Re: [Psidev-pi-dev] FW: Representing Sequences

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> >>>> I notice also that there is a small error in the schema in that on PeptideEvidence DBSequence_ref
> should be
> >>>> mandatory (and it is missing from the instance docs). I can fix this if there is agreement on this?
> >>> Yes, if <PeptideEvidence> stays optional.
> >> What about denovo where there is no database...
> > That is an argument to have PeptideEvidence optional, isn't it?
> > But DBSequence_ref  as attribute of it should be mandatory.
> Doh, sorry, yes you are totally correct. It should be mandatory.
Now it is.
ANd next problem: WE have two "Sequence_Ref" attributes, 
in <PeptideEvidence> and <ProteinHypothesis> (now both mandatory).
What if they are contradictory (validator?)?
If they are not contradictory, at least the one in <ProteinHypothesis> is redundant.

>  >(and it is missing from the instance docs).
> I believe it's in all the Mascot ones?
It is. 

> >>>> It is a database search parameter:
> >>>> <AdditionalSearchParams>
> >>>>    <pf:cvParam accession="PRIDE:0000162" name="Mass value type setting monoisotopic" cvRef="PRIDE"/>
> >>> Yes, it is, but in case we have more than one SpectrumIdentification, that could be conflicting.
> >>> http://code.google.com/p/psi-pi/issues/detail?id=37
> >> I'm not sure I understand whether this is OK or not now? (And why use
> >> Pride CV?)
> > I think the current schema is not okay, because it allows "average" in one SpecIdent and "mono" in
> another,
> > so it is not well-defined for the masses in elements or attributes.
> > We need a global attribute :-) or element. Or it can be done later in semantic validation :-( .
> I think it's actually _required_ to be like this. For example, at least
> one search engine allows you to specify mono for masses below x and
> average for masses above x. So, in this case, the output should be
> similar to the N15 example that I've supplied, with two separate mass
> tables. Maybe you could look at the Mascot_N15_example.xml and see if
> you think that this is OK.
It is okay with me; to answer Pierre-Alains original question then:
all mass values for peptides then depend on 
the type of search performed and the residue table used. ;-)

  Bye
    Martin


> Talk soon,
> 
> David
> 
> >
> >   Bye
> >     Martin
> >
> >
> >>>>> -----Original Message-----
> >>>>> From: psi...@li... [mailto:psidev-pi-dev-
> >>>>> bo...@li...] On Behalf Of Martin Eisenacher
> >>>>> Sent: 30 July 2008 13:05
> >>>>> To: 'Pierre-Alain Binz'
> >>>>> Cc: psi...@li...
> >>>>> Subject: Re: [Psidev-pi-dev] FW: Representing Sequences
> >>>>>
> >>>>> Hi Pierre-Alain, quite old posting, but I saw no answer yet, so I will try:
> >>>>>
> >>>>>> 2nd July, 2008:
> >>>>>> a couple of questions, just to make sure:
> >>>>>> 1) in case of top-down approach, do we have to duplicate sequenceCollection
> >>>>> information?
> >>>>> I hope not, by referencing the same identifier.
> >>>>>
> >>>>>> as SpectrumIdentificationResult contains a PeptideEvidence refering to a Peptide
> >>>>> element
> >>>>>> (and not to a DBSequence), identification is obligatory a Peptide?
> >>>>> At the moment I think it's possible to directly reference a DBSeq. At the time the
> >>>>> foreign key definitions are implemented we can forbid that.
> >>>>> But we should have in mind, that a peptide is a sequence plus modifications, so if
> >>>>> top-down
> >>>>> identifies only a sequence, we should allow that and if top-down identifies with
> >>>>> mods,
> >>>>> we should forbid that.
> >>>>> It would be quite helpful to have a top-down instance doc. To check
> >>>>> whether our thoughts are really deep enough...
> >>>>>
> >>>>>> 2) and what about spectral library searches, do we have to have Peptide
> >>>>>> elements with possibly undefined explicit sequences to refer to
> >>>>> >from the SpectrumIdentificationResult (because non peptidic, or because not
> >>>>> identified
> >>>>>> but good spectrum)
> >>>>> At the moment the sequence element can be empty or even left out.
