Add a script to QC the update-synonyms-sync target by ptgolden · Pull Request #10260 · monarch-initiative/mondo

ptgolden · 2026-05-19T19:04:41Z

This adds a script (synonym_sync_qc) that looks at mondo-edit.obo after update-synonyms-sync has been run (but before it has been committed). It runs two checks:

Are all unstaged changes to mondo-edit.obo confined to lines about synonyms? If not, that means that there are extraneous changes that shouldn't be happening with the synonym sync workflow.
Is the set of synonyms pre-sync the exact same set post-sync? And if so, what axioms (if any) have changed on those synonyms?

(1) uses git diff as the signal for analysis, (2) uses fastobo to actually parse mondo-edit.obo before and after sync. Because fastobo is fast, this runs an analysis on mondo-edit.obo in 6 seconds.

This script also writes a report formatted as markdown. The report details whether the checks passed, and then gives some details about how synonym axioms have changed.

The synonym-sync workflow has been updated to run this script. I also took out the make test invocation in there, since it will be run on the PR automatically anyway.

This adds a script (`synonym_sync_qc`) that looks at `mondo-edit.obo` after `update-synonyms-sync` has been run (but before it has been committed). It runs two checks: 1. Are all unstaged changes to `mondo-edit.obo` confined to lines about synonyms? If not, that means that there are extraneous changes that shouldn't be happening with the synonym sync workflow. 2. Is the set of synonyms pre-sync the exact same set post-sync? And if so, what axioms (if any) have changed on those synonyms? (1) uses `git diff` as the signal for analysis, (2) uses `fastobo` to actually parse `mondo-edit.obo` before and after sync. Because `fastobo` is fast, this runs an analysis on `mondo-edit.obo` in 6 seconds. --- This script also writes a report formatted as markdown. The report details whether the checks passed, and then gives some details about how synonym axioms have changed. --- The synonym-sync workflow has been updated to run this script. I also took out the `make test` invocation in there, since it will be run on the PR automatically anyway.

ptgolden · 2026-05-19T19:06:06Z

here's an example of the report generated from synonym sync run on current HEAD:

Synonym sync QC report

HEAD:mondo-edit.obo -> mondo-edit.obo

Pass 1 (diff confined to synonym: lines): PASS
Pass 2 ((term_id, literal) set invariant): PASS
Number of modifications on existing synonyms: 31

Pass 1: non-synonym line changes

No non-synonym lines changed.

Pass 2: synonym additions and deletions

No synonyms were added or removed.

Modifications by category

Category	Count
scope_change	0
modifier_change	2
provenance_change	29

Provenance xref changes by source prefix

Prefix	Added	Dropped
`DOID`	9	4
`OMIM`	5	7
`Orphanet`	0	6
`icd11.foundation`	1	0

modifier_change (2)

MONDO:0015912 — MATINS

- type=None
+ type=ABBREVIATION

MONDO:0017790 — polyposis of gastric fundus without polyposis coli

- type=None
+ type=ABBREVIATION

provenance_change (29)

MONDO:0001106 — renal insufficiency

- xrefs=['NCIT:C4376']
+ xrefs=['DOID:1074', 'NCIT:C4376']

MONDO:0001896 — non-communicating hydrocephalus

- xrefs=['NCIT:C116347']
+ xrefs=['DOID:14159', 'NCIT:C116347']

MONDO:0009106 — SCM type 1

- xrefs=['Orphanet:1671']
+ xrefs=[]

MONDO:0009106 — diastematomyelia

- xrefs=['ICD10CM:Q06.2', 'NCIT:C98913', 'OMIM:222500', 'Orphanet:573278', 'icd11.foundation:2070601288']
+ xrefs=['ICD10CM:Q06.2', 'NCIT:C98913', 'OMIM:222500', 'icd11.foundation:2070601288']

MONDO:0009106 — split cord malformation

- xrefs=['GARD:0001851', 'Orphanet:573278']
+ xrefs=['GARD:0001851', 'Orphanet:573278', 'icd11.foundation:2070601288']

MONDO:0009106 — split cord malformation type 1

- xrefs=['Orphanet:1671']
+ xrefs=[]

