Sweetpotato Trait Ontology is maintained by http://www.cropontology.org and https://sweetpotatobase.org
Request new traits/variables by submitting a new issue in this github repo, or by filling the trait request form http://submit.rtbbase.org
Focal point for requesting new terms: CIP
The following conventions are being used:
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‘Sweetpotato’ is written as one word following CIP style guide
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When requesting a new trait it should include detailed method and scale
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Variables are pre-composed of the trait, method, and scale
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Trait abbreviation should be a synonym, and is a 5-6 letter abbreviation for Object abbreviation as: [a-zA-Z]{3} plus attribute abbreviation as: [a-zA-Z0-9]{2-3}; so total: [a-zA-Z]{3}[a-zA-Z0-9]{2-3}
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Variable short synonym is name composed of Trait abbreviation + Method class abbreviation + Scale abbreviation following the IBP format and this regular expression: '[a-zA-Z]{3}[a-zA-Z0-9]{2-3}[_]{1}[A-Z]{1}{a-z}{1}[_]{1}[a-zA-Z0-9]{1,12}'
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Scale abbreviations must not contain special characters (as in regular expression above):
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Special scale abbreviations: categories with 1:9 should be as: 1to9; % as pct
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Extra columns from cropontology spreadsheet format are mapped to the comment field in the following format: "| 'column name': 'content'". The last pair is followed by a point to comply with the OBO format definition. For the moment no check is done if a comment already exists since there is no comment field in the spreadsheet.
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The columns 'Curation' and 'Crop' are currently ignored. 'Curation' could be added but unclear to what term level (trait, variable, method, scale?). 'Crop' column content is implied.
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Formula must not use 'x' to denote multiplication but '*' since everything starting with a letter is interpreted as a variable name for cross-referencing.
The following observations:
- Identifiers in xrefs must be using only English alphabet characters (no extended characters allowed by OBO-editor)
- The list of variables corresponds currenlty to those commonly used in sweetpotato trials. It will be expanded shortly to a larger list of 175+ variables.
TODOs in curation:
- Cross referencing to other ontologies
- Clearer separation of trait, method and variable definitions.