> >>>>> User or CV params are allowed.
> >>>>> How do they report results in spectral lib search if they identify non-peptidic or
> >>>>> unidentified?
> >>>>> We need CV terms for that...
> >>>>>
> >>>>>> 3) in the Peptide element, the Modifications are defined in a much more
> >>>>>> detailed manner than in ModificationParams (PSI-MOD is there for
> >>>>>> instance). Does this simply mean that The ModificationParams codes
> >>>>>> the search engine settings and the Peptide includes the formal PSI
> >>>>>> definition of the Mod? And the only reference is the ModName value?
> >>>>> I think that has changed meanwhile, in the MPC use case I used PSI-MOD terms
> >>>>> for both. If a search engine has its "own" mods, we need CV for that in PSI-PI CV
> >>>>> or
> >>>>> they can define their own.
> >>>>>
> >>>>>> 4) all mass values (sequenceMass, calculatedMassToCharge,
> >>>>> experimentalMassToCharge,
> >>>>>> are not specified whether monoisotopic or averaged.
> >>>>>> Do we assume that averaged does not exist anymore?
> >>>>> No, we decided to have only one type of masses in the whole analysisXML.
> >>>>> But I cannot find a note for that or a schema attribute... I will add an issue for that.
> >>>>>
> >>>>>
> >>>>>> 5) is sequenceMass the mass value with/without the mods? If with, the
> >>>>>> name might be missleading (peptideMass would be more appropriate)
> >>>>> It is indeed the mass of the sequence without mods.
> >>>>> THAT is described in http://code.google.com/p/psi-pi/wiki/NotesForFocumentation
> >>>>>
> >>>>>> 6) in case the DBSequence is nucleotide, is there a tag for saying
> >>>>>> this? (NB: MS on nucleotide molecules can be performed and analysed,
> >>>>>> not only MS on AA sequences that are interpreting nucleotide sequences).
> >>>>>> Or do we neglect MS experiments done on nucleotide molecules (and by
> >>>>>> the way on glycans...) and only represent the DBSequences as AA
> >>>>>> sequences (frame translations)? (and what about glycans?)
> >>>>>> Probaly can be solved if one can replace SequenceCollection by
> >>>>>> something else if needed (SmallMoleculeCollection, GlycanCollection,
> >>>>>> MoleculeCollection)... but the validator might not like this.
> >>>>> Mh, these can be extensions, I think they are not possible at the moment.
> >>>>> But a tag for the type can indeed be useful, it could be a CV param.
> >>>>> I will create an issue for that.
> >>>>>
> >>>>>> 7) in case that DBSequence is nucleotide, do we represent the
> >>>>>> Peptide as AA sequence in case of MS done on proteins?
> >>>>> I hope the following answers this:
> >>>>>
> >>>>> <DBSequence> is the nucleotide seq from the nucleotide DB,
> >>>>> <Peptide> is the identified amino acid sequence plus mods (without any translation
> >>>>> frame or something).
> >>>>> <PeptideEvidence> contains the DBSequence_Ref together with a frame and a
> >>>>> TranslationTable_Ref attribute.
> >>>>> (The Peptide_Ref is done in SpectrumIdentificationItem as in the amino acid DB
> >>>>> case.)
> >>>>> If a protein detection is performed, there are <PeptideHypothesis> elements
> >>>>> referencing
> >>>>> PeptideEvidence elements from SpectrumIdentificationItem sections.
> >>>>>
> >>>>>
> >>>>>
> >>>>>   Bye
> >>>>>     Martin
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> David Creasy wrote:
> >>>>> Thanks Andy,
> >>>>>
> >>>>> I've added an updated example document to SVN:
> >>>>> http://code.google.com/p/psi-
> >>>>> pi/source/browse/trunk/examples/schema_usecase_examples/working27June/F00
> >>>>> 1350.xml
> >>>>>
> >>>>> Problem is that we have now removed the main point of these recent changes
> >>>>> which was to add the decoy flag... I think
> >>>>> that we need to add isDecoy to SpectrumIdentificationItem.
