AlanSimmons
commented
3 months ago Basic query
// Obtain identifiers for rule-based datasets.
CALL
{
MATCH (p:Concept)<-[:isa]-(pRBD:Concept)-[:CODE]->(cRBD:Code)-[r:PT]->(tRBD:Term)
WHERE p.CUI = 'HUBMAP:C000004 CUI'
AND r.CUI=pRBD.CUI
RETURN pRBD.CUI AS CUIRBD,cRBD.CodeID AS CodeRBD,tRBD.name AS NameRBD
ORDER BY pRBD.CUI
}
// assaytype
CALL
{
WITH CUIRBD
MATCH (pRBD:Concept)-[:has_assaytype]->(passaytype:Concept)-[:PREF_TERM]->(tassaytype:Term)
WHERE pRBD.CUI=CUIRBD
RETURN REPLACE(tassaytype.name,'_assaytype','') AS assaytype
}
// dir-schema
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_dir_schema]->(pdir_schema:Concept)-[:PREF_TERM]->(tdir_schema:Term)
WHERE pRBD.CUI=CUIRBD
RETURN tdir_schema.name AS dir_schema
}
// tbl-schema
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_tbl_schema]->(ptbl_schema:Concept)-[:PREF_TERM]->(ttbl_schema:Term)
WHERE pRBD.CUI=CUIRBD
RETURN ttbl_schema.name AS tbl_schema
}
// vitessce_hints
// Strip the optional suffix '_vitessce_hint' from terms such as 'rna_vitessce_hint'.
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_vitessce_hint]->(pvitessce_hint:Concept)-[:PREF_TERM]->(tvitessce_hint:Term)
WHERE pRBD.CUI=CUIRBD
RETURN COLLECT(REPLACE(tvitessce_hint.name,'_vitessce_hint','')) AS vitessce_hints
}
// is_primary
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_process_state]->(pdsProcess:Concept)-[:isa]->(pProcessParent:Concept)
WHERE pRBD.CUI=CUIRBD
AND pProcessParent.CUI = 'HUBMAP:C004002 CUI'
RETURN CASE WHEN pdsProcess.CUI='HUBMAP:C004003 CUI' THEN true else false END AS is_primary
}
// dataset_type
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_dataset_type]->(pdataset_type:Concept)-[:PREF_TERM]->(tdataset_type:Term)
WHERE pRBD.CUI=CUIRBD
RETURN tdataset_type.name AS dataset_type, pdataset_type.CUI AS CUIDatasetType
}
// Pipeline Decision Rules category
CALL
{
WITH CUIDatasetType
OPTIONAL MATCH (pDatasetType:Concept)-[:has_pdr_category]->(pPDRCategory:Concept)-[:PREF_TERM]->(tPDRCategory:Term)
WHERE pDatasetType.CUI=CUIDatasetType
RETURN tPDRCategory.name AS pdr_category
}
// Fig 2 aggregated assay type
CALL
{
WITH CUIDatasetType
OPTIONAL MATCH (pDatasetType:Concept)-[:has_fig2_agg_assay_type]->(pFig2agg:Concept)-[:PREF_TERM]->(tFig2agg:Term)
WHERE pDatasetType.CUI=CUIDatasetType
RETURN tFig2agg.name AS fig2_aggregated_assaytype
}
// Fig2 modality
CALL
{
WITH CUIDatasetType
OPTIONAL MATCH (pDatasetType:Concept)-[:has_fig2_modality]->(pFig2modality:Concept)-[:PREF_TERM]->(tFig2modality:Term)
WHERE pDatasetType.CUI=CUIDatasetType
RETURN tFig2modality.name AS fig2_modality
}
// Fig2 category
CALL
{
WITH CUIDatasetType
OPTIONAL MATCH (pDatasetType:Concept)-[:has_fig2_category]->(pFig2category:Concept)-[:PREF_TERM]->(tFig2category:Term)
WHERE pDatasetType.CUI=CUIDatasetType
RETURN tFig2category.name AS fig2_category
}
// description
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_description]->(pdescription:Concept)-[:PREF_TERM]->(tdescription:Term)
WHERE pRBD.CUI=CUIRBD
