
>
> --------------------------------------------------------
> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC 
> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>
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>

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



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