search

monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
Creative Commons Attribution 4.0 International
223 stars 51 forks source link

Mondo-plus-NCIT-Cancer #3130

Open nicolevasilevsky opened 3 years ago

nicolevasilevsky commented 3 years ago

This will provide an extended version of Mondo that contains all of the NCIt neoplasm subtypes.

STEP 1: A. Find all NCIT classes that Are subClassOf+ neoplasm That are not equivalent any mondo class And are not superclasses of any equivalent to a mondo class Call this set C B. Return the ontology that includes these classes and their immediate superclasses, where the superclass is either in C or is equivalent to a mondo class C. Run the standard rewire operation (e.g. replace NCIT classes with their mondo equivalent) D. Merge into Mondo. Call this Mondo-plus-NCIT-Cancer E. [optional] subset this, including only subclasses of Neoplasm or susceptibility to Neoplasm [e.g. to include Lynch]

nicolevasilevsky commented 3 years ago
Here are some examples of NCIT terms that are needed: Label NCIT ID
AML with t(8;21)(q22;q22.1); RUNX1-RUNX1T1 NCIT:C9288
AML with inv(16)(p13.1q22) or t(16;16)(p13.1;q22); CBFB-MYH11 NCIT:C9287
APL with PML-RARA NCIT:C7968
AML with t(9;11)(p21.3;q23.3); KMT2A-MLLT3 NCIT:C82403
AML with t(6;9)(p23;q34.1);DEK-NUP214 NCIT:C82423
AML with inv(3)(q21.3q26.2) or t(3;3)(q21.3;q26.2); GATA2, MECOM NCIT:C82426
AML (megakaryoblastic) with t(1;22)(p13.3;q13.3); RBM15-MKL1 NCIT:C82427
Provisional Entity: AML with BCR-ABL1 NCIT:C129785
AML with Mutated NPM1 NCIT:C82431
AML with Biallelic Mutations of CEBPA NCIT:C129782
Provisional Entity: AML with Mutated RUNX1 NCIT:C129786
AML with Myelodysplasia-related Changes NCIT:C7600
Therapy-Related Myeloid Neoplasms NCIT:C27912
AML, Not Otherwise Specified NCIT:C27753
AML with Minimal Differentiation NCIT:C8460
AML without Maturation NCIT:C3249
AML with Maturation NCIT:C3250
Acute Myelomonocytic Leukemia NCIT:C7463
Acute Monoblastic/Monocytic Leukemia NCIT:C7318
Pure Erythroid Leukemia NCIT:C7467
Acute Megakaryoblastic Leukemia NCIT:C3170
Acute Basophilic Leukemia NCIT:C3164
Acute Panmyelosis with Myelofibrosis NCIT:C4344
Myeloid Sarcoma NCIT:C3520
Myeloid Proliferations Related to Down Syndrome NCIT:C82338
Transient Abnormal Myelopoiesis (TAM) NCIT:C82339
Myeloid Leukemia Associated with Down Syndrome NCIT:C43223
Unknown NCIT:C17998
Not Reported NCIT:C43234

matentzn commented 6 months ago

I wonder how we should proceed with this.

nicolevasilevsky commented 6 months ago

is that the correct PR, @matentzn? that is about syonyms.

This will add a lot of new terms to Mondo. But I think it would be good to have these and especially if we could create a subset, I like that idea.

I don't remember why this came up but I do remember Deanne asked for (some) of these at one point.

matentzn commented 6 months ago

I updated my comment was out of place. I meant this PR https://github.com/monarch-initiative/mondo/pull/3137

nicolevasilevsky commented 6 months ago

To me, this seems nice to have but probably not the highest priority, especially if no one is asking for it.