Closed GoogleCodeExporter closed 8 years ago
It would be useful to have a way of reporting custom databases - even if it is
just
free text to describe how the database was constructed?
It would also be beneficial to be able to report the number of peptides in the
search
database (in addition to the number of proteins searched).
Original comment by jensie...@gmail.com
on 27 Jun 2008 at 10:53
[deleted comment]
TeleCon, 10th July 2008: Seems like a hopeless expectation that there will be a
universal and unambiguous way of specifying search database. Where a custom
database
has been used, then this should be submitted along with the analysisXML file.
Original comment by eisena...@googlemail.com
on 15 Jul 2008 at 3:28
To close this issue (TeleCon 11th September, 2008):
- use CV to specify DB name for most important DBs (version etc. is specified as
attribute)
- use UserParam for database names not in the CV and submit them alongside the
data
set (or specify their publicly accessible URI in the location attribute)
Original comment by eisena...@googlemail.com
on 11 Sep 2008 at 4:13
At Turku meeting, decided to re-open this issue. Have the option of specifying a
miriam id rather than using CV. However, it would not be enough for mzIdentML
on it’s
own. For example, IPI is a single MIRIAM id, by the files are available as
IPI_Human,
IPI_Mouse etc. so it would also need a taxID coupled to it.
Original comment by dcre...@gmail.com
on 5 May 2009 at 10:46
E-Mail Comment from Pierre-Alain:
Hi:
a comment:
MIRIAM does not have an entry for Swiss-Prot, for TrEMBL, for uniparc,
for uniref etc. Only one for Uniprot (which is by the way not the
official abbreviation). Apparently, according to the information Luisa
had, ther is no intention to have separate entries for these Uniprot
"sub-"databases. It is therefore not usable so far.
Original comment by delag...@gmail.com
on 5 May 2009 at 1:33
E-Mail comment from David Creasy:
Hi Pierre-Alain,
Yes, it's not so useful at the moment. Even for IPI it isn't so useful
because there is no entry for MSIPI, and I guess it's unlikely that
there will be looking at the current strategy. Oh, and it also looks as
though the information about IPI is very out of date which doesn't
inspire confidence.
Um... also a bit strange that there is absolutely no mention of anything
from the NCBI.
The agreement at the Turku meeting was to make it an option to use
miriam *or* the existing the current method. My feeling is now that we
should defer supporting it until it's more comprehensive and a little
more 'neutral', but we can discuss on the next conference call.
Thanks,
David
Original comment by delag...@gmail.com
on 5 May 2009 at 1:34
I agree with David. Defer this until there is at least versioned database
support.
Original comment by delag...@gmail.com
on 5 May 2009 at 1:38
Hi,
This is what I found out after a meeting with the MIRIAM people today:
1. The only requirements for a database to be included in MIRIAM are: to be
freely
available, accessible on-line, to have stable and unique identifiers for the
entries
and no licence restriction for using it.
2.Apart from that, if any resource is not there yet is because noone has told
them
yet. They are very happy to add new ones and it should be a very
straightforward process.
3.I have told them about the fact that they have at present UniProt and
UniParc, for
instance, but no specific entries for UniProtKB/SwissProt, TrEMBL,
UniRef,...They are
going to think about this. Again, noone had told them before.
4.Both the MIRIAM identifier (for instance, for PRIDE MIR:00000065) or the
MIRIAM URN
(urn:miriam:pride) could be used for referencing the database.
5.For IPI, they do not want to split it by different species, but as pointed out
before, to add a new CV term (taxID) would be possible.
I think it is out of the scope here, but MIRIAM is being used in MIAME
documents to
assure that the identifiers reported match the corresponding referenced
database.
Original comment by javizca74@gmail.com
on 13 May 2009 at 2:01
Thanks for finding this out. I guess the most commonly used 'database' in the
mass
spec world is the NCBI 'nr' database. Be interesting to know if this is not
included
because of '1' or '2'.
Also, how about MSIPI. http://www.pil.sdu.dk/msipi.htm
Would they include this as a separate database?
Please let us know what they decide about '3'
Thanks,
David
Original comment by dcre...@gmail.com
on 13 May 2009 at 3:23
In TeleCon May 20th agreement, NOT to use MIRIAM, because:
Not suitable at the moment since MIRIAM cannot incorporate NCBI nr database or
differentiate between TrEMBL and SwissProt for instance.
Original comment by eisena...@googlemail.com
on 28 May 2009 at 3:25
Original comment by eisena...@googlemail.com
on 28 May 2009 at 3:26
Original issue reported on code.google.com by
philip.j...@gmail.com
on 18 Jun 2008 at 5:31