MONDO:0009106 — split spinal cord malformation

- xrefs=['GARD:0001851', 'Orphanet:573278']
+ xrefs=['GARD:0001851']

MONDO:0009366 — NPH

- xrefs=[]
+ xrefs=['DOID:1572']

MONDO:0009835 — Immunosuppressive measles encephalitis

- xrefs=['DOID:8970', 'icd11.foundation:1098683540']
+ xrefs=['icd11.foundation:1098683540']

MONDO:0010598 — glycogen storage disease IXa1

- xrefs=['OMIM:306000']
+ xrefs=['DOID:0111042', 'OMIM:306000']

MONDO:0010598 — glycogen storage disease type IXa

- xrefs=['DOID:0111042', 'https://www.ncbi.nlm.nih.gov/books/NBK55061/']
+ xrefs=['https://www.ncbi.nlm.nih.gov/books/NBK55061/']

MONDO:0011323 — BAM syndrome

- xrefs=['OMIM:603457', 'https://orcid.org/0000-0001-9310-0163']
+ xrefs=['https://orcid.org/0000-0001-9310-0163']

MONDO:0011323 — Bosma syndrome

- xrefs=['OMIM:603457', 'https://orcid.org/0000-0001-9310-0163']
+ xrefs=['https://orcid.org/0000-0001-9310-0163']

MONDO:0011323 — Ruprecht Majewski syndrome

- xrefs=['OMIM:603457', 'https://orcid.org/0000-0001-9310-0163']
+ xrefs=['https://orcid.org/0000-0001-9310-0163']

MONDO:0011996 — leukimia, chronic myeloid

- xrefs=['OMIM:608232']
+ xrefs=[]

MONDO:0013767 — RALD

- xrefs=['DOID:0110117', 'OMIM:614470', 'Orphanet:268114']
+ xrefs=['DOID:0110117', 'Orphanet:268114']

MONDO:0013767 — RAS-associated autoimmune leukoproliferative disorder

- xrefs=['DOID:0110117', 'OMIM:614470']
+ xrefs=['DOID:0110117']

MONDO:0013947 — Young adult-onset dHMN

- xrefs=['DOID:0111214', 'Orphanet:314485']
+ xrefs=[]

MONDO:0013947 — young adult-onset distal hereditary motor neuropathy

- xrefs=['DOID:0111214', 'Orphanet:314485']
+ xrefs=[]

MONDO:0014392 — SLC13A5 Citrate Transporter Disorder

- xrefs=['NORD:1914']
+ xrefs=['DOID:0080453', 'NORD:1914']

MONDO:0015912 — Alport syndrome with macrothrombocytopenia

- xrefs=['OMIM:155100']
+ xrefs=[]

MONDO:0015912 — FTNS

- xrefs=[]
+ xrefs=['OMIM:155100']

MONDO:0015912 — MATINS

- xrefs=['https://orcid.org/0000-0001-9310-0163']
+ xrefs=['OMIM:155100', 'https://orcid.org/0000-0001-9310-0163']

MONDO:0015912 — MHA

- xrefs=[]
+ xrefs=['OMIM:155100']

MONDO:0015912 — SBS

- xrefs=[]
+ xrefs=['OMIM:155100']

MONDO:0019719 — congenital anomalies of kidney and urinary tract

- xrefs=['OMIMPS:610805', 'Orphanet:93545']
+ xrefs=['DOID:0080205', 'OMIMPS:610805', 'Orphanet:93545']

MONDO:0032578 — CDCBM9

- xrefs=[]
+ xrefs=['DOID:0061138', 'OMIM:618174']

MONDO:0044640 — AR-CMT2T

- xrefs=['Orphanet:495274']
+ xrefs=['DOID:0110160', 'Orphanet:495274']

MONDO:0044640 — autosomal recessive axonal Charcot-Marie-Tooth disease type 2T

- xrefs=['Orphanet:495274']
+ xrefs=['DOID:0110160', 'Orphanet:495274']

Put rdfs:label in the header, and the text of the synonym beneath, showing what type of synonym it is in the synced version.

ptgolden · 2026-05-19T22:20:11Z

I changed the report a little bit, to make it clear what the label is and what the synonym is:

Synonym sync QC report

HEAD:mondo-edit.obo -> mondo-edit.obo

Pass 1 (diff confined to synonym: lines): PASS
Pass 2 ((term_id, literal) set invariant): PASS
Number of modifications on existing synonyms: 31

Pass 1: non-synonym line changes

No non-synonym lines changed.

