MedDRA to DOID cross-references

[ireneisdoomed]

Hi,

from an analysis of FAERS data, we have obtained a list of 11 MedDRA to DOID mappings that we believe have a very high level of confidence:

+----------+---------------------+-----+--------------------------+-------------------------------+
|efoId     |efoName              |score|traitId                   |traitName                      |
+----------+---------------------+-----+--------------------------+-------------------------------+
|DOID_10718|giardiasis           |0.999|10018261                  |Giardia lamblia infection      |
|DOID_7551 |gonorrhea            |1.0  |10018610-10018611-10018604|Gonorrhea                      |
|DOID_10718|giardiasis           |1.0  |10018262                  |Giardiasis                     |
|DOID_1947 |trichomoniasis       |1.0  |10044620-10044623         |Trichomoniasis                 |
|DOID_1947 |trichomoniasis       |0.999|10044618                  |Trichomonas infections         |
|DOID_10718|giardiasis           |0.999|10018260                  |Giardia infections             |
|DOID_10718|giardiasis           |0.996|10064239                  |Lambliasis                     |
|DOID_7551 |gonorrhea            |0.996|10053842                  |Gianotti-Crosti syndrome       |
|DOID_7551 |gonorrhea            |0.999|10051970                  |Neisseria gonorrhoeae infection|
|DOID_10113|trypanosomiasis      |1.0  |10044710-10044707         |Trypanosomiasis                |
|DOID_13406|pulmonary sarcoidosis|1.0  |10037430                  |Pulmonary sarcoidosis          |
+----------+---------------------+-----+--------------------------+-------------------------------+

meddra-doid-xref-0995-1.json.zip

This is part of an emerging pipeline we are working on to integrate the different methods of automatic disease mapping into a single tool. The algorithm performs very well as long as it is already captured in the ontology.

Could you please examine the mappings and consider how best to include this annotation in the ontology? The SPOT team has already imported the MedDRA xrefs whose labels match an EFO/Orphanet term and are now in the process of curating the ones of less confidence. Both EFO and Open Targets would benefit a lot if you could include them similarly.

Any feedback or comments is much appreciated.

Thanks!

[lschriml]

I have added:

giardiasis. MEDDRA:0017536 gonorrhea MEDDRA:10018604 trichomoniasis MEDDRA:10044620 trypanosomiasis. MEDDRA:10044707 pulmonary sarcoidosis MEDDRA:10037430

Cheers, Lynn

[ireneisdoomed]

Hi Lynn, thank you so much for checking these out!

There's a 1 to many relationship between DOID and MedDRA and this is not captured. Is the ontology constrained to having only one cross-reference to MedDRA?

[lschriml]

We can include multiple MedDRA IDs.

On Jun 9, 2021, at 4:55 AM, Irene López @.***> wrote:

 Hi Lynn, thank you so much for checking these out!

There's a 1 to many relationship between DOID and MedDRA and this is not captured. Is the ontology constrained to having only one cross-reference to MedDRA?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or unsubscribe.

[linikujp]

Why do you have multiple IDs for a MedDRA term. For example : |10018610-10018611-10018604|Gonorrhea

Also, please clarify if you are mapping PT terms only or you include other terms as well.

Thanks, Asiyah

On Wed, Jun 9, 2021, 09:55 lschriml @.***> wrote:

We can include multiple MedDRA IDs.

On Jun 9, 2021, at 4:55 AM, Irene López @.***> wrote:

 Hi Lynn, thank you so much for checking these out!

There's a 1 to many relationship between DOID and MedDRA and this is not captured. Is the ontology constrained to having only one cross-reference to MedDRA?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/947#issuecomment-857715388, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACCPEPNJCLS4J3RF57CL6G3TR5XFHANCNFSM457BCTUQ .

[ireneisdoomed]

Hi @linikujp! Sorry for the delayed answer. We are working with a specific version of the MedDRA dictionary and as far as I understand, these 3 terms all refer to the disease Gonorrhea, which is what the column traitName refers to.

Given this, all three terms are mapped to the same EFO ID.

And regarding your other question, we are not restricting ourselves to a specific therapeutic area.

Many thanks!