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 2 years ago

2022-06-22 Wednesday

Since last Wednesday

First steps for EFO/VT alignment #101
- Ran EFO(GWAS)-VT-OBA trait alignment pipeline and reviewed the produced EFO-OBA and VT-OBA pattern matches - PR obophenotype/human-phenotype-ontology#104
Got phenotype curator community feedback on
- uPheno obophenotype/human-phenotype-ontology#828 Dislocated anatomical entity pattern template
- uPheno obophenotype/human-phenotype-ontology#830 Obstructed anatomical entity pattern template
- uPheno obophenotype/human-phenotype-ontology#834 Exserted anatomical entity pattern template
- uPheno obophenotype/human-phenotype-ontology#836 Abnormally protruding anatomical entity pattern template

Blockers

Need input on EFO obophenotype/human-phenotype-ontology#1436

rays22 commented 2 years ago

Since last Wednesday

Updated some VT-OBA mapping tables #106
Completed fix for Remove CHEBI role classes that cause logical errors in OBA obophenotype/human-phenotype-ontology#99 in PR OBA obophenotype/human-phenotype-ontology#99
Preparations for OBA curation call.
Followed up MP pattern call
Continued EFO/VT alignment work #101
- Reviewed some EFO-OBA pipeline suggested patterns
Solved issues with adding ORCIDs as DOS-DP data_list_vars: #418
Partially debugged response to chemical stimulus trait pattern templates #87
Next
Create new upheno phenotype patterns
Continue EFO/VT-OBA alignment work [#101](https://github.com/obophenotype/bio-attribute-ontology/issues/101
Blockers
Debug response to chemical stimulus trait pattern templates #87

rays22 commented 2 years ago

2022-07-06.

Since last Wednesday

Resolving remaining tasks with New 'trait in response' pattern involving CHEBI roles obophenotype/human-phenotype-ontology#96
Preparations for uPheno curation call.
Reviewed CL PR obophenotype/human-phenotype-ontology#1626
Troubleshooting slow protege
Cleaning EFO/GO 'response to drug' term tables related to https://github.com/geneontology/go-ontology/issues/22210

2022-07-13.

Since last Wednesday

Provided overview and training to new phenotype ontology editor
Created new uPheno DOS-DP phenotype pattern drafts:
- PATO:0001478 collapsed Collapsed anatomical entity pattern template
- PATO:0001514 delaminated Delaminated anatomical entity pattern template
- PATO:0002175 deviation Deviation of anatomical entity pattern template
- PATO:0000122 length Abnormal length of anatomical entity pattern template
Fixed and finalised uPheno phenotype patterns based on community feedback, merged related pull requests, and created related PATO tickets:
- uPheno issue obophenotype/human-phenotype-ontology#828 Dislocated anatomical entity pattern template
- uPheno issue obophenotype/human-phenotype-ontology#830 Obstructed anatomical entity pattern template
- uPheno issue obophenotype/human-phenotype-ontology#834 Exserted anatomical entity pattern template
- uPheno issue obophenotype/human-phenotype-ontology#836 Abnormally protruding anatomical entity pattern template
- uPheno issue obophenotype/human-phenotype-ontology#840 Perforate anatomical entity pattern template
- uPheno issue obophenotype/human-phenotype-ontology#842 Abnormal thickness of anatomical entity template
- uPheno issue obophenotype/human-phenotype-ontology#844 Non-functional anatomical entity pattern template
  Next
  1. Import VT terms into OBA #85
  2. Continue EFO/VT alignment work #101
  3. Follow up PATO tickets
    Blockers
    
    None.

rays22 commented 2 years ago

2022-07-20.

Since last Wednesday

Preparations for uPheno Phenotype Editors Call.
Reviewed synonym pipeline PR obophenotype/human-phenotype-ontology#107.
Closed OBA action potential issue obophenotype/human-phenotype-ontology#1
Completed the necessary term additions for OBA ticket: Add new disease onset terms obophenotype/human-phenotype-ontology#111 and related EFO tickets and PR:
- #1658
- #1693
- #1697
Reviewed PATO PR obophenotype/human-phenotype-ontology#472.
Started mapping some VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.

Blockers

How to fix the issue with GO:0014024 neural rod cavitation? immaterial entity (luminal space) <--> equivalent to material entity (via range restriction? by 'results in formation of' range: 'connected anatomical structure' == 'material entity')
- It appears that he class 'GO:0014024 neural rod cavitation' that is un-satisfiable in OBA has been replaced in GO by GO:0014020.
- It appears that this class is coming into OBA via PATO (pato_import.owl)
- TO FIX: Run a PATO release and refresh imports.

rays22 commented 2 years ago

2022-07-22.

