Weekly progress report on uPheno and OBA

[matentzn]

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]

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

Next

• Remove CHEBI role classes that cause logical errors in OBA obophenotype/human-phenotype-ontology#99
• Continue EFO/VT alignment work #101
  • Review EFO-OBA pipeline suggested patterns
  • Second iteration of EFO(GWAS)-VT-OBA trait alignment using the pipeline

Blockers

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

[rays22]

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]

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

Next

• Create new upheno phenotype patterns
• Continue EFO/VT-OBA [alignment work](https://github.com/obophenotype/bio-attribute-ontology/issues/101

Blockers

• Time

[rays22]

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]

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.

Next

• Continue mapping some VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
• Follow up uPheno pattern feedback from the last Phenotype Editors Call
• Continue EFO/VT alignment work #101

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]

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

Next

• Merge open OBA PRs
• Run an OBA release
• Hand over new terms to EFO
• Facilitate OBA update in OLS
• Continue mapping the remaining 154 VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
• Continue EFO/VT alignment work #101

Blockers

None.

[rays22]

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.

Next

• Preparations for Monarch Huddle on August 16th
• Preparations for phenotype ontology editors call
• Continue mapping the remaining 154 VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
• Continue EFO/VT alignment work #101

Blockers

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

[rays22]

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

Next

• Preparations for OBA call
• Preparations for uPheno phenotype editors call
• Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
• Continue EFO/VT alignment work #101

Blockers

None.

[rays22]

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

Next

• Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA.
• Continue EFO/VT alignment work #101

Blockers

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

[rays22]

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]

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.

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:0001606 greasy
  • PATO:0001373 glistening

Blockers

None.

[rays22]

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]

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.
  • Added new entity_attribute term OBA:VT0010917 obophenotype/human-phenotype-ontology#143
  • Added 41 new entity_attribute_location terms obophenotype/human-phenotype-ontology#144
  • Added VT pigmentation and content terms obophenotype/human-phenotype-ontology#148
  • 'mass' related terms from VT obophenotype/human-phenotype-ontology#146
  • VT thickness terms obophenotype/human-phenotype-ontology#147
  • Quantity related VT terms and synonyms obophenotype/human-phenotype-ontology#149
• Reviewed PR Edits to annotations on RateOfBehavior patterns obophenotype/human-phenotype-ontology#888

Next

• 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:
  • 'mass' related terms from VT obophenotype/human-phenotype-ontology#146
  • VT thickness terms obophenotype/human-phenotype-ontology#147
  • Quantity related VT terms and synonyms obophenotype/human-phenotype-ontology#149
• 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]

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

Next

• Continue 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]

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]

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]

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.

Next

• Complete PRs in preparation of a new OBA release.
• Continue EFO-OBA alignment #101
• Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA

Blockers

[rays22]

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.

Next

• Complete PRs in preparation of a new OBA release.
• Continue EFO-OBA alignment #101
• Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA

Blockers

[rays22]

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

Next

• OBA manuscript preparations
• Continue EFO-OBA alignment #101
• Continue mapping the remaining VT terms used by the Mouse Phenome Database so that they can be imported into or mapped to OBA

Blockers

[rays22]

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

Next

• 2022-11-21 EBI/SPOT talk preparations: Integrated Trait and Phenotype Ontologies
• OBA manuscript preparations
• Fix deprecated GO classes in OBA
• Obsolete 'deviation from normal' subclasses in OBA

Blockers

[rays22]

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]

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]

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]

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]

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]

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]

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.

Next

• Submit OBA manuscript
• Issues related to phenotype editors call (uPheno)
• Import the remaining VT terms relevant to MPD into OBA #85

Blockers

[rays22]

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]

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]

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