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Updated efo-mondo-mapping module for v12 data release #526

Closed ewafula closed 1 year ago

ewafula commented 1 year ago

What analysis module should be updated and why?

efo-mondo-mapping

What changes need to be made? Please provide enough detail for another participant to make the update.

Update EFO, MONDO, and NCIT codes for v12 cancer groups

What input data should be used? Which data were used in the version being updated?

Use the updated v12 efo-mondo-map-prefill.tsv files on the PR #336

When do you expect the revised analysis will be completed?

1 day

Note:

Who will complete the updated analysis?

@sangeetashukla

ewafula commented 1 year ago

Moving this comment from @sangeetashukla on the PR here on the ticket @jharenza @chinwallaa @ewafula Final summary of changes that need reviewing before merging into dev:

As of now, the list of cancer_groups in the results/efo-mondo-map.tsv in this branch matches the v12 histologies.tsv. As per that list, below are the notes.

Diffuse hemispheric glioma NA NA NA - No codes were found, and need to be added manually.

Epstein-Barr virus-related tumor MONDO_0017342 MONDO_0017342 NA - NCIT code is pending.

Extraventricular neurocytoma EFO_1000856 MONDO_0016727 NCIT_C92555 - EFO code needs review.

Glial-neuronal tumor NA NA NA - No codes were found, and need to be added manually.

Mesenchymal tumor EFO_1000473 MONDO_0003512 NCIT_C7059 - needs review because description for each of the codes is not necessarily the same.

Other EFO_0030051 GO_0051707 NCIT_C17649 - needs review since this is not specific at all.

Perineuroma NA NA NA - was added but is missing all codes, therefore needs review.

Pheochromocytoma and Paraganglioma EFO_0020005 MONDO_0035540 NA - NCIT code is pending.

SEGA NA NA NA - was added but is missing all codes, therefore needs review.

High-grade glioma and Low-grade glioma need additional review since High-grade glioma/astrocytoma and Low-grade glioma/astrocytoma are also included, although the codes are different.

T Acute Lymphoblastic Leukemia/Lymphoma EFO_0000209 MONDO_0004963 NCIT_C3183 EFO_1001936 MONDO_0003537 NCIT_C8694 The codes need to be re-visited. Alternatives are suggested here based on the automated search results captured in results/efo-mondo-map-prefill-auto.tsv

Uterine Corpus Endometrial Carcinoma EFO_0007532 MONDO_0000553 NCIT_C159413 EFO_1000238 MONDO_0000553 NCIT_C159413 - EFO code seems to have changed, needs review.

ewafula commented 1 year ago

@sangeetashukla,

SEGA seems to have an NCIT code here: https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C3696

Perineuroma has MONDO code here: https://monarchinitiative.org/disease/MONDO:0019404

