[Babase] AMOK/Billy Questions

Jeanne Altmann altj at Princeton.EDU
Tue Dec 30 16:29:48 EST 2008


Sounds right,
j 

-----Original Message-----
From: babase-bounces at eeblistserv.princeton.edu
[mailto:babase-bounces at eeblistserv.princeton.edu] On Behalf Of Susan
Alberts
Sent: Tuesday, December 30, 2008 2:52 PM
To: lacey.maryott at duke.edu; The Baboon Database Project
Subject: Re: [Babase] AMOK/Billy Questions

See below.

On 30 Dec 2008, at 09:28, Lacey Maryott wrote:

> 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)

The decision that Jeanne made, which I support, is that we should use
BIL's parity for AMO.
>
>>
>> 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?

That is 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?

We'll retain the pid for BIL/AMO so we can put this question on back
burner for now.

S

>
>>>
>>
>>
>> Jeanne, thoughts? Others?
>>
>> Susan
>>
>> --------------------------------------------------------
>> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham  
>> NC 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>
>> _______________________________________________
>> Babase mailing list
>> Babase at www.eco.princeton.edu
>> http://www.eco.princeton.edu/mailman/listinfo/babase
>>
>
> -- 
> Lacey Maryott
> 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, Department of Biology, Duke University, Box 90338,  
Durham NC 27708 USA,  Phone 919-660-7272, FAX 919-660-7293,
alberts at duke.edu




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