> >>>>>
> >>>>> And yes, I suspect that we should go back to using the
> >>>>> ConceptualMoleculeCollection
> >>>>> Um, and since we've not actually ended up adding anything to DBSequence... we
> >>>>> haven't actually achieved anything?
> >>>>> I think we need to discuss this again at the next telecon.
> >>>>>
> >>>>> David
> >>>>>
> >>>>> Jones, Andy wrote:
> >>>>> Hi all,
> >>>>>
> >>>>> Ive updated the schema in SVN with the following main changes:
> >>>>>
> >>>>> PeptideEvidence is now part of SpectrumIdentificationItem as discussed on the
> >>>>> call (simple mappings to proteins are done
> >>>>> at this level)
> >>>>> Added DBSequence that should be used instead of Sequence (following some of
> >>>>> the discussion below)
> >>>>> Created a new collection class SequenceCollection (rather than
> >>>>> ConceptualMoleculeCollection) so that only references can
> >>>>> be given to DBSequence and Peptide
> >>>>> In fact, Im not sure if this is sensible since it prevents other types of
> >>>>> ConceptualMolecule being added later... to
> >>>>> discuss
> >>>>> In FuGE on cvParam, the value attribute is no longer mandatory
> >>>>>
> >>>>> Ive added a simple example that validates under
> >>>>> examples\schema_usecase_examples\working27June
> >>>>>
> >>>>> Feel free to mail me any changes to make on Monday,
> >>>>> Cheers
> >>>>> Andy
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: psi...@li... [mailto:psidev-pi-dev-
> >>>>> bo...@li...] On Behalf Of
> >>>>> Jones, Andy
> >>>>> Sent: 27 June 2008 16:24
> >>>>> To: Angel Pizarro
> >>>>> Cc: psi...@li...
> >>>>> Subject: Re: [Psidev-pi-dev] FW: Representing Sequences
> >>>>>
> >>>>> I think Angels response below might not have made it round the list yet.
> >>>>>
> >>>>> I tend to agree that isDecoy is redundant information and perhaps this is not the
> >>>>> best place to encode semantic
> >>>>> information. An alternative would be to have a parameter, say on
> >>>>> SpectrumIdentification for  cvParam = decoy_string
> >>>>> value = Rev. This would be a more compact representation and we would not
> >>>>> have to add what is quite a specific
> >>>>> attribute type (isDecoy) to Sequence.
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: an...@it... [mailto:an...@it...] On Behalf Of Angel
> >>>>> Pizarro
> >>>>> Sent: 27 June 2008 15:59
> >>>>> To: Jones, Andy
> >>>>> Cc: psi...@li...
> >>>>> Subject: Re: [Psidev-pi-dev] FW: Representing Sequences
> >>>>>
> >>>>> my 2¢ :
> >>>>> You need to be able to extend this to all molecule types, or am I missing the point
> >>>>> of this thread, and you mean that
> >>>>> this would be a suclass of the conceptual molecule element?
> >>>>>
> >>>>> Second, and this is is tangentially related, but are decoy sequences really a
> >>>>> problem we should be putting our effort
> >>>>> into? Is it in our domain to encode semantic information about a sequence, and
> >>>>> possibly relating reported sequences as
> >>>>> part of our schema?
> >>>>> On a personal level I could care less if "isDecoy" is an attribute or not, but the
> >>>>> temptation then would be for folks to
> >>>>> encode the same accession for two different sequences, effectively making the
> >>>>> primary key of the sequence object
> >>>>> (accession, isDecoy)
> >>>>>
> >>>>>
> >>>>> Do we want to go there?
> >>>>> On Fri, Jun 27, 2008 at 10:21 AM, Jones, Andy <And...@li...>
> >>>>> wrote:
> >>>>> So how about include length as an attribute and then let all other things go in the
> >>>>> CV (pI, mass, etc.)?