Since last Wednesday

Continued mapping the VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
- Made a PR to update response to chemical stimulus data table obophenotype/human-phenotype-ontology#115
- Made another PR to Sync sssom tsv tables with google sheet data obophenotype/human-phenotype-ontology#116 to reduce the number of VT terms to be mapped to or to be included in OBA from 216 to 154.
#511 -- Made a PATO release (v2022-07-21)
Fixed and finalised uPheno phenotype pattern Collapsed anatomical entity pattern template obophenotype/human-phenotype-ontology#848 based on community feedback.
Created new uPheno
- folded anatomical entity DOS-DP pattern draft PR obophenotype/human-phenotype-ontology#859 and issue #857 and
- wrinkled anatomical entity DOS-DP pattern draft PR obophenotype/human-phenotype-ontology#860 and issue #858

Blockers

None.

rays22 commented 2 years ago

2022-08-10 Wednesday

Since last Wednesday

Completed GWAS/EFO related issue Add new disease onset terms obophenotype/human-phenotype-ontology#111
Responded to GWAS related EFO New term requests for age at initiation/occurrence of behaviours, treatments and procedures. obophenotype/human-phenotype-ontology#1659
OBA release and troubleshooting errors -- New OBA release obophenotype/human-phenotype-ontology#118
Checked latest PATO and OBA releases in OLS and found Obsolete PATO:0002419 showing up in release file pato.owl and on OLS obophenotype/human-phenotype-ontology#512)
Added an abnormally curled anatomical entity pattern template draft for community review.

Blockers

How to fix Obsolete PATO:0002419 showing up in release file pato.owl and on OLS obophenotype/human-phenotype-ontology#512) ?

rays22 commented 2 years ago

2022-08-17 Wednesday

Since last Wednesday

New PATO release
Finalised DOS-DP templates based on community feedback and merged them into master branch:
- Deviation towards the medial side of anatomical entity -- PR obophenotype/human-phenotype-ontology#833
- Deviation towards the lateral side of anatomical entity -- PR obophenotype/human-phenotype-ontology#839
- Spatial deviation of anatomical entity -- PR obophenotype/human-phenotype-ontology#854
- Abnormal length of anatomical entity -- PR obophenotype/human-phenotype-ontology#856
- Folded anatomical entity -- PR obophenotype/human-phenotype-ontology#859
- Wrinkled anatomical entity -- PR obophenotype/human-phenotype-ontology#860
- Abnormally curled anatomical entity -- PR obophenotype/human-phenotype-ontology#862

Blockers

None.

rays22 commented 1 year ago

2022-08-24 Wednesday

Since last Wednesday

Renamed 'deviation' to 'spatial deviation' in PATO -- obophenotype/human-phenotype-ontology#520
New uPheno phenotype pattern template: Abnormally opaque anatomical entity
Thought about the problem of multi-cell-part structure DisjointWith multicellular anatomical structure and commented on UBERON issue obophenotype/human-phenotype-ontology#2495
Fixing draft bone length from to DOSDP pattern template obophenotype/human-phenotype-ontology#75
Fixing draft pattern for bone length along an axis obophenotype/human-phenotype-ontology#81
Add new disease age of onset terms for GWAS #122
PR: Add bird traits from obophenotype/human-phenotype-ontology#52 obophenotype/human-phenotype-ontology#95
Reviewing PR Replace sagittal crest (Issue 1849) obophenotype/human-phenotype-ontology#2161

Blockers

OBA PR #52: what to do with anatomical entity terms (for example from HAO) that are outside of the scope of Uberon?

rays22 commented 1 year ago

2022-09-07 Wednesday

Since last Wednesday

Drafted an abnormally dry anatomical entity pattern template - obophenotype/human-phenotype-ontology#873
Drafted an abnormally decreased wetness of anatomical entity pattern template - obophenotype/human-phenotype-ontology#875
Started OBA training of new ontology editor
New OBA release
- Debugging OBA issue obophenotype/human-phenotype-ontology#130
Created a potential fix for unsatisfiable classes in OBA and CL in upstream RO PR obophenotype/human-phenotype-ontology#624. Tickets:
- Unsatisfiable classes in cl.obo obophenotype/human-phenotype-ontology#1692
- Remove axiom drains only 'connected anatomical structure' obophenotype/human-phenotype-ontology#623
EFO PR: Add Mondo URIs obophenotype/human-phenotype-ontology#1749
Next
Implement community suggestions in uPheno phenotype pattern templates
- DOS-DP 'opaque' phenotype pattern template obophenotype/human-phenotype-ontology#866
- delaminated anatomical entity pattern template obophenotype/human-phenotype-ontology#851
Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
OBA training of new ontology editor
Blockers

