search

mwalzer / psi-pi

Automatically exported from code.google.com/p/psi-pi
0 stars 0 forks source link

mzIdentML version1.1: dbSequence_ref on PDH should be mandatory #72

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
It appears that dbSequence_ref on PDH is an optional attribute when in fact 
this was certainly intended to be mandatory.

Possible solutions:

1. Update this in the schema as a version 1.1.1 release - does this count as a 
backwards compatible change? Newer software would be fine but older export 
software may not export this value.

2. Accept this as a bug and make sure our import software handles this i.e. 
checks down the tree in PeptideHypothesis to retrieve the corresponding 
referenced protein via PeptideEvidence?

3. Any other options?

Everyone writing export software, please be careful to include this attribute!

Original issue reported on code.google.com by andrewro...@googlemail.com on 2 Nov 2012 at 11:03

GoogleCodeExporter commented 9 years ago 
Further investigation shows that we thought about this but decided otherwise. 
Documentation:

<xsd:complexType name="ProteinDetectionHypothesisType">
        <xsd:annotation>
            <xsd:documentation>A single result of the ProteinDetection analysis (i.e. a protein).</xsd:documentation>
        </xsd:annotation>
        <xsd:complexContent>
            <xsd:extension base="IdentifiableType">
                <xsd:sequence>
                    <xsd:element name="PeptideHypothesis" type="PeptideHypothesisType" maxOccurs="unbounded"/>
                    <xsd:group ref="ParamGroup" minOccurs="0" maxOccurs="unbounded">
                        <xsd:annotation>
                            <xsd:documentation>Scores or parameters associated with this ProteinDetectionHypothesis e.g. p-value</xsd:documentation>
                        </xsd:annotation>
                    </xsd:group>
                </xsd:sequence>
                <xsd:attribute name="dBSequence_ref" type="xsd:string">
                    <xsd:annotation>
                        <xsd:documentation>A reference to the corresponding DBSequence entry. This optional and redundant, because the PeptideEvidence elements referenced from here also map to the DBSequence. </xsd:documentation>
                    </xsd:annotation>

Making this attribute optional seems rather odd, since it forces readers to 
look at PeptideHypothesis_ref instead. However, for now code will have to do 
this.

Original comment by andrewro...@googlemail.com on 23 Jan 2013 at 3:31

GoogleCodeExporter commented 9 years ago 
Discussed at PSI2013 -  decision to make an update to the specification 
document, encouraging exporters to include the attribute, but noting that 
reading software will have to check for the attribute and otherwise read it 
from PeptideEvidence.

ACTION: Andy to draft update to spec doc.

Issue will be closed when the spec doc update has been made

Original comment by andrewro...@googlemail.com on 17 Apr 2013 at 12:19