Update pride_cv.obo

[nithujohn]

User description

changes in definition @ypriverol

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PR Type

Documentation

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Description

• Replaced comment fields with def fields for better term definitions.

• Added detailed descriptions to numerous ontology terms in pride_cv.obo.

• Improved clarity and consistency of term definitions and descriptions.

• Enhanced the ontology file for better usability and understanding.

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Changes walkthrough 📝

	Relevant files
Documentation	pride_cv.obo Added detailed definitions and replaced comments in ontology terms pride_cv.obo Replaced comment fields with def fields for term definitions. Added detailed definitions for existing ontology terms. Improved clarity and consistency in term descriptions. Enhanced ontology usability with better documentation. +143/-75

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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, which contradicts its name and purpose def: "Describes isotope labeling quantification techniques detectable at MS1 level." [PRIDE:PRIDE] Formatting Issue The TMT term (PRIDE:0000314) has an incorrectly formatted definition that spans multiple lines and contains an embedded synonym def: "Tandem Mass Tag is a MS2 based isotope labeling quantification technique synonym: "Tandem Mass Tag" EXACT []" [PRIDE:PRIDE]

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Category	Suggestion	Score
Possible issue	Fix incorrect namespace separator in term definition to maintain consistent syntax Fix syntax error in definition of 'Protonated setting MH+' term - incorrect separator used between namespace and term pride_cv.obo [561] -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]: 8 Why: The incorrect separator (;) instead of (:) in [PRIDE;PRIDE] could cause parsing errors in tools that process the ontology. This is a critical syntax fix.	8
General	Fix typographical error in term definition that impacts readability and clarity Fix typo in definition of 'Precursor ion mass tolerance' term - "efines" should be "defines" pride_cv.obo [75] -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]: 7 Why: The typo "efines" instead of "defines" affects readability and could cause confusion. Fixing this improves the clarity of an important technical definition.	7
	Improve definition clarity by fixing capitalization, punctuation and sentence structure Fix typo in definition of 'mass error type setting ppm' term - missing closing quote and incorrect punctuation pride_cv.obo [531] -def: "the mass error type is set to ppm (parts per million), it specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion, and it is expressed as parts per million (ppm). " [PRIDE:PRIDE] +def: "The mass error type is set to ppm (parts per million), which specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion and is expressed as parts per million (ppm)" [PRIDE:PRIDE] Apply this suggestion Suggestion importance[1-10]: 6 Why: The suggested changes improve readability and professionalism of the definition by fixing multiple style issues including capitalization, punctuation, and sentence structure.	6

[ypriverol]

@nithujohn this is failing validation.