Pass 2: synonym additions and deletions

No synonyms were added or removed.

Modifications by category

Category	Count
scope_change	0
modifier_change	2
provenance_change	29

Provenance xref changes by source prefix

Prefix	Added	Dropped
`DOID`	9	4
`OMIM`	5	7
`Orphanet`	0	6
`icd11.foundation`	1	0

modifier_change (2)

MONDO:0015912 macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

EXACT ABBREVIATION synonym: "MATINS"

- type=None
+ type=ABBREVIATION

MONDO:0017790 gastric adenocarcinoma and proximal polyposis of the stomach

EXACT ABBREVIATION synonym: "polyposis of gastric fundus without polyposis coli"

- type=None
+ type=ABBREVIATION

provenance_change (29)

MONDO:0001106 kidney failure

EXACT synonym: "renal insufficiency"

- xrefs=['NCIT:C4376']
+ xrefs=['DOID:1074', 'NCIT:C4376']

MONDO:0001896 obstructive hydrocephalus

EXACT synonym: "non-communicating hydrocephalus"

- xrefs=['NCIT:C116347']
+ xrefs=['DOID:14159', 'NCIT:C116347']

MONDO:0009106 diastematomyelia

NARROW ABBREVIATION synonym: "SCM type 1"

- xrefs=['Orphanet:1671']
+ xrefs=[]

MONDO:0009106 diastematomyelia

EXACT synonym: "diastematomyelia"

- xrefs=['ICD10CM:Q06.2', 'NCIT:C98913', 'OMIM:222500', 'Orphanet:573278', 'icd11.foundation:2070601288']
+ xrefs=['ICD10CM:Q06.2', 'NCIT:C98913', 'OMIM:222500', 'icd11.foundation:2070601288']

MONDO:0009106 diastematomyelia

EXACT synonym: "split cord malformation"

- xrefs=['GARD:0001851', 'Orphanet:573278']
+ xrefs=['GARD:0001851', 'Orphanet:573278', 'icd11.foundation:2070601288']

MONDO:0009106 diastematomyelia

NARROW synonym: "split cord malformation type 1"

- xrefs=['Orphanet:1671']
+ xrefs=[]

MONDO:0009106 diastematomyelia

EXACT synonym: "split spinal cord malformation"

- xrefs=['GARD:0001851', 'Orphanet:573278']
+ xrefs=['GARD:0001851']

MONDO:0009366 normal pressure hydrocephalus

EXACT ABBREVIATION synonym: "NPH"

- xrefs=[]
+ xrefs=['DOID:1572']

MONDO:0009835 subacute sclerosing panencephalitis

EXACT synonym: "Immunosuppressive measles encephalitis"

- xrefs=['DOID:8970', 'icd11.foundation:1098683540']
+ xrefs=['icd11.foundation:1098683540']

MONDO:0010598 glycogen storage disease IXa1

EXACT synonym: "glycogen storage disease IXa1"

- xrefs=['OMIM:306000']
+ xrefs=['DOID:0111042', 'OMIM:306000']

MONDO:0010598 glycogen storage disease IXa1

EXACT synonym: "glycogen storage disease type IXa"

- xrefs=['DOID:0111042', 'https://www.ncbi.nlm.nih.gov/books/NBK55061/']
+ xrefs=['https://www.ncbi.nlm.nih.gov/books/NBK55061/']

MONDO:0011323 arhinia, choanal atresia, and microphthalmia

EXACT synonym: "BAM syndrome"

- xrefs=['OMIM:603457', 'https://orcid.org/0000-0001-9310-0163']
+ xrefs=['https://orcid.org/0000-0001-9310-0163']

MONDO:0011323 arhinia, choanal atresia, and microphthalmia

EXACT synonym: "Bosma syndrome"

- xrefs=['OMIM:603457', 'https://orcid.org/0000-0001-9310-0163']
+ xrefs=['https://orcid.org/0000-0001-9310-0163']

