Comments (4)
i am thinking of a complete rework of the parsing. I think we should use ARCtrl's composite column model.
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iirc ARCtrl parses annotation tables like this:
- pattern match and assign grouping
- everything not assignes is
Freetext
if that is true, then it should be easy to use for tokenization as well, by filling these composite columns with CvParams in an additional step.
Sounds good? @HLWeil
from arctokenization.
Yup that's pretty much it.
It sounds fine with me, provided that it doesn't fail in some specific cases which should be checked. But as a starting point for getting your tokens for further use it should be good!
from arctokenization.
Closing this as we use ARCtr's ARCTable parser now, which we then tokenize. See #48
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Related Issues (20)
- Use new equals overrides for testing CvParam equality in ARCTokenizarion tests
- Transfer ArcGraph into ARCTokenization
- `Study.parseMetadataSheetfromFile` does not parse metadata sheet: says worksheet is not present HOT 4
- `Assay.parseMetadataSheetfromFile` does not parse metadata sheet: says worksheet is not present
- [BUG] Annotation table parsing can result in CvParam lists of incorrect length when parsing incorrect building blocks HOT 1
- [Feature Request] Annotation Table Graph
- [Discussion] is it really necessary to nest static ontology terms HOT 2
- [BUG] Study structural ontology has incorrect ID links in some cases HOT 2
- [BUG] When parsing User Comments, the name of the comment (not the value!) gets lost
- Make ARCMock accessible for consumption in other libraries HOT 1
- Refactor FileSystem token-based metadata parsing from ValidationPackage POC into ARCTokenization
- [BUG] `ARCMock.AssayMetadataTokens` misses Assay Technology Type TAN HOT 1
- `ARCMock` does not allow adding of User Comments HOT 1
- ProcessGraph parsing function (Study & Assay) only works with full paths but a function for tokens (like those for metadata sheets) would be nice
- Feature Request - Enhanced Tokenization for Specific Folders and Files
- Add integration tests for parsing ISA files from tokens
- Add CodeGenerator for structural ontologies HOT 1
- Move ControlledVocabulary to own repo HOT 1
- Use OBO.NET.CodeGeneration for structural ontology generation
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