None.

rays22 commented 1 year ago

2022-09-14 Wednesday

Since last Wednesday

OBA training of new ontology editor
Assigned new OBA editor id ranges in PR #132
Implemented community suggestions in uPheno DOS-DP phenotype pattern templates
- 'delaminated' anatomical entity pattern template obophenotype/human-phenotype-ontology#851
- 'opaque' phenotype pattern template obophenotype/human-phenotype-ontology#866
Obtained feedback from uPheno ontology editors on phenotype pattern drafts and implemented them:
- abnormally dry anatomical entity pattern template
- abnormally decreased wetness of anatomical entity pattern template
Updated cystInLocation logical definition -- Issue #878
Continued mapping VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.

Blockers

None.

rays22 commented 1 year ago

2022-09-21 Wednesday

Since last Wednesday

Mapping new VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
- Updated the alignment files in PR obophenotype/human-phenotype-ontology#141.
- Added new terms in PR obophenotype/human-phenotype-ontology#142.
  Next
Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
Create new uPheno phenotype pattern drafts that use:
- PATO:0001373 glistening

Blockers

None.

rays22 commented 1 year ago

2022-09-28 Wednesday

Since last Wednesday

Created a new uPheno phenotype pattern draft:
- Abnormally glistening anatomical entity pattern template obophenotype/human-phenotype-ontology#884
Continued mapping and importing VT terms used by the Mouse Phenome Database into OBA.
Reviewed PR Edits to annotations on RateOfBehavior patterns obophenotype/human-phenotype-ontology#888

Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA and fix PRs:
EFO-OBA alignment #101
- Identify matching DOS-DP patterns for EFO terms in oba-efo-unreviewed.dosdp.tsv
GWAS-OBA-EFO: New term request for Sun PMID 34320236 obophenotype/human-phenotype-ontology#1764
- Requires new OBA release.

Blockers

None.

rays22 commented 1 year ago

2022-10-05 Wednesday

Since last Wednesday

Continued OBA training of new ontology editor
- Adding new diameter terms to OBA in PR obophenotype/human-phenotype-ontology#151
Updated OBA DOS-DP template entity_attribute.yaml in PR obophenotype/human-phenotype-ontology#65
Updated CL DOS-DP template cellPartOfAnatomicalEntity.yaml in PR obophenotype/human-phenotype-ontology#1277

Blockers

None.

rays22 commented 1 year ago

2022-10-12 Wednesday

Since last Wednesday

Wrote an SOP on how to add new GWAS requested trait terms to OBA and EFO obophenotype/human-phenotype-ontology#154
Tested Protege Desktop Version 5.6.0, Build beta-1-SNAPSHOT
Examined partonomy in modelling traits and phenotypes #156
EFO/GWAS clinical temporal measurement-related traits obophenotype/human-phenotype-ontology#105
- Clarified which terms in this ticket remain to be mapped
- Identified some trait patterns to target
  Next
Continue EFO-OBA alignment #101
Follow up uPheno ontology editors' meeting action items
Improve SOP on how to add new GWAS requested trait terms to OBA and EFO obophenotype/human-phenotype-ontology#154
GWAS-OBA-EFO: New term request for Sun PMID 34320236 obophenotype/human-phenotype-ontology#1764
Add some new terms related to EFO/GWAS clinical temporal measurement-related traits obophenotype/human-phenotype-ontology#105
Complete PRs in preparation of a new OBA release.
Blockers
Need clarification of partonomy in modelling traits and phenotypes #156

rays22 commented 1 year ago

2022-10-19 Wednesday

Since last Wednesday

Created a new uPheno herniated anatomical entity pattern template draft
- PR #890
Created a new uPheno abnormally dilated cellular component pattern template
- PR #892
Followed up uPheno ontology editors' meeting action items
- Finalised the abnormally glistening anatomical entity pattern template in PR #885 based on community feedback.
- Finalised the abnormally greasy anatomical entity pattern templatein PR #881 based on community feedback.
Debugged DOS-DP pattern files in UBERON PR#2467 tooth patterns
Reviewed OBA PR replacing zone of skin with skin of body obophenotype/human-phenotype-ontology#134
Reviewed OBA PR creating diastema trait terms obophenotype/human-phenotype-ontology#136
Wrote a new SOP Release Workflow for the Ontology of Biological Attributes (OBA) as part of OBA issue #154.
Helped fix MPO release in #3674 and #3675
Next
GWAS-OBA-EFO: New term request for Sun PMID 34320236 obophenotype/human-phenotype-ontology#1764
Add some new terms related to EFO/GWAS clinical temporal measurement-related traits obophenotype/human-phenotype-ontology#105
Complete PRs in preparation of a new OBA release.
Continue EFO-OBA alignment #101
Blockers

