[Babase] More on snames not in biograph
Lacey Maryott
lacey.maryott at duke.edu
Thu May 7 12:44:27 EDT 2009
Susan Alberts wrote:
> Hi all,
>
> Tabby found a file on her computer called snames not in biograph, it
> was by Daphne, and she sent it to Lacey. This was after I had already
> extracted snames not in biograph on Friday.
>
> This new file from Daphne/Tabby provides some information and raises
> some questions.
>
> 1. There were three snames in Daphne's file that were in not in the
> file I made last Friday. These were:
> UNK for Unknown
> HAD for HADADA
> TUR for TURKANA
>
> Lacey, please add these to the table "snames not in biograph" in
> babase_pending.
As per e-mails that followed this one, I Will only enter UNK for
Unknown. This is now done.
>
> These also need to be added to the list for the team. I will email the
> team and ask them to just write them in by hand, rather than producing
> a new version, since they may have already started working with the
> one I sent last week.
>
> 2. There was one name in the list that I had that was not in Daphne's
> list: RUF for Ruffle. No changes need to be made to any file, I am
> just noting this. But, I am puzzled by this and not sure where it came
> from. Any ideas? Jeanne? Does this really appear anywhere in the data?
>
> 3. I noticed a typo in the file that I made on Friday. Sname SON has
> the name SONY associated with it, not SON, as I wrote in the field on
> Friday. Lacey, in babase_pending can you change the name to SONY (no
> changes to the sname)?
Yes, done.
>
> 4. Daphne's file includes a whole set of "Snames" that are listed as
> human samples for DNA extractions. There are some question/issues with
> this list.
>
> -First, I am not sure where these came from. Why am I SSL, for
> instance? Why is Jenny JTG? I think what needs to happen here is we
> need to look through the Tissue Inventory and see whether these
> "snames" are used, and whether my samples are really listed as SSL in
> there, etc. If not, then this list definitely needs to be expunged, as
> it is very confusing. If so, then I think we need to figure out why,
> and make some changes to samples and to the inventory. Lacey, can you
> do some work with the inventory on these?
I'll look through and see how the snames list matches up to the
inventory list
>
> -Second, I am not sure that this list has a proper place in babase.
> Given that it is clear in the inventory that the samples belong to
> humans (is it lacey?)
It is (in most cases) clearly Marked. Some human samples are listed as
'Population: Amboseli' but the name on them will say the humans name,
ie: Kinyua or Serahs' full names
> do we need to do anything with these? What is the risk that (a) the
> team would choose a baboon name that began with one of these, (b) that
> we would mix up a human and a baboon sample or be confused about
> these? I think the risk is small?
>
> -Third, they are not in the list that the team has been using, so they
> have never been banned as snames. Do we want to start now?
>
> Thoughts?
>
> 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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