Weekly progress report on uPheno and OBA

matentzn commented 2 years ago

At the end of every week (after our meetings), we should provide a summary of the work we have done in the last week, in 4 - 10 bullet points.

@rays22 can you please, for every week, make a comment here to describe what has happened in the last week, and what is happening in the next? This is for @dosumis because he has less and less time to chase up the stuff we do.

For now, can you make a comment here, and describe what you have done in the last week on OBA or uPheno (pull requests, issues, whatever you did) and what you are planning to do until next Wednesday? Kinda like a sprint summary.

Sections:

Work finished in the last seven days
Work planned for the next seven days
Blockers (tickets that need input and pull requests that need reviews)

rays22 commented 1 year ago

2023-10-18 -- 2023-10-25

Since last Wednesday

Added NCIT measurement term related OBA traits (which also overlap with laboratory measurement terminology) in PR obophenotype/human-phenotype-ontology#297
Researched what is actually being measured in mammography for OBA PR review obophenotype/human-phenotype-ontology#294
Made preparations for 2023-10-24 Monarch Huddle - Ontology WG
Started mapping laboratory measurement terminology codes.
Next
uPheno2 manuscript.
Continue OBA trait terms/mappings to laboratory measurement terminology.
Transfer data files from EBI laptop.
Blockers

rays22 commented 12 months ago

2023-10-25 -- 2023-11-01

Since last Wednesday

Progressed on mapping of some of the laboratory measurement terminology to OBA trait terms.
Next
Continue the mapping of laboratory measurement terminology to OBA trait terms.
uPheno2 manuscript.
Blockers

rays22 commented 11 months ago

2023-11-01 -- 2023-11-08

Since last Wednesday

Progress on mapping of some of the laboratory measurement terminology to OBA trait terms.:
- Identified 79 new trait terms to be added to OBA in the first batch of 350 laboratory measurement terms
Commented on uPheno/zfin ameliorated and exacerbated phenotype modelling
Next
Continue the mapping of laboratory measurement terminology to OBA trait terms.
uPheno2 manuscript.
Blockers

rays22 commented 11 months ago

2023-11-08 -- 2023-11-15

Since last Wednesday

Created a PR with new OBA terms as part of the mapping of clinical laboratory measurement terms to OBA.
Wrote a paragraph to the uPheno2 manuscript.
Next
Continue the mapping of clinical laboratory measurement terms to OBA.
uPheno2 manuscript.
Blockers

rays22 commented 10 months ago

2023-12-01 -- 2023-12-06

Since last Wednesday

Mapped 351 clinical measurement related traits to OBA #300,
- and added 49 new related OBA trait classes in PR obophenotype/human-phenotype-ontology#303
EMBL-EBI SPOT team retreat
Reviewed OBA PR obophenotype/human-phenotype-ontology#305
Fixed OBA PR obophenotype/human-phenotype-ontology#185
Next
uPheno2 manuscript.
Revisit new OBA patterns (e.g. for ratio-related traits)
Continue the mapping of clinical measurement related traits to OBA
Blockers

rays22 commented 10 months ago

2023-12-06 -- 2023-12-14

Since last Wednesday

Helped troubleshoot OBA PR obophenotype/human-phenotype-ontology#305
Reviewed and helped fix OBA PR obophenotype/human-phenotype-ontology#294
Mapped and added 'mass' related trait terms to OBA from VT in PR obophenotype/human-phenotype-ontology#146
Reviewed OBA PR obophenotype/human-phenotype-ontology#306
Published new release of OBA -- v2023-12-07
Next
uPheno2 manuscript.
Continue the mapping of clinical measurement related traits to OBA
Blockers

rays22 commented 9 months ago

2024-01-02 -- 2024-01-10

Since last Wednesday

Commented on uPheno-pattern related HP issue#7388
Commented on uPheno pattern-alignment related HP issue #7389
Reviewed OBA PR obophenotype/human-phenotype-ontology#308
Reviewed OBA PR obophenotype/human-phenotype-ontology#309
Reviewed chebi slim obo PR obophenotype/human-phenotype-ontology#23
Continued mapping clinical measurement related traits to OBA.
Next
uPheno2 manuscript.
Create a new OBA release.
Get input on ratio pattern
Continue the mapping of clinical measurement related traits to OBA
Blockers

rays22 commented 9 months ago

2024-01-11 -- 2024-01-17

Since last Wednesday

Reviewed PR for chebi obo slim release v2024-01-11
Improved OBA documentation in PR obophenotype/human-phenotype-ontology#265
Reviewed and helped debug OBA PR obophenotype/human-phenotype-ontology#310
Updated the uPheno, Uberon, CL progress slide for 2024-01-16 Monarch Huddle - Ontology Technology WG
Created a new OBA release (v2024-01-12) in PR obophenotype/human-phenotype-ontology#311
Next
uPheno2 manuscript.
Investigate ratio pattern(s) for OBA and uPheno.
Continue the mapping of clinical measurement related traits to OBA.
Blockers