rays22 commented 1 year ago

2022-10-26 Wednesday

Since last Wednesday

Added new OBA term as requested by GWAS age of onset of cervical dystonia obophenotype/human-phenotype-ontology#157.
Finalised the uPheno herniated anatomical entity pattern template draft based on community feedback in #890.
Did some investigations on partonomy in modelling traits and phenotypes to better understand how to proceed with phenotype modelling in OBA #156
Preparations for EFO-GWAS meeting on 2022-10-26.

Blockers

-

rays22 commented 1 year ago

2022-11-02 Wednesday

Since last Wednesday

New uPheno pattern template drafts:
- 'abnormally arched anatomical entity' #895
- 'abnormally scaly anatomical entity' #896
Added suggestion to solve uPheno issue #872 Patterns with "part of" have the same name as counterparts.
Helped MP to Remove obsolete EQs attached to some of the patternized terms obophenotype/human-phenotype-ontology#3688
Literature search for OBA trait paper.
Preparations for HPO pattern review meeting.

Blockers

-

rays22 commented 1 year ago

2022-11-09 Wednesday

Since last Wednesday

HPO pattern review preparations
Proofread NHGRI-EBI GWAS Catalog manuscript
Preparations for uPheno editors' call
Reviewed PATO 2022-11-03 release #536
Identified matching HPO and MP terms that can use identical EQs - uPheno obophenotype/human-phenotype-ontology#898
OBA manuscript preparations

Blockers

-

rays22 commented 1 year ago

2022-11-16 Wednesday

Since last Wednesday

OBA manuscript preparations
Reviewed a new PATO release #538
uPheno--MP: Align abnormal morphology of anatomical entity EQs with HPO obophenotype/human-phenotype-ontology#3692
Fixed hypoplastic wikipedia xref in PATO
Checked how many OBA classes with trait in their name are subclasses of OBA:0000001 biological attribute OBA issue obophenotype/human-phenotype-ontology#88

Blockers

-

rays22 commented 1 year ago

2022-11-23

Since last Wednesday

Prepared my 2022-11-21 EBI/SPOT talk: Integrated Trait and Phenotype Ontologies
OBA manuscript preparation
- Collected background information on the purpose and design of OBA
- Collected references on work related to phenotype ontologies
- Developed ides for figures to illustrate main points in the manuscript
Tested new Protege version (5.6.0 beta snapshot 3)
Next
OBA manuscript preparation
- Assigning tasks to contributors
Review some of the EFO/GWAS related OBA PRs
Blockers

ar-ibrahim commented 1 year ago

24-11-2022

EFO-OBA mapping tickets:

based on list of terms in unreviewed EFO-OBA mappings list

issue#150 3/7 terms mapped, PR approved
issue#160 50 terms mapped, PR approved
issue#166 45 terms mapped, pending PR review

OBA paper:

background literature search
finding examples of OBA trait terms that can link mouse (Mouse Phenome Database) and human genomic variants (GWAS)

rays22 commented 1 year ago

2022-11-30

Since last Wednesday

OBA manuscript preparation
- divided work and created slides to explain tasks for co-authors of the manuscript
Reviewed OBA PRs and helped resolve conflicts
- 50 EFO-OBA volume terms
- 45 EFO-OBA terms
Made preparations for 2022-11-25 GWAS-EFO-OBA alignment meeting
Checked diff for UBERON base approach issue obophenotype/human-phenotype-ontology#2664
Completed GWAS/EFO related new OBA term request: age of onset of cervical dystonia obophenotype/human-phenotype-ontology#157
Reviewed Add entity_attribute_partOf.yaml pattern to OBA obophenotype/human-phenotype-ontology#153
Next
Focus: OBA manuscript preparation
- Write text
Request that OBA in OLS is displayed in an improved and more user friendly way:
- OLS uses preferred root node OBA:0000001
- OLS shows materialised part-of relationships in OBA (obo:part_of hierarchical)
  Blockers
  
  Overstretched.

rays22 commented 1 year ago

2022-12-06

Since last Wednesday

Requested an update of OBA in OLS #653 and made a PR to propose configuration changes in OLS so that a materialised OBA part_of hierarchy is displayed in the EBI OLS browser.
Completed the abnormally arched anatomical entity pattern template based on community feedback.
Installed and started testing Protege v5.6.0-beta-1
Added some test and figures to the OBA manuscript
Next
Focus: OBA manuscript preparation
Blockers