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: Jones, Andy
> >>>>> Sent: 27 June 2008 14:54
> >>>>> To: 'David Creasy'
> >>>>> Subject: RE: [Psidev-pi-dev] Representing Sequences
> >>>>>
> >>>>> id and name are standard for all elements that inherit from FuGE identifiable  this
> >>>>> is perhaps a separate discussion as
> >>>>> to whether the optional name attribute should be there.
> >>>>>
> >>>>> I agree that length may be useful  is this just an integer value with no unit?
> >>>>> Yes,  I think so.
> >>>>> I'm less sure about pI and mass since mass at least can be calculated very simply
> >>>>> Only if you have the sequence... (we have residue masses in the file).
> >>>>>
> >>>>>
> >>>>> , and pI values (in my opinion) are pretty inaccurate and fairly meaningless
> >>>>> Scandalous! (I happen to agree, but now some people will never speak to either of
> >>>>> us ever again).
> >>>>>
> >>>>> The main problem with mass and pI is that these are 'irrelevant' if the sequence is
> >>>>> nuleic acid rather than residues.
> >>>>> Why not just allow CV there? We can share the same CV as the PEFF format,
> >>>>> which includes, taxonomy, sequence type, gene
> >>>>> ID, and lots of wonderful other things?
> >>>>>
> >>>>>
> >>>>>  unless someone can convince me otherwise?
> >>>>> Cheers
> >>>>> Andy
> >>>>>
> >>>>>
> >>>>> From: David Creasy [mailto:dc...@ma...]
> >>>>> Sent: 27 June 2008 14:51
> >>>>> To: Jones, Andy
> >>>>> Cc: psi...@li...
> >>>>> Subject: Re: [Psidev-pi-dev] Representing Sequences
> >>>>>
> >>>>> Hi Andy,
> >>>>>
> >>>>> length may be useful, because some people won't want to output the actual
> >>>>> sequence for space reasons. The other things
> >>>>> we wanted to add before were pI and mass.
> >>>>> Why do we want name? Is this for, say, a description line?
> >>>>> (Also, identifier -> id?)
> >>>>>
> >>>>> David
> >>>>>
> >>>>> Jones, Andy wrote:
> >>>>> Hi all,
> >>>>>
> >>>>> It was decided on the call that we would like to flag that Sequences in the
> >>>>> ConceptualMoleculeCollection should have a
> >>>>> Boolean attribute to capture if they are decoy sequences. At the moment we are
> >>>>> using the FuGE:Sequence element. I don't
> >>>>> really want to add another attribute to this (it's less problematic cutting down FuGE
> >>>>> than adding new things), so I'm
> >>>>> wondering if we should define our own Sequence type in AnalysisXML. This
> >>>>> would also allow us to choose exactly the
> >>>>> relevant attributes. At the moment, Sequence can have all of the following:
> >>>>>
> >>>>>                         <pf:Sequence isCircular="true" sequence="String" length="0"
> >>>>> isApproximateLength="true"
> >>>>> SequenceAnnotationSet_ref="String" start="0" end="0" identifier="String"
> >>>>> name="String">
> >>>>>
> >>>>> Several of these attributes were created to represent concepts that probably will
> >>>>> never be required or implemented in
> >>>>> AnalysisXML. How about the following:
> >>>>>
> >>>>> <DBSequence identifier = "" name = "" isDecoy = "true">
> >>>>>                 <seq>MCTMG...</seq>
> >>>>>                 <pf:DatabaseReference Database_ref=""
> >>>>> accession="Rev_IPI00013808.1"/>
> >>>>> </DBSequence>
> >>>>>
> >>>>> Are any of the other attributes on Sequence actually required? I'll post a new
> >>>>> version of the schema with other changes
> >>>>> WRT to PeptideEvidence shortly,
> >>>>> Cheers
> >>>>> Andy
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
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> >>>>> Matrix Science
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> >>>>> London W1U 7GB, UK
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> >>
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> 
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> 
> dc...@ma...
> http://www.matrixscience.com
> 
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898