rays22 commented 9 months ago

2024-01-18 -- 2024-01-24

Since last Wednesday

Proposed two new pattern templates for ratio-related biological attributes in OBA PR obophenotype/human-phenotype-ontology#312
Investigated ['Vulvar hemangioma' logical definition problem - HPO obophenotype/upheno#958] (https://github.com/obophenotype/upheno/issues/958)
Created a new occupational_exposure_to_material pattern for ECTO in PR obophenotype/human-phenotype-ontology#252
Next
uPheno2 manuscript.
Investigate level vs amount vs concentration patterns and qualities for uPheno.
Blockers

rays22 commented 9 months ago

2024-01-25 -- 2024-01-31

Since last Wednesday

Researched TO ratio patterns for OBA PR obophenotype/human-phenotype-ontology#312
Researched uPheno issue #925
Mapped APO modifiers to PATO -- uPheno issue obophenotype/human-phenotype-ontology#927
Next
uPheno2 manuscript.
Blockers

rays22 commented 8 months ago

2024-02-01 -- 2024-02-07

Since last Wednesday

uPheno manuscript: incremental progress
Followed up on MP-HPO phenotype alignment
Next
uPheno manuscript writing
Blockers

rays22 commented 8 months ago

2024-02-08 -- 2024-02-14

Since last Wednesday

Investigated alleged missing text definitions of uPheno patterns
uPheno manuscript: incremental progress
Next
uPheno manuscript writing
Blockers

rays22 commented 8 months ago

2024-02-15 -- 2024-02-21

Since last Wednesday

Reconsidered the use of PRO homology classes in OBA -- obophenotype/human-phenotype-ontology#269.
Added EFO-OBA protein level mapping terms to efo_oba.sssom..
Created a PR #3227 to fix pancreas-related UBERON issue #3208..
Reviewed UBERON PR #3126.
Incremental progress on writing the uPheno manuscript.
Investigated RO issues #774 and #775 relevant to ratio-related traits and phenotypes
Next
Continue uPheno manuscript writing.
Follow up RO issues #774 and #775 relevant to ratio-related traits and phenotypes
Map APO entities to OBA / GO.
Blockers
Need new RO arithmetic relationships requested in #774 and #775 to make progress on modelling ratio-related traits

rays22 commented 8 months ago

2024-02-22 -- 2024-02-28

Since last Wednesday

Reviewed an OBA PR related to a new GWAS trait
Requested an RO id range so I can edit the ontology
Investigated problematic high-level hierarchy classes in OBA
Updated the Ontology Tech WG 2024-02-27 report slides
Created new RO properties has numerator and has denominator in PR obophenotype/human-phenotype-ontology#792 to help model ratio-type traits (and thereby resolving RO #774 and #775).
Helped solve ChEBI import problem in HPO
Requested 'ratio' to be the primary label of PATO:0001470 in PR obophenotype/human-phenotype-ontology#556 and improved definitions of related terms.
Next
Follow up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312
Continue uPheno manuscript writing.
Map APO entities to OBA / GO.
Review AVI documents
Blockers

rays22 commented 7 months ago

2024-02-29 -- 2024-03-06

Since last Wednesday

Reviewed documents describing uPheno, UBERON, OBA for the Association for Veterinary Informatics (AVI) Standards Workgroup to consider using in veterinary electronic health records.
Responded to GWAS Catalog queries about traits related to obsolete GO processes.
Researched the literature for the uPheno2 manuscript.
Next
Continue uPheno manuscript writing.
Follow up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312
Blockers

rays22 commented 7 months ago

2024-03-07 -- 2024-03-13.

Since last Wednesday

Updated the 2024-03-12 Monarch Huddle - Ontology Curation WG report slides.
Supporting the use of uPheno phenotype patterns in HP.
Supporting the GWAS Catalog with their queries.
Next
Continue uPheno manuscript writing.
Complete PR #556 to replace label of PATO "proportionality to" with "ratio"
Follow up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312
Blockers

rays22 commented 7 months ago

2024-03-14 -- 2024-03-20.

Since last Wednesday

Renamed PATO "proportionality to" to "ratio" in PR obophenotype/human-phenotype-ontology#556
Debugging OBA PR ##318
As part of the work needed to fix uPheno issue obophenotype/human-phenotype-ontology#928, I have mapped and curated 89 new OBA classes related to APO traits.
Next
Continue uPheno manuscript writing.
Follow up APO-related uPheno issue obophenotype/human-phenotype-ontology#928
Blockers

rays22 commented 7 months ago

2024-03-21 -- 2024-03-27

Since last Wednesday

Troubleshooting new APO-related OBA terms
Troubleshooted/prepared the OBA v2024-03-27 release artefacts.
uPheno manuscript.
Next
Continue uPheno manuscript writing.
Follow up APO-related OBA PR obophenotype/human-phenotype-ontology#325
Follow up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312
Blockers

rays22 commented 6 months ago

2024-03-28 -- 2024-04-03

Since last Wednesday

Reviewed the uPheno editors' meeting SOP.
Continued troubleshooting APO-related OBA PR obophenotype/human-phenotype-ontology#325.
Next
Continue uPheno manuscript writing.
Continue mapping APO terms for uPheno issue obophenotype/human-phenotype-ontology#928
Follow up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312.
Blockers