Time

rays22 commented 1 year ago

2023-01-11 Wednesday

Since last Wednesday

OBA manuscript preparation
Investigated HPO pattern review related issues
Investigated the cause of unsatisfiable classes in OBA
Next
Focus: OBA manuscript preparation
Blockers

rays22 commented 1 year ago

2023-01-18

Since last Wednesday

OBA manuscript preparation: text, tables and figures.
Continued investigating the cause of unsatisfiable classes in OBA
Next
Finalise OBA manuscript
Fix unsatisfiable classes in OBA
Blockers

rays22 commented 1 year ago

2023-01-25

Since last Wednesday

CL call (2023-01-18)
OBA curation call (2023-01-20)
EFO-OBA Mapping of traits related to entities in blood/serum obophenotype/human-phenotype-ontology#166
HP-MP phenotype ontology alignment (uPheno): generated some helper tables to help align HP and MP logical axioms. The goal is to improve the semantic similarity of terms of biologically similar or identical phenotypes in different model organisms.

Blockers

-

rays22 commented 1 year ago

2023-02-01 Wednesday

Finalised OBA manuscript
- Preprint published on bioRxiv
Reviewed IMPC related attributes for OBA PR obophenotype/human-phenotype-ontology#192 and
Fixed unsatisfiable classes in OBA by refreshing external ontology imports in PR obophenotype/human-phenotype-ontology#203
Fixed duplicate terms in OBA PR obophenotype/human-phenotype-ontology#202
Next
VT-OBA trait term alignment: finish remaining term mapping
EFO-OBA trait term alignment: continue term addition and mapping
Blockers

rays22 commented 1 year ago

2023-02-08

Since last Wednesday

Reviewed OBA PR obophenotype/human-phenotype-ontology#207 related to a new GWAS/EFO term request.
Helped MP fix duplicate EQs in PR obophenotype/human-phenotype-ontology#3712 and PR obophenotype/human-phenotype-ontology#3713
Tried to update SSSOM mapping files #208
Mapped sleep-related EFO terms to OBA traits #209
Patternised entity homeostasis traits in #211
- This PR has also fixed issues related to obsolete GO homeostasis process terms
  Next
Create a new OBA release
Complete SSSOM mapping file update #208
Run OBA alignment pipelines
VT-OBA trait term alignment: finish remaining term mapping
- Import the remaining VT terms relevant to MPD into OBA #85
EFO-OBA trait term alignment: continue term addition and mapping
Blockers

rays22 commented 1 year ago

2023-02-15

Since last Wednesday

OBA issue: Added some CPATH related OBA traits
Reviewed OBA PR obophenotype/human-phenotype-ontology#214 and fixed QC errors: morphology and related traits
Reviewed OBA PR obophenotype/human-phenotype-ontology#135 and fixed QC errors and conflicts
New public OBA release: v2023-02-14
Updated release SOP document
Next
Follow up EFO/GWAS catalogue related issue: coordinate with SIB on conversion of swisslipids# 140
Follow up OBA issue: Design patterns for describing protein molecular attributes for UniProtKB/Swiss-Prot obophenotype/human-phenotype-ontology#219
Complete SSSOM mapping file update #208
VT-OBA trait term alignment: finish remaining term mapping
- Import the remaining VT terms relevant to MPD into OBA #85
  Blockers

rays22 commented 1 year ago

2023-02-22

Since last Wednesday

Reviewed OBA PR 221 and the parent issue.
Investigated possible ways to model 'bone length from to' FOVT-requested traits in OBA obophenotype/human-phenotype-ontology#73
Made some phenotype pattern suggestions that are related to Retiring the NBO Phenotype branch obophenotype/human-phenotype-ontology#3717
Documentation: Added new document to obook on how to install Protege
Preparations before the uPheno editors' call
Next
Explore pyOBO to help map swisslipid identifiers to ChEBI
Complete EFO-OBA SSSOM mapping file update and run EFO-OBA alignment workflow
VT-OBA trait term alignment: finish remaining term mapping
Design patterns for describing protein molecular attributes for UniProtKB/Swiss-Prot
Refresh imports and new OBA release
Blockers

