ALS TDI OMOP Data Set

Release notes: version 0.2.0, 2026 refresh

The ALS TDI ARC Study mapped to the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM). This release restructures the ARC Natural History Study into OMOP CDM v5.4 and maps it to standardized vocabularies.

Version 0.2.0 is the first release to include linked electronic health record laboratory data alongside the self-reported registry surveys and central-laboratory results that made up version 0.1.0.

This is part of a larger harmonization effort with Answer ALS and the Critical Path Institute.

EHR data is produced by Registry Forge ALS

The EHR component of this release is built with Registry Forge ALS, ALS TDI's open-source pipeline for turning raw C-CDA and FHIR exports into research-ready, OMOP-mapped data.

Project site and documentation: alstdi.github.io/RegistryForgeALS

Preprint: Boyce D, et al. Registry Forge: an open-source pipeline for transforming patient-mediated electronic health record exports into research-ready OMOP data. medRxiv 2026.06.02.26354637. https://doi.org/10.1101/2026.06.02.26354637

At a glance


Release	0.2.0, 2026 refresh
CDM version	OMOP CDM v5.4, full column set on every table (reference)
Vocabulary	Athena OMOP Standardized Vocabularies v5.0, release 27-FEB-2026
Participants	708 — the ARC participants with linked biological samples, drawn from a registry of 2,014
Data types	Self-reported surveys, ALSFRS-R, central-laboratory blood chemistry and haematology, self-reported ALS gene results, linked EHR laboratory results, mortality
Access	ARC Data Commons, at no cost to academic and nonprofit researchers under a Data Use Agreement
Portal	Neuromine Data Portal

Citation: ALS Therapy Development Institute (ALS TDI). (2023). ALS Research Collaborative (ARC) [Data set]. ALS Therapy Development Institute. https://doi.org/10.71944/C3NA-9124

For background on the ARC resource itself, see the preprint Boyce et al., The ALS Research Collaborative: A Long Running Multimodal ALS Natural History Resource.

What changed since version 0.1.0

	Version 0.1.0	Version 0.2.0
Vocabulary edition	Athena v5.0, 30-AUG-2024	Athena v5.0, 27-FEB-2026
EHR data	Not included	EHR laboratory results for 47 participants, on the registry analyte concepts
ALS diagnosis and El Escorial certainty	One row per surveyed instance	One row per participant, resolved to the current recorded status
Anatomical site of symptom onset	Repeated across follow-up rounds	One row per site per participant
Personal medical history (conditions)	Round 1 only	Affirmatives from all four survey rounds, dated to first report
Self-reported medications	Full list repeated at every submission	Deduplicated, one row per distinct medication record
Visit linkage	Partial	Every measurement and observation row resolves to a visit
Units	Source labels carried verbatim, unit concepts unmapped	Corrected unit labels and mapped unit concepts
ALS gene concepts	Not resolvable against the bundled vocabulary	Resolvable — the 2026 edition adds OMOP Genomic

No new survey instruments or measurement analytes were added; see the 2026 Data Refresh page for details and known limitations.

Replace any earlier extract with this release

Diagnosis, El Escorial certainty and onset site now resolve to a single current value per participant, and measurements, medications and visit structure all differ. Version 0.1.0 reports different values. Replace it rather than pooling the two.

Participant summary

Participants fall into three groups, identified by the prefix on person.person_source_value:

Prefix	Group	Participants
`CASE_`	People with ALS	604
`ASYMP_`	Asymptomatic carriers of an ALS-linked variant	48
`CONTROL_`	Healthy controls	56

The trailing integer of person_source_value is the ARC subject identifier — the supported route from a CDM row back to a participant. It is deliberately not carried as a column inside the CDM tables. Not all participants answered all surveys; controls and asymptomatic carriers generally have fewer records than people with ALS.

Table counts

Table	Rows
person	708
observation	230,364
measurement	73,459
visit_occurrence	22,969
condition_occurrence	606
drug_exposure	3,142
observation_period	698
death	268
care_site	2

Other OMOP domains, including procedure_occurrence, are not populated.

Telling EHR rows from registry rows

Use the standard type concepts:

`*_type_concept_id`	Meaning
`32817`	EHR
`32856`	Central-laboratory blood draw
`32862`	Participant self-report, including ALSFRS-R and gene results
`32879`	Registry-derived observation period

EHR-derived visits additionally carry care_site_id 21; all registry-side visits carry 20.

