Open GoogleCodeExporter opened 8 years ago
Hi all,
I would favour options 2 or 3. Option 2 is a hack and Option 3 implies a schema
change. If the idea is to support "properly" de novo approaches, option 3 would
be the preferred one.
But I have the feeling that option 1 (which also implies a schema change) will
make files potentially less consistent, and will make life much harder for
readers.
Best regards,
Juan
Original comment by javizca74@gmail.com
on 24 Jan 2014 at 7:46
Discussed today - we favour option 1; and document that file readers may choose
to ignore PSMs (from database search) if they do not have PeptidEvidenceRef
Original comment by andrewro...@googlemail.com
on 31 Jan 2014 at 4:17
In the mzid1.2-draft schema I have provisionally made this change, and updated
DBSequence to be 0..many (from 1..many in mzid1.1). I still have some
reservations about it though.
I would be happier if we could add a validation rule that says if the search is:
<SearchType>
<cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
</SearchType>
PeptideEvidenceRef MUST be present on every SpectrumIdentificationItem. I worry
that we will get lots of badly exported files, with no links at all from PSMs
to proteins, due to the spec document not being read properly.
Salvador - would this be possible to implement?
Original comment by andrewro...@googlemail.com
on 27 Feb 2014 at 1:50
I guess that any of the following cvParams should "trigger" the MUST rule on
SII:
ID: MS:1001584
Name: combined pmf + ms-ms search
ID: MS:1001083
Name: ms-ms search
ID: MS:1001081
Name: pmf search
Do you agree?
Original comment by smartinez@proteored.org
on 27 Feb 2014 at 6:51
Original issue reported on code.google.com by
andrewro...@googlemail.com
on 23 Jan 2014 at 5:38