Definitions added

[nithujohn]

User description

Hi @ypriverol there are few terms I can't find definitions. I am posting it down.
[Term]
id: PRIDE:0000058
name: z

[Term]
id: PRIDE:0000089
name: Protonated setting Mr

[Term]
id: PRIDE:0000367
name: subsample 1 description

[Term]
id: PRIDE:0000368
name: subsample 2 description

[Term]
id: PRIDE:0000369
name: subsample 3 description

[Term]
id: PRIDE:0000370
name: subsample 4 description

[Term]
id: PRIDE:0000371
name: subsample 5 description

[Term]
id: PRIDE:0000372
name: subsample 6 description

[Term]
id: PRIDE:0000373
name: subsample 7 description

[Term]
id: PRIDE:0000374
name: subsample 8 description

[Term]
id: PRIDE:0000375
name: standard deviation subsample 1

[Term]
id: PRIDE:0000376
name: standard deviation subsample 2

[Term]
id: PRIDE:0000377
name: standard deviation subsample 3

[Term]
id: PRIDE:0000378
name: standard deviation subsample 4

[Term]
id: PRIDE:0000379
name: standard deviation subsample 5

[Term]
id: PRIDE:0000380
name: standard deviation subsample 6

[Term]
id: PRIDE:0000381
name: standard deviation subsample 7

[Term]
id: PRIDE:0000382
name: standard deviation subsample 8

id: PRIDE:0000383
name: standard error subsample 1

[Term]
id: PRIDE:0000384
name: standard error subsample 2

[Term]
id: PRIDE:0000385
name: standard error subsample 3

[Term]
id: PRIDE:0000386
name: Standard error subsample 4

[Term]
id: PRIDE:0000387
name: standard error subsample 5

[Term]
id: PRIDE:0000388
name: standard error subsample 6

[Term]
id: PRIDE:0000389
name: standard error subsample 7

[Term]
id: PRIDE:0000390
name: standard error subsample 8

[Term]
id: PRIDE:0000391
name: quantification parameter

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PR Type

Documentation

---

Description

• Added detailed definitions for numerous PRIDE ontology terms.

• Updated ontology metadata, including version and date.

• Introduced new terms and restructured existing ones for clarity.

• Enhanced descriptions for Olink instruments and quantification methods.

---

Changes walkthrough 📝

	Relevant files
Documentation	pride_cv.obo Added definitions and updated ontology terms                          pride_cv.obo Replaced comments with detailed definitions for ontology terms. Updated metadata fields like data-version and date. Added new terms for Olink instruments and quantification methods. Improved descriptions for existing terms to enhance clarity. +161/-82
Additional files	pride_cv.owl +1010/-84

---

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PR Reviewer Guide 🔍

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⏱️ Estimated effort to review: 3 🔵🔵🔵⚪⚪

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⚡ Recommended focus areas for review Incorrect Definition The definition for MS2 based isotope labeling (PRIDE:0000317) incorrectly states it is detectable at MS1 level, but it should be MS2 level based on the term name and usage. def: "Describes isotope labeling quantification techniques detectable at MS1 level." [PRIDE:PRIDE] Syntax Error The definition for TMT reagent 88 (PRIDE:0000560) has an incorrectly formatted citation with missing closing bracket [PRIDE;PRIDE] instead of [PRIDE:PRIDE]. def: "protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton." [PRIDE;PRIDE]

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	Fix definition syntax error Fix incorrect syntax in protonated setting MH+ definition - semicolon used instead of colon pride_cv.obo [560] -def: "protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton." [PRIDE;PRIDE] +def: "protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton." [PRIDE:PRIDE] Apply this suggestion Suggestion importance[1-10]: 6 __ Why: Corrects an incorrect syntax in the ontology definition format (semicolon instead of colon), which could potentially cause issues with ontology parsing tools.	Low
	Fix definition typo Fix typo in definition of 'Precursor ion mass tolerance' - change "efines" to "defines" pride_cv.owl [480] -<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Precursor ion mass tolerance efines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches</obo:IAO_0000115> +<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Precursor ion mass tolerance defines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches</obo:IAO_0000115> Apply this suggestion Suggestion importance[1-10]: 5 __ Why: The suggestion fixes a clear typo in the definition text ("efines" -> "defines"), which improves readability and professionalism of the documentation.	Low
	Fix definition typo Fix typo in definition of precursor ion mass tolerance term - "efines" should be "defines" pride_cv.obo [74] -def: "Precursor ion mass tolerance efines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches" [PRIDE:PRIDE] +def: "Precursor ion mass tolerance defines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧) of a precursor ion and its theoretical (m/z) value during database searches" [PRIDE:PRIDE] Apply this suggestion Suggestion importance[1-10]: 5 __ Why: Fixes a minor typo in the definition text that could affect readability and professionalism of the documentation, though not impacting functionality.	Low