rays22 commented 5 months ago

2024-05-02 -- 2024-05-08

Since last Wednesday

Helped fix PR Update imports and definitions.owl obophenotype/human-phenotype-ontology#331
Reviewed PR obophenotype/human-phenotype-ontology#328
Next
Follow up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312.
Blockers

rays22 commented 5 months ago

2024-05-09 -- 2024-05-15

Since last Wednesday

Tested PR that fixes part_of cycles in OBA -- obophenotype/human-phenotype-ontology#314.
Updated the release workflow documents in PR obophenotype/human-phenotype-ontology#332 and #334.
Reviewed OBA PR obophenotype/human-phenotype-ontology#333 v2024-05-13 release artefacts.
Next
uPheno manuscript.
Follow up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312.
Blockers

rays22 commented 5 months ago

2024-05-16 -- 2024-05-22

Since last Wednesday

Updated one of the report slides for the 2024-05-21 Monarch Huddle - Ontology Technology WG.
Followed up OBA ratio related patterns and examples in PR obophenotype/human-phenotype-ontology#312.
Expanded and edited the uPheno manuscript.
Next
uPheno manuscript.
Support MP in migrating https://github.com/mgijax/mammalian-phenotype-ontology/blob/main/.github/workflows/imports.yml To using a normal ubuntu base image like https://github.com/pato-ontology/pato/blob/master/.github/workflows/build.yml#L12
Blockers
PR #312 needs review.

rays22 commented 5 months ago

2024-05-23 -- 2024-05-29

Since last Wednesday

Added a figure and some text to uPheno manuscript.
Next
uPheno manuscript.
Complete PR #312.
Blockers
PR #312 needs reviewers.

rays22 commented 4 months ago

2024-05-30 -- 2024-06-05

Since last Wednesday

Added a new ratio-related OBA-trait DOS-DP pattern template -- issue obophenotype/human-phenotype-ontology#272 and PR obophenotype/human-phenotype-ontology#312.
Continued writing the uPheno manuscript.
Next
uPheno manuscript.
Add new APO-related traits to OBA -- PR obophenotype/human-phenotype-ontology#325.
Blockers
None.

rays22 commented 4 months ago

2024-06-06 -- 2024-06-12

Since last Wednesday

Reviewed Uberon PR obophenotype/human-phenotype-ontology#3289 - blood vasculature design pattern and 55 blood terms from VCCF.
Continued writing and collecting information for the uPheno manuscript.
Next
uPheno manuscript.
Restructure amount in PATO - issue obophenotype/human-phenotype-ontology#554.
Blockers
None.

rays22 commented 4 months ago

2024-06-13 -- 2024-06-19.

Since last Wednesday

Restructured PATO:0000070 amount in PR obophenotype/human-phenotype-ontology#560.
Updated the report slides for the 2024-06-18 Monarch Huddle - Ontology Curation WG.
Investigated the HP issue obophenotype/human-phenotype-ontology#7534 Acidosis & Alkalosis logical definition causes lots of bad inference.
- Created a PR to fix logical acid-base homeostasis related axioms -- obophenotype/human-phenotype-ontology#10581.
  Next
uPheno manuscript.
Add new APO-related traits to OBA -- PR obophenotype/human-phenotype-ontology#325.
Create a new OBA release.
Blockers
None.

rays22 commented 4 months ago

2024-06-20 -- 2024-06-26

Since last Wednesday

Researched cross-taxon phenotypes for the uPheno manuscript.
Provided feedback on the Monarch Initiative browser:
1. Regarding false inferences about human gene-phenotype associations and contributed to the discussions on the issue.
2. Regarding a usability issue.
Dropped invalid ChEBI identifiers from seed.txt in chebi_obo_slim PR obophenotype/human-phenotype-ontology#33.
Next
uPheno manuscript.
Create a new chebi_obo_slim release.
Create a new OBA release.
Blockers
None.

rays22 commented 3 months ago

2024-06-27 -- 2024-07-03.

Since last Wednesday

Created a new OBA release (v2024-06-27).
Updated the OBA SSSOM mapping files in PR obophenotype/human-phenotype-ontology#339.
Investigated obsoletion-candidate NBO phenotype terms used in HP EQ definitions as part of HP issue obophenotype/human-phenotype-ontology#9628.
Created an availability poll for a 2 hr workshop in September 2024 regarding uPheno high level structure.
Reviewed HPO PR update stenosis EQs obophenotype/human-phenotype-ontology#10610.
Next
uPheno manuscript.
Blockers
None.

rays22 commented 3 months ago

2024-07-04 -- 2024-07-17

Since last Wednesday

Created a PR to import term PATO:0005013 incomplete structure into HP #10631.
- Addresses HPO/uPheno issue obophenotype/human-phenotype-ontology#955.
Investigated the uPheno issue Abnormality of lingual tonsil (transitively) a subclass of Abnormality of face -- obophenotype/human-phenotype-ontology#957 and facilitated a fix in Uberon.
Next
uPheno manuscript.
Blockers

obophenotype / upheno