jharenza commented 1 year ago

Hi @sangeetashukla. See my comments below. cc @ewafula 

Diffuse hemispheric glioma NA NA NA - No codes were found, and need to be added manually. - this is a new entity. use MONDO:0016680 for now
Epstein-Barr virus-related tumor MONDO_0017342 MONDO_0017342 NA - NCIT code is pending. - OK
Extraventricular neurocytoma EFO_1000856 MONDO_0016727 NCIT_C92555 - EFO code needs review. - MONDO_0016727 and NCIT_C92555 correct. EFO not correct
Glial-neuronal tumor    NA  NA  NA - No codes were found, and need to be added manually. - NCIT_C4747
Mesenchymal tumor EFO_1000473 MONDO_0003512 NCIT_C7059 - needs review because description for each of the codes is not necessarily the same. - NCIT:C7059 seems best here
Other EFO_0030051 GO_0051707 NCIT_C17649 - needs review since this is not specific at all. - this should be removed totally, will update PR prior to this
Perineuroma NA NA NA - was added but is missing all codes, therefore needs review. - MONDO:0019404
Pheochromocytoma and Paraganglioma  EFO_0020005 MONDO_0035540   NA - NCIT code is pending. - OK to be blank NCIT
SEGA    NA  NA  NA - was added but is missing all codes, therefore needs review. - NCIT:C3696 and will update PR to use long name
High-grade glioma and Low-grade glioma need additional review since High-grade glioma/astrocytoma and Low-grade glioma/astrocytoma are also included, although the codes are different. 
T Acute Lymphoblastic Leukemia/Lymphoma EFO_0000209 MONDO_0004963 NCIT_C3183 EFO_1001936 MONDO_0003537 NCIT_C8694 The codes need to be re-visited. Alternatives are suggested here based on the automated search results captured in results/efo-mondo-map-prefill-auto.tsv - use these: EFO_0000209 MONDO_0004963 NCIT_C3183
Uterine Corpus Endometrial Carcinoma EFO_0007532 MONDO_0000553 NCIT_C159413 EFO_1000238 MONDO_0000553 NCIT_C159413 - EFO code seems to have changed, needs review. - http://purl.obolibrary.org/obo/NCIT_C159413 this seems to be nothing. Use EFO_0007532 MONDO_0000553
sangeetashukla commented 1 year ago

Hi @sangeetashukla. See my comments below. cc @ewafula

Diffuse hemispheric glioma NA NA NA - No codes were found, and need to be added manually. - this is a new entity. use MONDO:0016680 for now
Epstein-Barr virus-related tumor MONDO_0017342 MONDO_0017342 NA - NCIT code is pending. - OK
Extraventricular neurocytoma EFO_1000856 MONDO_0016727 NCIT_C92555 - EFO code needs review. - MONDO_0016727 and NCIT_C92555 correct. EFO not correct
Glial-neuronal tumor  NA  NA  NA - No codes were found, and need to be added manually. - NCIT_C4747
Mesenchymal tumor EFO_1000473 MONDO_0003512 NCIT_C7059 - needs review because description for each of the codes is not necessarily the same. - NCIT:C7059 seems best here
Other EFO_0030051 GO_0051707 NCIT_C17649 - needs review since this is not specific at all. - this should be removed totally, will update PR prior to this
Perineuroma NA NA NA - was added but is missing all codes, therefore needs review. - MONDO:0019404
Pheochromocytoma and Paraganglioma    EFO_0020005 MONDO_0035540   NA - NCIT code is pending. - OK to be blank NCIT
SEGA  NA  NA  NA - was added but is missing all codes, therefore needs review. - NCIT:C3696 and will update PR to use long name
High-grade glioma and Low-grade glioma need additional review since High-grade glioma/astrocytoma and Low-grade glioma/astrocytoma are also included, although the codes are different. 
T Acute Lymphoblastic Leukemia/Lymphoma EFO_0000209 MONDO_0004963 NCIT_C3183 EFO_1001936 MONDO_0003537 NCIT_C8694 The codes need to be re-visited. Alternatives are suggested here based on the automated search results captured in results/efo-mondo-map-prefill-auto.tsv - use these: EFO_0000209 MONDO_0004963 NCIT_C3183
Uterine Corpus Endometrial Carcinoma EFO_0007532 MONDO_0000553 NCIT_C159413 EFO_1000238 MONDO_0000553 NCIT_C159413 - EFO code seems to have changed, needs review. - http://purl.obolibrary.org/obo/NCIT_C159413 this seems to be nothing. Use EFO_0007532 MONDO_0000553

Thank you @jharenza I will review your comments and update the mapping file.

sangeetashukla commented 1 year ago

@ewafula The older PR attached to the issue has been merged. I will create a new PR with the efo-mondo-map.tsv updated.

ewafula commented 1 year ago

Sure, @sangeetashukla. Create a v12-efo-mondo branch off the v12-post-release PR branch as you did before.

jharenza commented 1 year ago

Closed with https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/321