rays22 commented 1 year ago

2023-03-01

Since last Wednesday

Installed and evaluated pyOBO and gilda to help map free text chemical names and swisslipid identifiers to ChEBI terms.
1. They can be used to map free text chemical names to ChEBI IDS, but the success rate depends on the quality of the source material.
2. I can confirm that there is no quick and trivial way to map of swisslipid IDs to ChEBI IDs.
Assessed the amount of work needed to add replacement OBA trait terms for NBO phenotype branch terms.
Assessed the amount of work needed to deal with GWAS/EFO traits involving proteins and chemicals in blood or serum obophenotype/human-phenotype-ontology#222.
Reviewed NBO PR #158 and made some suggestions for a fix in relation to traits and phenotypes.
Next
Provide mapping between EFO response to terms and new OBA replacements obophenotype/human-phenotype-ontology#1436
Reconcile the content of the OBA Google sheet obophenotype/human-phenotype-ontology#108
Traits involving proteins and chemicals in blood or serum obophenotype/human-phenotype-ontology#222
Blockers

rays22 commented 1 year ago

2023-03-08

Since last Wednesday

Added new DOS-DP data filler and updated the pattern template for OBA bone length from to DOSDP pattern template obophenotype/human-phenotype-ontology#73 based on recent discussions
Reviewed OBA-EFO alignment PR new term 'gene expression amount' obophenotype/human-phenotype-ontology#224
Created a new partial uPheno pattern for grouping phenotypes PR obophenotype/human-phenotype-ontology#905
Created gene expression trait related OBA pattern templates in PR obophenotype/human-phenotype-ontology#226
Next
Provide mapping between EFO response to terms and new OBA replacements obophenotype/human-phenotype-ontology#1436
Reconcile the content of the OBA Google sheet obophenotype/human-phenotype-ontology#108
Create a PATO term shortlist for GWAS curators
Investigate and fix QC errors for several OBA PRs
Blockers
Issues with refreshing OBA imports

ar-ibrahim commented 1 year ago

Summary of Phenomics First work

**1. EFO-OBA mapping and term requests** a. oba-efo-unreviewed.dosdp.tsv #150; #160; #162 #166; #213; #215; #220; #223; #225 b. EFO measurement branch mega tickets #1848; #1905; #1882 c. EFO response to OBA mappings #1436 d. #205 GWAS Age of onset term request

**2. OBA paper** (status: submitted, currently working on reviewer comments)

**3. Documentation** a. #229 Refreshing DOSDP patterns with CHEBI and PRO imports b. #249 as part of OBO Academy Hackathon

**4. IMPC mapping** #174

**5. uPheno paper** (status: started, ongoing)

6. OBA curation calls, uPheno Working Group calls, uPheno editors calls, Monarch meetings and tutorials, OBO Academy sessions, Ontology Summit 2023

rays22 commented 1 year ago

2023-03-30

Since last Wednesday

Fixed a github RSA SSH host key issue
Added new editors workflow document in PR obophenotype/human-phenotype-ontology#911
Revised the OBA manuscript as requested by the editorial office of the journal
Created a PATO term shortlist for GWAS curators
Next
uPheno manuscript preparation
Fix a formatting issue in entity_attribute_location.tsv
Provide mapping between EFO response to terms and new OBA replacements obophenotype/human-phenotype-ontology#1436
Reconcile the content of the OBA Google sheet obophenotype/human-phenotype-ontology#108
Create a PATO term shortlist for GWAS curators
Investigate and fix QC errors for several OBA PRs
Blockers
Issues with refreshing OBA imports

rays22 commented 1 year ago

2023-05-10

Since last Wednesday

Collected and read papers for the uPheno manuscript
Uploaded 6 new templates from src/patterns/data/matches to a gsheet data tables to be reviewed: Human Phenotype Ontology (HPO) - EQ Review
Reviewed OBA PR obophenotype/human-phenotype-ontology#237: new trait terms for EFO/GWAS
Fixed the logical definition of OBA:VT0008211 mature B cell quantity in #240, because it was using a decreased amount quality.
Added new chemical amount in location trait terms #245
Next
uPheno manuscript
OBA clean up and release
HP-MP alignment
Improve documentation
Blockers