Domain mappings

person

year_of_birth, sex, race and ethnicity, with sequential person_id and the group prefix retained on person_source_value. Unknown, multiple or unselected race, ethnicity or sex maps to concept_id = 0.

Reading ethnicity_concept_id in this data set

A participant who selects Hispanic or Latino receives 38003563. Everyone else receives 0. The concept for "Not Hispanic or Latino" is deliberately not used, because the instrument asks a single combined race question — a participant who did not select Hispanic or Latino has not asserted that they are not Hispanic. Treat 0 as unknown, not as non-Hispanic, in any network study that expects standard ethnicity coding.

observation

observation_type_concept_id = 32862 on all rows. Every row links to a visit.

Content	Concept	Notes
ALSFRS-R, 12 items plus total score	`42529071`–`42529084`	`value_as_number` carries the score; one row per item per assessment
ALS diagnosis and El Escorial certainty	`2000000061`	Custom concept, one row per participant
Anatomical site of symptom onset	`2000000396`	Custom concept, one row per site
Family medical history	`4167217` plus per-condition standard concepts	One row per reported condition, per relative
Personal medical history	Per-condition standard concepts	One row per participant per condition, from all survey rounds
History of head or neck injury	`1340204`	Screening question only
Lifestyle, tobacco use	`3012697`	Lifetime-history flag only
Military service	`37162399`	Flag
Occupational industry	`36204389`	One row per reported industry

observation_date is the survey or assessment date (conditions: the date of the round that first reported the condition). value_source_value preserves the raw response verbatim.

El Escorial criteria — harmonized with Answer ALS and the Critical Path Institute; self-reported, then validated by ALS TDI staff. Custom concepts: Definite 2000000057, Possible 2000000058, Probable 2000000059, Probable laboratory-supported 2000000060 (defined but unpopulated), Suspected 2000000062.

Anatomical site of symptom onset — fine anatomy rolls up (hand becomes arm, foot becomes leg); the verbatim site is always in value_source_value. Left arm 4215746, right arm 4286959, left leg 4136825, right leg 4268743; bulbar and other sites map to 0 because no suitable standard concept was identified — read value_source_value to recover the site.

measurement

Three sources, partitioned by measurement_type_concept_id:

Central-laboratory blood draws (32856) — 35 analytes covering a comprehensive metabolic panel and complete blood count with differential: A/G Ratio, Albumin, Alkaline Phosphatase, Basophils and Basophils Abs, Bilirubin Total, BUN, BUN/Creatinine Ratio, Calcium, Chloride, CO2, Creatinine, EGFR, Eosinophils and Eosinophils Abs, Globulin, Glucose, Hematocrit, Hemoglobin, Lymphocytes and Lymphocytes Abs, MCH, Monocytes and Monocytes Abs, Neutrophils and Neutrophils Abs, Platelet Count, Potassium, RDW, Red Blood Cell Count, SGOT (AST), SGPT (ALT), Sodium, Total Protein, White Blood Cell Count. Seven further analytes are present in the source but not mapped, matching version 0.1.0: MCV, MCHC, Mean Platelet Volume, IMM Grans and IMM Grans Abs, Nucleated RBC and Nucleated RBC Abs.

EHR laboratory results (32817) — restricted to the same 35 analytes and mapped onto the same registry concepts, with the original LOINC code preserved in measurement_source_value. Deduplicated; the only rows with measurement_datetime populated. Join registry and EHR laboratory data directly on measurement_concept_id.

