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 lower eyelid hooded / Eyelid partly covered by skin when eyes are open; hooding human-phenotype-ontology#828 Dislocated anatomical entity pattern template
  • uPheno thickened eyelids / Not swollen human-phenotype-ontology#830 Obstructed anatomical entity pattern template
  • uPheno Mouth: tongue lipomas human-phenotype-ontology#834 Exserted anatomical entity pattern template
  • uPheno Mouth: tonsils absent or hypoplastic 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 [Neoplasms #101](First steps for EFO/VT alignment bio-attribute-ontology#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 Transferring some "response to [drug]" terms to EFO geneontology/go-ontology#22210

Next

• Create new upheno phenotype patterns
• Continue EFO/VT-OBA [alignment work](First steps for EFO/VT alignment bio-attribute-ontology#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 lower eyelid hooded / Eyelid partly covered by skin when eyes are open; hooding human-phenotype-ontology#828 Dislocated anatomical entity pattern template
  • uPheno issue thickened eyelids / Not swollen human-phenotype-ontology#830 Obstructed anatomical entity pattern template
  • uPheno issue Mouth: tongue lipomas human-phenotype-ontology#834 Exserted anatomical entity pattern template
  • uPheno issue Mouth: tonsils absent or hypoplastic human-phenotype-ontology#836 Abnormally protruding anatomical entity pattern template
  • uPheno issue Nails, pointed / Beaked human-phenotype-ontology#840 Perforate anatomical entity pattern template
  • uPheno issue Nails: fast growing  human-phenotype-ontology#842 Abnormal thickness of anatomical entity template
  • uPheno issue Nails: platonychia / Flat and broad 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]

2023-10-11 -- 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

[rays22]

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]

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]

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]

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]

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]

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]

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]

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]

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 'Vulvar hemangioma' logical definition problem #958] ('Vulvar hemangioma' logical definition problem #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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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 Acidosis & Alkalosis logical definition causes lots of bad inference  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]

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]

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]

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