[Psidev-pi-dev] Release candidate 4.0.10_rc1 of psi-ms.obo

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Dear proteomics community,

attached there's the release candidate 4.0.10_rc1 of the psi-ms.obo file.

It contains corrections for the names of is_a relationships for several 
terms,
which result from our ontology reorganisation last summer.

Thanks Hannes, for pointing out these inconsistencies.

New CV terms in version 4.0.10_rc1 of psi-ms.obo:
=================================================
************ No new terms

Changed CV terms in version 4.0.10_rc1 of psi-ms.obo:
=====================================================
************ is_a: MS:1001105 ! peptide result details
************ replaced by
************ is_a: MS:1001105 ! peptide sequence-level identification 
attribute
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." 
[PSI:PI]
comment: This term was made obsolete because scan start time 
(MS:1000016) should be used instead.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

************ is_a: MS:1001092 ! peptide identification confidence metric
************ replaced by
************ is_a: MS:1001092 ! peptide sequence-level identification 
statistic
[Term]
id: MS:1001191
name: p-value
def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
comment: This term was made obsolete because now is split into peptide 
and protein terms.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001198 ! protein identification confidence metric
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ MS:1001116 ! single protein identification statistic
[Term]
id: MS:1001198
name: protein identification confidence metric
def: "Identification confidence metric for a protein." [PSI:PI]
is_a: MS:1001116 ! single protein identification statistic

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ is_a: MS:1001116 ! single protein identification statistic
[Term]
id: MS:1002268
name: Byonic:Best LogProb
def: "Best (most negative) log p-value of an individual PSM." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002109 ! lower score better

************ is_a: MS:1002405 ! protein cluster details
************ replaced by
************ is_a: MS:1002405 ! protein group-level result list attribute
[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein group-level result list attribute

************ is_a: MS:1002358 ! search engine specific score for 
distinct peptides
************ replaced by
************ is_a: MS:1002358 ! search engine specific peptide 
sequence-level identification statistic
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific peptide sequence-level 
identification statistic
is_obsolete: true

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
************ in the following six OpenXQuest terms
[Term]
id: MS:1002681
name: OpenXQuest:combined score
def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002682
name: OpenXQuest:xcorr xlink
def: "OpenXQuest's cross-correlation of cross-linked ions subscore." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002683
name: OpenXQuest:xcorr common
def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002684
name: OpenXQuest:match-odds
def: "OpenXQuest's match-odds subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002685
name: OpenXQuest:intsum
def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002686
name: OpenXQuest:wTIC
def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ is_a: MS:1001073 ! database type
************ replaced by
************ is_a: MS:1001073 ! database type amino acid
[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type amino acid

************ Removed
************ is_a: MS:1001153 ! search engine specific score
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_obsolete: true

Best Regards,
Gerhard

-- 

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*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

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