There is an option to include non-standard concepts in Usagi:
Including non-standard concepts in the STCM table (does anyone already do this?) would add an extra step but seems doable, given the self-referencing relationships that exist in the concept_relationship table (i.e. x maps to x).
Something along the lines of:
INSERT INTO [observation]
(
...
,[observation_concept_id]
,[value_as_concept_id]
...
)
SELECT
...
,obs_concepts.concept_id_2
,value_concepts.concept_id_2
....
FROM
(
...
) source_data
INNER JOIN source_to_concept_map stcm
ON source_data.code = stcm.source_code
INNER JOIN
(
SELECT concept_id_1, concept_id_2
FROM concept_relationship cr
INNER JOIN concept c
ON cr.concept_id_2 = c.concept_id
WHERE cr.relationship_id = 'Maps to'
and c.domain_id = 'Observation'
and c.standard_concept = 'S'
) obs_concepts
ON stcm.target_concept_id = obs_concepts.concept_id_1
LEFT OUTER JOIN
(
SELECT concept_id_1, concept_id_2
FROM concept_relationship cr
INNER JOIN concept c
ON cr.concept_id_2 = c.concept_id
WHERE cr.relationship_id = 'Maps to value'
) value_concepts
ON stcm.target_concept_id = value_concepts.concept_id_1
Anyway, as @schuemie has advocated above, it would benefit us in the long term to be consistent and choose a single method to represent the data.