MONDO:0011323 arhinia, choanal atresia, and microphthalmia

EXACT synonym: "Ruprecht Majewski syndrome"

- xrefs=['OMIM:603457', 'https://orcid.org/0000-0001-9310-0163']
+ xrefs=['https://orcid.org/0000-0001-9310-0163']

MONDO:0011996 chronic myeloid leukemia

EXACT synonym: "leukimia, chronic myeloid"

- xrefs=['OMIM:608232']
+ xrefs=[]

MONDO:0013767 autoimmune lymphoproliferative syndrome type 4

EXACT ABBREVIATION synonym: "RALD"

- xrefs=['DOID:0110117', 'OMIM:614470', 'Orphanet:268114']
+ xrefs=['DOID:0110117', 'Orphanet:268114']

MONDO:0013767 autoimmune lymphoproliferative syndrome type 4

EXACT synonym: "RAS-associated autoimmune leukoproliferative disorder"

- xrefs=['DOID:0110117', 'OMIM:614470']
+ xrefs=['DOID:0110117']

MONDO:0013947 neuronopathy, distal hereditary motor, autosomal recessive 5

BROAD synonym: "Young adult-onset dHMN"

- xrefs=['DOID:0111214', 'Orphanet:314485']
+ xrefs=[]

MONDO:0013947 neuronopathy, distal hereditary motor, autosomal recessive 5

BROAD synonym: "young adult-onset distal hereditary motor neuropathy"

- xrefs=['DOID:0111214', 'Orphanet:314485']
+ xrefs=[]

MONDO:0014392 developmental and epileptic encephalopathy, 25

EXACT synonym: "SLC13A5 Citrate Transporter Disorder"

- xrefs=['NORD:1914']
+ xrefs=['DOID:0080453', 'NORD:1914']

MONDO:0015912 macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

EXACT synonym: "Alport syndrome with macrothrombocytopenia"

- xrefs=['OMIM:155100']
+ xrefs=[]

MONDO:0015912 macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

EXACT ABBREVIATION synonym: "FTNS"

- xrefs=[]
+ xrefs=['OMIM:155100']

MONDO:0015912 macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

EXACT ABBREVIATION synonym: "MATINS"

- xrefs=['https://orcid.org/0000-0001-9310-0163']
+ xrefs=['OMIM:155100', 'https://orcid.org/0000-0001-9310-0163']

MONDO:0015912 macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

EXACT ABBREVIATION synonym: "MHA"

- xrefs=[]
+ xrefs=['OMIM:155100']

MONDO:0015912 macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

EXACT ABBREVIATION synonym: "SBS"

- xrefs=[]
+ xrefs=['OMIM:155100']

MONDO:0019719 congenital anomaly of kidney and urinary tract

EXACT synonym: "congenital anomalies of kidney and urinary tract"

- xrefs=['OMIMPS:610805', 'Orphanet:93545']
+ xrefs=['DOID:0080205', 'OMIMPS:610805', 'Orphanet:93545']

MONDO:0032578 cortical dysplasia, complex, with other brain malformations 9

EXACT ABBREVIATION synonym: "CDCBM9"

- xrefs=[]
+ xrefs=['DOID:0061138', 'OMIM:618174']

MONDO:0044640 Charcot-Marie-Tooth disease type 2T

EXACT ABBREVIATION synonym: "AR-CMT2T"

- xrefs=['Orphanet:495274']
+ xrefs=['DOID:0110160', 'Orphanet:495274']

MONDO:0044640 Charcot-Marie-Tooth disease type 2T

EXACT synonym: "autosomal recessive axonal Charcot-Marie-Tooth disease type 2T"

- xrefs=['Orphanet:495274']
+ xrefs=['DOID:0110160', 'Orphanet:495274']

matentzn

This is great! Looks amazing. Can we wrap the detailed lists in <details>...</details> and add some way to crop the list at say 30 entries per category in case the PR has MAAAANY changes (that would make the github PR field blow up)?

