[Psidev-ms-dev] Release candidate 3.89.0_rc3 of psi-ms.obo

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Dear proteomics community,

attached there's the release candidate 3.89.0_rc3 of the psi-ms.obo file.

New CV terms in version 3.89.0_rc3 of psi-ms.obo:
=================================================
************ Added a string value slot holding the molecular formula in 
Hill notation
[Term]
id: MS:1000336
name: neutral loss
def: "The loss of an uncharged species during a rearrangement process. 
The value slot holds the molecular formula in Hill notation of the 
neutral loss molecule, see PMID: 21182243. This term must be used in 
conjunction with a child of the term MS:1002307 (fragmentation ion 
type)." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

************ New terms for reporter ions
************ The mass can be specified in the value slot.
[Term]
id: MS:1002668
name: frag: iTRAQ 4plex reporter ion
def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the 
mass of the iTRAQ 4Plex reporter ion." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002669
name: frag: iTRAQ 8plex reporter ion
def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the 
mass of the iTRAQ 8Plex reporter ion." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002670
name: frag: TMT reporter ion
def: "Standard reporter ion for TMT. The value slot holds the mass of 
the iTRAQ 8Plex reporter ion and can be suffixed with either N or C, 
indicating whether the mass difference is encoded at a Nitrogen or 
Carbon atom." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002671
name: frag: TMT ETD reporter ion
def: "Standard reporter ion for TMT with ETD fragmentation. The value 
slot holds the mass of the iTRAQ 8Plex reporter ion and can be suffixed 
with either N or C, indicating whether the mass difference is encoded at 
a Nitrogen or Carbon atom." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002672
name: no modification threshold
def: "No statistical threshold for accepting or rejecting that a 
modification position." [PSI:PI]
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002673
name: OpenXQuest
def: "Cross-Linking MS search engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

Changed CV terms in version 3.89.0_rc3 of psi-ms.obo:
=====================================================
************ Changed the regular expression to allow null for the 
interaction position
[Term]
id: MS:1002665
name: regular expression for protein interaction scores derived from 
cross-linking
def: 
"([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression

************ Obsoleted the following terms.
[Term]
id: MS:1002455
name: H2O neutral loss
def: "OBSOLETE Neutral loss of water." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value H2O.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "OBSOLETE Neutral loss of ammonia." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value NH3.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "OBSOLETE Neutral loss of phosphoric acid." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value H3PO4.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

************ REARRANGEMENT OF PSM-level result details BRANCH 
************ (see attached figure)
************ The following two terms moved from
************ is_a: MS:1001872 ! distinct peptide-level e-value
************ to is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1001328
name: OMSSA:evalue
def: "OMSSA E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value

[Term]
id: MS:1001330
name: X\!Tandem:expect
def: "The X!Tandem expectation value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value

************ The following two terms moved from
************ is_a: MS:1001870 ! distinct peptide-level p-value
************ to is_a: MS:1002352 ! PSM-level p-value
[Term]
id: MS:1001329
name: OMSSA:pvalue
def: "OMSSA p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002352 ! PSM-level p-value

[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002352 ! PSM-level p-value

************ The following two terms moved from
************ is_a: MS:1002347 ! PSM-level identification confidence metric
************ to is_a: MS:1001092 ! peptide identification confidence metric
[Term]
id: MS:1001872
name: distinct peptide-level e-value
def: "Estimation of the e-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
MS:1001092 ! peptide identification confidence metric
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1001870
name: distinct peptide-level p-value
def: "Estimation of the p-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
MS:1001092 ! peptide identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

Best Regards,
Gerhard

-- 

*--*

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

*PhD student*

*Medizinisches Proteom-Center*

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