rays22 commented 1 year ago

2023-05-17

Since last Wednesday

uPheno 2 manuscript preparations
New OBA release
Imported new lipid amount trait terms into EFO from OBA #1999
- Provided advice on EFO/GWAS lipid trait terms
EFO/GWAS: Fixed a SPAQL query to help find PR terms%0A(STR(%3Flbl)%20AS%20%3FLABEL)%0AWHERE%20%7B%0A%20%20%20%20%3Fterm%20rdfs%3Alabel%20%3Flbl%20.%0A%20%20%20%20VALUES%20%3Fqlist%20%7B%0A%20%20%20%20%20%20%20%20%22%5Et-cell%20surface%20glycoprotein%20cd4%22%0A%20%20%20%20%7D%0A%20%20%20%20FILTER%20(STRENDS(%20(LCASE(STR(%3Flbl)))%2C%20%22(human)%22)%20).%20%23%20label%20string%20ends%20with%20%22(human)%22%0A%20%20%20%20FILTER%20REGEX%20(%20%3Flbl%2C%20%3Fqlist%2C%20%22i%22%20).%20%23%20label%20string%20contains%20a%20given%20pattern%20from%20the%20list%20(case%20insensitive)%0A%7D&endpoint=https%3A%2F%2Fsparql.proconsortium.org%2Fvirtuoso%2Fsparql&requestMethod=POST&tabTitle=Query&headers=%7B%7D&contentTypeConstruct=text%2Fturtle%2C%2F%3Bq%3D0.9&contentTypeSelect=application%2Fsparql-results%2Bjson%2C%2F%3Bq%3D0.9&outputFormat=table)
Next
uPheno 2 manuscript
Improve OBA documentation
Blockers

dosumis commented 1 year ago

CC @udp

rays22 commented 1 year ago

2023-06-01 -- 2023-06-07

Since last Wednesday

Researched PRO to help complete OBA PR obophenotype/human-phenotype-ontology#251 with ~4.7k requested new protein level traits.
- Added 'level of protein in blood serum' traits in PR obophenotype/human-phenotype-ontology#253
Curated standard protein identifiers from research paper PMID:36349687 for GWAS - EFO issue obophenotype/human-phenotype-ontology#1851.
- In order to address EFO obophenotype/human-phenotype-ontology#1851, I have updated pro_obo_sim - obophenotype/human-phenotype-ontology#24 and
- added another set of new 'level of protein in blood serum' traits - obophenotype/human-phenotype-ontology#254.
Gave an introduction to uPheno DOS-DP template workflow to colleague.
Added v2023-06-07 release artefacts obophenotype/human-phenotype-ontology#255.
Next
Create a new OBA release.
Import OBA trait terms created for the GWAS Catalog into EFO.
Investigate PR Add Swisslipid import to OBA obophenotype/human-phenotype-ontology#252.
Update uPheno documentation and oba-release-sop.
Update OBA documentation: Phenotype Ontology Editors' Workflow.
Blockers
Gaps in documentation and SOPs.

rays22 commented 1 year ago

2023-06-07 -- 2023-06-14

Since last Wednesday

Published new 2023-06-07 release of OBA
Imported OBA trait terms created for the GWAS Catalog into EFO -- PR obophenotype/human-phenotype-ontology#2027
- Provided OBA trait terms for EFO/GWAS Catalog issue obophenotype/human-phenotype-ontology#1848
- Provided OBA trait terms for EFO/GWAS Catalog issue obophenotype/human-phenotype-ontology#1851
Reviewed uPheno PR obophenotype/human-phenotype-ontology#914
Updated the uPheno dos-dp template workflow document -- PR obophenotype/human-phenotype-ontology#915
Investigated PR Add Swisslipid import to OBA obophenotype/human-phenotype-ontology#252.
- Lipid Maps to ChEBI/Swisslipids to InChiKey mapping
- CheBI to Lipid Maps to InChiKey mapping
  Next
Fix PR Add Swisslipid import to OBA obophenotype/human-phenotype-ontology#252.
Update oba-release-sop.
uPheno manuscript preparation
Blockers
Lipid Maps SPARQL endpoint is often down.

rays22 commented 1 year ago

2023-06-14 -- 2023-06-21

Since last Wednesday

uPheno: Updated abnormalConstrictionOfAnatomicalEntity.yaml-- obophenotype/human-phenotype-ontology#914
OBA: Refreshed chebi_obo_slim after adding terms for OBA obophenotype/human-phenotype-ontology#9 and
- made a new chebi slim release
Added 29 new OBA lipid trait terms for GWAS/EFO in PR obophenotype/human-phenotype-ontology#258
uPheno: Prepared slides and content for the internal uPheno project meeting on 2023-06-21.
Next
Fix PR Add Swisslipid import to OBA obophenotype/human-phenotype-ontology#252.
Create new OBA release.
Blockers

rays22 commented 1 year ago

2023-06-21 -- 2023-06-28

Since last Wednesday

Fixed missing Cl axioms in OBA imports for PR Add Swisslipid import to OBA obophenotype/human-phenotype-ontology#252.
Updated the citation information for OBA.
Next
uPheno manuscript preparation.
Follow up OBA-EFO mapping tasks.
Blockers
Need reviewer to progress with v2023-06-27 OBA release.

