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#181
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#181
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- Update: Now adding synonyms for alt & included symbols, w/ type of mondo#abbreviation. - Misc updates: Todo comments. Renamed variables/methods for consistency and accuracy. Refactored some things.
- In previous commits, stated that this would also include 'included' symbols, but for now we have decided not to proceed with that. - Update: Now adding synonyms for alternative symbols, w/ type of mondo#abbreviation. - Update: Now stripping the text ', INCLUDED' from symbols. Previously was only doing for titles. - Update: For included & alternative titles/symbols ending in ', FORMERLY', these are being added as relatedSynonyms, and also being marked as owl:deprecated. - Misc updates: Updated some comments and codestyle.
- Bug fix: mondo#ABBREVIATION URI - Update: Typo and codestyle of cleanup_label()
- Update: Docstring to make clearer - Update: Typo fix - Update: Now "former" included titles/symbols are also being processed
- Update: Refactor: Cleaned some redundancy in how this was being called. Simplified code. Modularized other parts of code.
- Update: Now considering all abbreviations when checking a title and uppercasing them. Previously was only looking at the first preferred symbol. - Update: Refactored, added comments and todos, simplified code. - Bug fix: Was not actually uppercasing previously. The .replace() usage was incorrect.
- Add: A todo
- Upgrade to v1.5.3. Has a bugfix for SSSOM and includes dotenv package.
- Bug fix: Need to add '--user --break-system-packages' due to new nature of ODK security.
- Analysis: Self-referential “phenotype in the gene position + Phenotype field without a MIM” + "morbidmap.txt entry not in Phenotype-Gene Relationships table" case
- Update: No longer just analysis. Now filtering these out.
- Update: Revert filtering out. Now log as a review.tsv case.
- Update: README: general documentation for d2g pipeline
- Updates to README.md docs: (i) changed verbiage 'related' to 'pattern', (ii) added an example from morbidmap.txt. - Updates: Code comments: Added verbiage 'disease-defining'
Update morbidmap analysis notebook
- Update: Docs: Fixed a few places where the phrase Gene->Disease was used but should have been Disease->Gene, and vice versa. - Update: Some additional rephrasing.
Disease-Gene: Self-referential cases
Title cleaning updates
- Delete: some files somehow accidentally added
ODK Upgrade
Update `requirements-unlocked.txt`
- Renamed function: Now more accurate and shorter - Codestyle: Line length - Code quality: Redundant imports - Update comments
- Add: New cases: '3. D2G: somatic', '4. D2G: Phenotype is gene', and '5. D2G: Phenotype type error'. - Renamed the classLabel for the 2 existing review cases to be shorter / simpler. - Refactored code for DRYness, adding _add_to_review_tsv() and REVIEW_CASE_NAME_MAP. Also streamlined the values / error messages for these to be more consistent and easier to read.
- Bug fix: Fixed a sorting issue for the 'self-referential' review case. - Codestyle: Added a space after comma - Docs: Added clarifying text about how to easily identify individual cases when a case contains multiple rows. - Docs: Added text about the relationship between review cases 2 and 3
- Refactor: Moved review.tsv code into a separate function in order to make the disease2gene section more readable.
- Docs: Updated docs for 'D2G: self-referential' representation within review.tsv itself to be more clear.
- Updated some comments to be clearer
- Update: Verbiage for case 3 for additional clarity
`review.tsv` updates
Abbreviation recasing: use all abbreviations
Added a way for us to manually make exclusions, such that entries in morbidmap.txt will not get populated as disease-genes associations. - Add: data/exclusions-disease-gene.tsv: Manually curated file. - Update: Logic to utilize the above TSV.
- Update: Added Sabrina's ORCID to exclusions file. - Bug fix: Was still not filtering exlcusions correctly; was missing a logical condition. - Bug fix?: Added RO:0003302 entries to disease-gene-relationships (.sparql / .tsv). I think these were previously left out by mistake. - Update: A comment to be more clear
Disease-Gene exclusions
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@twhetzel I guess there is no super hurry to merge review / merge this, as I'm making a release tomorrow off of the branch I just worked on. I don't mind reviewing this by myself but if you want to give it a look-over, feel free! |
joeflack4
commented
Dec 15, 2024
This was referenced Dec 17, 2024
Merged
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