Self-reported ALS-linked gene results (32862) — C9orf72, SOD1, TARDBP, FUS, NEK1, PFN1, SPG11 and VCP, one row per participant per gene, on OMOP Genomic concepts (2026 vocabulary edition or later required).

drug_exposure

Self-reported medications; supplements are not included. drug_concept_id comes from an ingredient-level lookup, and every released row is mapped to a standard concept. Dosage is not calculated; source values are retained. Missing start dates use the placeholder 1900-01-01; a missing end date reuses the start date. The source re-exports each participant's full list at every survey submission, so this release deduplicates on participant, ingredient, drug name, reference drug, dates, form, dosage and frequency — medication counts are not comparable with version 0.1.0.

condition_occurrence

The participant's ALS diagnosis only, condition_concept_id = 373182, one row per participant. condition_source_value records the self-reported diagnosis status.

visit_occurrence

Five visit classes: survey submissions, ALSFRS-R self-assessments, participant-data submissions, central-laboratory blood draws, and EHR laboratory extract dates. Registry survey-derived visits carry visit_concept_id = 38004259 ("Research Clinic/Center"); laboratory visits carry 32036. EHR-derived visits are date-based extract visits (one per participant per date), not reconstructions of source encounters, and carry care_site_id 21.

death

One row per deceased participant. death_date is set to 31 December of the year of death, so that no day or month of death is disclosed, and is capped at the extraction date. Nine rows carry the placeholder 1900-01-01 — a death with an unknown date, not an event in 1900.

Dates and timing

Dates may be shifted for de-identification, following Hripcsak et al., JAMIA 2016.
Where a date is missing, the survey date is used if available, otherwise an approximate date, otherwise the placeholder 1900-01-01.
observation_period spans each participant's earliest to latest recorded event date, deliberately including retrospective self-reported dates such as symptom onset. Death dates are year-imputed and excluded from the calculation, so a period may end before a recorded death date. See the 2026 Data Refresh page before using it for person-time.
Registry dates are written in US format; EHR dates are ISO 8601. Parse the two explicitly if you combine them.

Custom concepts

ALS-specific variables with no standardized OMOP vocabulary use local concepts above 2,000,000,000: 2000000061 (El Escorial question), 2000000057–2000000060 and 2000000062 (El Escorial statuses), 2000000396 (onset-site question).

Custom concepts do not exist in Athena

These are local by design and appear in no Athena release. Load the supplied local concept definitions alongside your Athena tables, or handle the range above 2,000,000,000 explicitly.

Guidance for data use

Read *_source_value and *_source_concept_id to trace any row back to the original survey response or EHR code.
Explore concept definitions with OHDSI Athena; use the 27-FEB-2026 release or later.
Recover the ARC subject identifier from the trailing integer of person.person_source_value.
Distinguish EHR from registry rows using *_type_concept_id.
Join registry and EHR laboratory data on measurement_concept_id; the EHR rows' LOINC detail is in measurement_source_value.
Treat ethnicity_concept_id = 0 as unknown, not as non-Hispanic.
Do not compare medication row counts against version 0.1.0, and replace any pre-2026 extract with this release rather than pooling.

Detailed ETL documentation, the person-level accounting of which participants are included, and the data quality results are available to data recipients on request.

Surveys mapped in this release

The ARC study fields far more instruments than this release maps; the OMOP release deliberately keeps the version 0.1.0 content footprint so the two remain comparable.

Mapped: enrollment and general information, Your ALS Experience, New Enrollee Survey, Family History, Medical History Conditions rounds 1–4, Medical History Injuries round 1, Lifestyle round 1 tobacco flag, Occupation round 1 (military service and occupational industry), ALSFRS-R, medications, blood draw results, gene results, mortality.

Collected by ARC but not mapped in this release: education, marital status, employment status, smoking sub-detail, current smoking status from follow-up rounds, physical activity, hospitalization and emergency visits, clinical trial participation, geography and residential history, diet, supplements, anthropometrics, handedness and footedness, military deployment arenas, age at diagnosis, ALS complications, free-text "other" write-in fields, the swallowing, speech, bladder and bowel symptom items, and follow-up rounds 2–4 of the lifestyle and occupation modules. These are available through ARC Data Commons outside the OMOP release; see the ARC preprint and the data dictionary for the complete picture.

Caution

These data are participant self-report plus central-laboratory results plus patient-mediated EHR laboratory extracts. They are not a clinician-adjudicated chart review, and condition_occurrence carries the participant's own account of their ALS diagnosis status.
Treat ethnicity_concept_id = 0 as unknown, not as non-Hispanic.
Diagnosis, El Escorial certainty and onset site resolve differently than in version 0.1.0. Replace earlier extracts rather than pooling.

Problems with the data, or questions about a specific row: dboyce@als.net.

For full OMOP domain details, see the OMOP CDM v5.4 Reference Guide.