rays22 commented 1 year ago

2023-06-28 -- 2023-07-05

Since last Wednesday

Published a new OBA release
Provided new OBA trait and related terms for EFO/GWAS obophenotype/human-phenotype-ontology#2039
Reviewed and helped fix OBA PR obophenotype/human-phenotype-ontology#264
Next
uPheno manuscript preparation.
Follow up OBA-EFO mapping tasks.
Blockers

rays22 commented 1 year ago

2023-07-05 -- 2023-07-12

Since last Wednesday

Updated some of the OBA documents.
Updated the SSSOM mapping files that are needed for EFO-OBA alignment.
Created a SPARQL query to generate table with PRO superclass to PRO Homo sapiens specific subclasses.
Next
uPheno manuscript preparation.
Follow up OBA-EFO mapping tasks.
Blockers
open PRs need review

rays22 commented 11 months ago

2023-09-01 -- 2023-09-13

Since last Wednesday

Added new OBA trait terms that map to EFO measurement classes PR obophenotype/human-phenotype-ontology#290
Reviewed and debugged OBA PR obophenotype/human-phenotype-ontology#291
Fixed incorrectly labelled serum non-albumin term in PR obophenotype/human-phenotype-ontology#289
Updated chebi_obo_slim with OBA component terms
Reviewed OBA PR obophenotype/human-phenotype-ontology#291
Completed the OBA and GO sections of the GPT-ontology definition evaluation template
Next
Add more OBA trait terms related toEFO measurement branch terms -- issue obophenotype/human-phenotype-ontology#276
MP-HPO phenotype alignment: check if axiom matches agree with text definitions obophenotype/human-phenotype-ontology#921
uPheno2 manuscript
Blockers

rays22 commented 11 months ago

2023-09-13 -- 2023-09-20

Since last Wednesday

MP-HPO phenotype alignment: generated EQ tables to check if axiom matches agree with manual mapping annotations -- obophenotype/human-phenotype-ontology#921
Completed the mapping of the remaining amount and diameter related EFO measurement branch terms to OBA as part of issue obophenotype/human-phenotype-ontology#276
Next
Create or map OBA trait terms related to EFO volume measurement branch terms -- as part of issue obophenotype/human-phenotype-ontology#276
uPheno2 manuscript
Blockers

rays22 commented 11 months ago

2023-09-20 -- 2023-09-27

Since last Wednesday

Added new EFO measurement related traits in OBA PR obophenotype/human-phenotype-ontology#293 including EFO volume measurement branch terms -- as part of issue obophenotype/human-phenotype-ontology#276
Updated the EFO-OBA SSSOM mapping table with newly curated matches -- as part of issue obophenotype/human-phenotype-ontology#276
Next
uPheno2 manuscript
New OBA release
Blockers

rays22 commented 10 months ago

2023-09-27 -- 2023-10-04

Since last Wednesday

Completed the manual mapping of 92.6% of the targeted 769 EFO measurement-branch terms to OBA trait terms -- issue obophenotype/human-phenotype-ontology#276.
- updated the EFO-OBA SSSOM mapping table with newly curated matches
- the remaining unmapped EFO terms are either out of scope for OBA or need new DOS-DP templates
Fixed some of my laptop user account configurations after my username had been changed by EBI.
Next
Get laptop account/Docker fixed
uPheno2 manuscript
New OBA release
Blockers
Docker has not been working on my laptop since the EBI-mandated username change.

rays22 commented 10 months ago

2023-10-04 -- 2023-10-11

Since last Wednesday

Set up an alternative Linux workstation for ODK workflow in place of my EBI laptop.
Fixed unsats and duplicates in OBA PR obophenotype/human-phenotype-ontology#293.
Next
New OBA release.
- Depends on a refreshed PRO slim.
uPheno2 manuscript.
Create OBA trait terms/mappings to laboratory measurement terminology.
Transfer data files from EBI laptop.
Blockers
Docker is broken on my laptop due to EBI-mandated username change.

rays22 commented 10 months ago

2023-10-11 -- 2023-10-18

Since last Wednesday

Expanded PRO OBO Slim in PR obophenotype/human-phenotype-ontology#37.
Created a new public release of PRO OBO Slim.
Fixed some OBA trait labels in PR obophenotype/human-phenotype-ontology#295
New OBA release v2023-10-18
Next
uPheno2 manuscript.
Create OBA trait terms/mappings to laboratory measurement terminology.
Transfer data files from EBI laptop.
Blockers

obophenotype / upheno