And then I am just happy to go ahead and try!

matentzn

And the <details> thing i mentioned earlier

matentzn · 2026-05-20T13:08:44Z

          make GITHUB_ACTION=true IMP=false PAT=false update-synonyms-sync -B

-      - name: QC to ensure that nothing other than provenance has changed
-        run: cd src/ontology; make GITHUB_ACTION=true IMP=false PAT=false test -B


Make sure make test REALLY runs as you say - I dont think so without additional prodding (action triggering action)

here's a PR from a previous run: #10194

That QC is run from a PR event.

The QC in the sync workflow runs before the PR is created, on the exact same SHA, but it doesn't count as the required QC check. That makes it totally superfluous.

ptgolden · 2026-05-20T13:37:59Z

This is great! Looks amazing. Can we wrap the detailed lists in <details>...</details> and add some way to crop the list at say 30 entries per category in case the PR has MAAAANY changes (that would make the github PR field blow up)?

Yep, good idea.

Should there possibly be some diagnostic about synonyms that have lost all provenance?

matentzn · 2026-05-20T14:01:07Z

Should there possibly be some diagnostic about synonyms that have lost all provenance?

For now just a number; maybe broken by "prefix that used to support it". But we have not yet decided how exactly SOP these cases.

1. Allow calling the script on a specific ref, to get a summary of changes for commits in the past (not just unstaged changes) 2. Add an option to export a short summary, appropriate for a pull request body. 3. Add that summary as the PR body in the synonyms.yaml workflow, and attach the full report as an artifact that is hyperlinked. (To prevent a super long commit message).

ptgolden · 2026-05-26T19:02:53Z

Make sure make test REALLY runs as you say - I dont think so without additional prodding (action triggering action)

You were completely right about this. And it led me to an interesting conclusion.

We have been talking about the limitations of using the built-in $GITHUB_TOKEN vs using a personal-access token (PAT) or a GitHub Actions token. What I'm realizing is that I strongly suspect that you have already uploaded a PAT to this repository, and it was being used by this workflow along with a few others. You can see it here:

mondo/.github/workflows/synonyms.yaml

Lines 26 to 35 in 265623d

    
           - name: Create Pull Request 
        
             uses: peter-evans/create-pull-request@v5 
        
             with: 
        
               branch-suffix: short-commit-hash 
        
               labels: automated 
        
               body: "Update the confirmed synonyms axiom annotation." 
        
               title: "Monthly confirmed synonyms evidence update" 
        
               base: ${{ github.head_ref }} 
        
               branch: "confirmed_synonyms_evidence" 
        
               token: ${{ secrets.GH_TOKEN }}

{{ secrets.GH_TOKEN }} is pointing to your personal PAT. What this means is that a PR created from this workflow does re-trigger workflows.

In my view, it would be good to stop relying on this, and remove instances of your PAT, if possible. I have changes coming into #10244 which will do just that. I'll wait on this one until we finish that.

matentzn · 2026-05-29T05:29:48Z

In my view, it would be good to stop relying on this, and remove instances of your PAT, if possible. I have changes coming into #10244 which will do just that. I'll wait on this one until we finish that.

Please micromanage my reviews on slack on this - happy to follow your nose on this one! Whats the next step then?

ptgolden requested a review from matentzn as a code owner May 19, 2026 19:04

ptgolden self-assigned this May 19, 2026

Improve synonym sync report

066922c

Put rdfs:label in the header, and the text of the synonym beneath, showing what type of synonym it is in the synced version.

matentzn requested changes May 20, 2026

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ptgolden mentioned this pull request May 29, 2026

Change normalization/QC workflow to use custom statuses #10244

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Add a script to QC the update-synonyms-sync target#10260

Add a script to QC the update-synonyms-sync target#10260
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synonym-sync-qc

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ptgolden commented May 19, 2026

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ptgolden commented May 19, 2026

Synonym sync QC report

Pass 1: non-synonym line changes

Pass 2: synonym additions and deletions

Modifications by category

Provenance xref changes by source prefix

modifier_change (2)

provenance_change (29)

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ptgolden commented May 19, 2026

Synonym sync QC report

Pass 1: non-synonym line changes

Pass 2: synonym additions and deletions

Modifications by category

Provenance xref changes by source prefix

modifier_change (2)

provenance_change (29)

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