El Escorial criteria for ALS

[dicorey4]

For Amyotrophic Lateral Sclerosis, there are revised El Escorial criteria that are used to classify ALS diagnosis with indicators and symptoms of the motor system to help determine which criteria determination to categorize a patient. There are guidelines as part of the ALS NINDS CDE located under the Disease/Injury Related Events/Classification/Symptom, Sign, Diagnosis links (https://www.commondataelements.ninds.nih.gov/amyotrophic%20lateral%20sclerosis). There are no definitive diagnostic tests for ALS, so these criteria are important to help categorize patients consistently.

These criteria and indicators/symptoms do not reside in any of the vocabularies within OMOP right now. These criteria are used as inclusion/exclusion criteria for a lot of studies and would prove extremely valuable to making sure all studies can map these criteria to the same concepts for analysis purposes.

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[m-khitrun]

Hello, @dicorey4!

Thank you for your contribution!
Please follow the instructions and upload your content using our templates by the end of December so we can add them during the Winter release.
If you need any help with the templates, feel free to contact me by e-mail: [email protected].

Regards,
Masha

[dicorey4]

I have added the template1 with our new additions here: https://drive.google.com/drive/u/0/folders/1m6_kutvbpfqzGtGqegcg8nDBO9a5_XDd

Some explanation: in the concept_manual tab - rows 4-8 are answers to row3 and represents the categorization of someone with ALS.

Rows 32-34 are answers to rows 9-31. We are not sure if new terminology should be created so they are associated with only the criteria and indicator variables or if existing LOINC codes should be used.

This is our first terminology submission, so please let me know if you need anything else or if I failed to fill something out properly.

[m-khitrun]

Hello Diane, The concepts you provided refer to so-called Survey data, and there are many issues around their standardization. I'd like to encourage you to contact the Survey WG, a lot of interesting discussions go on there. The current best practice to store this data is the precoordinated pairs approach, as in UK Biobank<https://athena.ohdsi.org/search-terms/terms?vocabulary=UK+Biobank&conceptClass=Precoordinated+pair&page=1&pageSize=15&query=> or other concepts in OMOP Extension. OMOP CDM is not supposed to store negative information therefore you need to add concepts 3 and 9-31 as pre-coordinated pairs of criteria + positive answer, e.g.: Bulbar lower motor neuron clinical indicator: yes In this case, the concept_class_id would be a ‘Precoordinated pair’. Also, you should adjust concept names as follows to make them more specific: El Escorial criteria - revised: Left lower extremity upper motor neuron clinical indicator El Escorial criteria - revised: Bulbar lower motor neuron clinical indicator Please, note that when we add concepts to OMOP Extension, we assign them specific OMOP-generated concept codes. You should map your raw source codes to the new standard concepts to use them. So, you can let the concept_code field empty. Best, Masha

…

________________________________ From: dicorey4 ***@***.***> Sent: Friday, December 20, 2024 18:19 To: OHDSI/Vocabulary-v5.0 ***@***.***> Cc: Maria Khitrun ***@***.***>; Assign ***@***.***> Subject: Re: [OHDSI/Vocabulary-v5.0] El Escorial criteria for ALS (Issue #1082) I have added the template1 with our new additions here: https://drive.google.com/drive/u/0/folders/1m6_kutvbpfqzGtGqegcg8nDBO9a5_XDd Some explanation: in the concept_manual tab - rows 4-8 are answers to row3 and represents the categorization of someone with ALS. Rows 32-34 are answers to rows 9-31. We are not sure if new terminology should be created so they are associated with only the criteria and indicator variables or if existing LOINC codes should be used. This is our first terminology submission, so please let me know if you need anything else or if I failed to fill something out properly. — Reply to this email directly, view it on GitHub<#1082 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXY5773LX5YZK5O2DIDRMK32GQ7SHAVCNFSM6AAAAABTQATRJSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNJXGMYDONRQG4>. You are receiving this because you were assigned.Message ID: ***@***.***>

[dicorey4]

Hi Masha, Thank you for your response. I will work with my colleagues to update this, however, with the holidays I’m not sure if that will be possible by the end of this year. We may have to push off our submission until the next release. I will update the github issue before the end of the year if possible, otherwise will this issue get pushed to the next release automatically or do I have to do something to facilitate that? Thank you for all your help, Diane From: Masha Khitrun ***@***.***> Sent: Friday, December 20, 2024 12:33 PM To: OHDSI/Vocabulary-v5.0 ***@***.***> Cc: Diane Corey ***@***.***>; Mention ***@***.***> Subject: Re: [OHDSI/Vocabulary-v5.0] El Escorial criteria for ALS (Issue #1082) [External Message] Hello Diane, The concepts you provided refer to so-called Survey data, and there are many issues around their standardization. I'd like to encourage you to contact the Survey WG, a lot of interesting discussions go on there. The current best practice to store this data is the precoordinated pairs approach, as in UK Biobank<https://athena.ohdsi.org/search-terms/terms?vocabulary=UK+Biobank&conceptClass=Precoordinated+pair&page=1&pageSize=15&query=> or other concepts in OMOP Extension. OMOP CDM is not supposed to store negative information therefore you need to add concepts 3 and 9-31 as pre-coordinated pairs of criteria + positive answer, e.g.: Bulbar lower motor neuron clinical indicator: yes In this case, the concept_class_id would be a ‘Precoordinated pair’. Also, you should adjust concept names as follows to make them more specific: El Escorial criteria - revised: Left lower extremity upper motor neuron clinical indicator El Escorial criteria - revised: Bulbar lower motor neuron clinical indicator Please, note that when we add concepts to OMOP Extension, we assign them specific OMOP-generated concept codes. You should map your raw source codes to the new standard concepts to use them. So, you can let the concept_code field empty. Best, Masha

…

________________________________ From: dicorey4 ***@***.***<mailto:***@***.***>> Sent: Friday, December 20, 2024 18:19 To: OHDSI/Vocabulary-v5.0 ***@***.***<mailto:***@***.***>> Cc: Maria Khitrun ***@***.***<mailto:***@***.***>>; Assign ***@***.***<mailto:***@***.***>> Subject: Re: [OHDSI/Vocabulary-v5.0] El Escorial criteria for ALS (Issue #1082) I have added the template1 with our new additions here: https://drive.google.com/drive/u/0/folders/1m6_kutvbpfqzGtGqegcg8nDBO9a5_XDd Some explanation: in the concept_manual tab - rows 4-8 are answers to row3 and represents the categorization of someone with ALS. Rows 32-34 are answers to rows 9-31. We are not sure if new terminology should be created so they are associated with only the criteria and indicator variables or if existing LOINC codes should be used. This is our first terminology submission, so please let me know if you need anything else or if I failed to fill something out properly. — Reply to this email directly, view it on GitHub<#1082 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXY5773LX5YZK5O2DIDRMK32GQ7SHAVCNFSM6AAAAABTQATRJSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNJXGMYDONRQG4>. You are receiving this because you were assigned.Message ID: ***@***.***<mailto:***@***.***>> — Reply to this email directly, view it on GitHub<#1082 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BNU57YCSZDRXFT3WQXPGK6D2GRIFJAVCNFSM6AAAAABTQATRJSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNJXGQZTKOJZG4>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[m-khitrun]

Hi Diane,

If you complete your contribution by Jan 10th, it will work. Otherwise, we can move it to the next release.
If you need any help, please feel free to reach out to me by email.

Masha