Re: [Psidev-ms-dev] New version 4.1.25 of psi-ms.obo

[Felipe da V. L. <lep...@gm...>]

Thanks Gerhard

On Tue, Apr 9, 2019, 9:09 AM mayerg97 via Psidev-ms-dev <
psi...@li...> wrote:

> Dear proteomics/metabolomics community,
>
> following are the new/changed terms for the version 4.1.25 of the
> psi-ms.obo file. It can be downloaded from
> https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
>
>
> @Felipe: I left out PTMProphet:PTM Score (see Eric's last email):
> "
> PTM Prophet has quite a substantial number of metrics.
>      At the PSM level, we have:
>          normalized information content
>          number of localized modifications
>      At the site level, we have:
>          modification localization probability
>          O-score
>          M-score
> "
>
> If you need such PTMProphet metrics, then please send me a list with
> proposal for their exact name and definitions.
>
>
>
> New CV terms in version 4.1.25 of psi-ms.obo:
> =============================================
> [Term]
> id: MS:1003011
> name: pFind
> def: "Sequence-tag-based search engine pFind." [PMID:30295672]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1003012
> name: KSDP score
> def: "Kernel mass spectral dot product scoring function." [PMID:15044235]
> is_a: MS:1001143 ! PSM-level search engine specific statistic
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1003013
> name: i3tms
> def: "i3-tms search engine and data-analysis software." [PSI:PI]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1003014
> name: MSFragger
> def: "A database search-based peptide identification tool." [PMID:28394336]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1003015
> name: razor peptide
> def: "A peptide which is shared between protein groups and assigned to
> the protein group with the largest number of identified peptides." [PSI:PI]
> is_a: MS:1000860 ! peptide
>
> [Term]
> id: MS:1003016
> name: ProteinProphet:peptide weight
> def: "Fraction of peptide evidence attributable to a protein or a set of
> indistinguishable proteins." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002490 ! peptide-level scoring
> 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
>
> [Term]
> id: MS:1003017
> name: ProteinProphet:peptide group weight
> def: "Fraction of peptide evidence attributable to a group of proteins."
> [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002490 ! peptide-level scoring
> 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
>
> [Term]
> id: MS:1003018
> name: Philosopher
> def: "General proteomics processing toolkit for shotgun proteomics."
> [https://philosopher.nesvilab.org/]
> is_a: MS:1001456 ! analysis software
>
>
>
> Changed CV terms in version 4.1.25 of psi-ms.obo:
> =================================================
> ************ adde synonym 'InterProphet'
> [Term]
> id: MS:1002288
> name: iProphet
> def: "A program in the TPP that calculates distinct peptide
> probabilities based on several lines of corroborating evidence including
> search results from multiple search engines via the pepXML format."
> [PMID:21876204]
> synonym: "InterProphet" EXACT []
> is_a: MS:1002286 ! Trans-Proteomic Pipeline software
>
>
> Best Regards,
> Gerhard
>
> --
>
> ----------------------------------------------------------------------
>
> Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
>
> Scientific assistant
>
> Medizinisches Proteom-Center
>
> DEPARTMENT Medical Bioinformatics
>
> Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum
>
> Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554
>
> E-mail ger...@ru...
>
> www.medizinisches-proteom-center.de
>
>
>
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