RETURN REPLACE(tdescription.name,'_description','') AS description
}
// pipeline-shorthand
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_pipeline_shorthand]->(pshorthand:Concept)-[:PREF_TERM]->(tshorthand:Term)
WHERE pRBD.CUI=CUIRBD
RETURN tshorthand.name AS pipeline_shorthand
}
// is multi-assay
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:isa]->(pMulti:Concept)
WHERE pRBD.CUI=CUIRBD
AND pMulti.CUI = 'HUBMAP:C004033 CUI'
RETURN CASE WHEN pMulti.CUI IS NOT NULL THEN True ELSE False END AS is_multiassay
}
// must_contain
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:must_contain]->(pDT:Concept)-[:PREF_TERM]->(tDT:Term)
WHERE pRBD.CUI=CUIRBD
RETURN COLLECT(tDT.name) AS must_contain
}
// measurement assay CUI
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_measurement_assay]->(pMeas:Concept)
WHERE pRBD.CUI=CUIRBD
RETURN pMeas.CUI as CUIMeas
}
// Optional measurement codes
CALL
{
WITH CUIMeas
MATCH (pMeas:Concept)-[:CODE]->(cMeas:Code)-[:PT]->(tMeas:Term)
WHERE pMeas.CUI = CUIMeas
RETURN COLLECT(DISTINCT {code:cMeas.CodeID,term:tMeas.name}) AS MeasCodes
}
// whether the measurement assay contains full_genetic_sequencesi
CALL
{
WITH CUIMeas
OPTIONAL MATCH (pRBD:Concept)-[:contains]->(ppii:Concept)
WHERE pRBD.CUI=CUIMeas
AND ppii.CUI = 'HUBMAP:C004009 CUI'
RETURN CASE WHEN NOT ppii.CUI IS null THEN true ELSE false END AS contains_full_genetic_sequences
}
// provider
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_provider]->(pProvider:Concept)-[:PREF_TERM]->(tProvider:Term)
WHERE pRBD.CUI=CUIRBD
RETURN tProvider.name AS provider
}
// active status
CALL
{
WITH CUIRBD
OPTIONAL MATCH (pRBD:Concept)-[:has_active_status]->(pStatus:Concept)-[:PREF_TERM]->(tStatus:Term)
WHERE pRBD.CUI=CUIRBD
RETURN tStatus.name AS active_status
}
CALL
{
WITH CodeRBD, NameRBD, assaytype, dir_schema, tbl_schema, vitessce_hints,is_primary,pipeline_shorthand,description,dataset_type,pdr_category,fig2_aggregated_assaytype,fig2_modality,fig2_category,is_multiassay,must_contain,MeasCodes,contains_full_genetic_sequences,provider,active_status
RETURN
{
rule_description:
{ code:CodeRBD,name:NameRBD
},
value:
{
assaytype:assaytype, dir_schema:dir_schema, tbl_schema:tbl_schema, vitessce_hints:vitessce_hints, primary:is_primary,
pipeline_shorthand:pipeline_shorthand, description:description,
is_multiassay:is_multiassay, must_contain:must_contain,
provider:provider,
active_status:active_status,
dataset_type:
{
dataset_type:dataset_type, PDR_category:pdr_category,
fig2:
{
aggregated_assaytype:fig2_aggregated_assaytype, modality:fig2_modality, category:fig2_category
}
},
measurement_assay:{
codes:MeasCodes,
contains_full_genetic_sequences:contains_full_genetic_sequences
}
}
} AS rule_based_dataset
}
WITH rule_based_dataset
RETURN rule_based_dataset```
To do
Deprecate the following endpoints:
Create new endpoints that return information from the new UBKG model for rule-based datasets. The endpoints will replicate the testing_rules_chain.json.
Reference
https://github.com/x-atlas-consortia/ubkg-etl/issues/148