diff --git a/macros/dumps_data_condition.sql b/macros/dumps_data_condition.sql
index dc54245ee46cf4fad584e4b1fa2d6859b1c7aaae..42aa62b90b05725ba02898e3952d64127c60f14b 100644
--- a/macros/dumps_data_condition.sql
+++ b/macros/dumps_data_condition.sql
@@ -1,4 +1,4 @@
--- This macro filters data showed in SQL dumps
+-- This macro filters data showed in the ChEBI Data products: SQL DUMPS, Ontology, TSV Files
-- It receives two table aliases: compound_table alias which as an alias for the compounds table
-- And table_name alias which is an alias for a table you want to filter (structure, chemical_data, etc)
{% macro dumps_data_condition(table_name_alias, compounds_table_alias='c') -%}
diff --git a/macros/ontology_data_condition.sql b/macros/ontology_data_condition.sql
deleted file mode 100644
index e8425c989da378888e0680e632d59bc0b3fa76e8..0000000000000000000000000000000000000000
--- a/macros/ontology_data_condition.sql
+++ /dev/null
@@ -1,4 +0,0 @@
--- This macro filters data showed in the ontology. Ontology includes compound with 1,2 and 3 stars.
-{% macro ontology_data_condition(table_name_alias, compounds_table_alias='c') -%}
- ({{- compounds_table_alias -}}.stars IN (1, 2, 3) AND {{ table_name_alias -}}.status_id IN (1, 3, 9, 7))
-{%- endmacro %}
\ No newline at end of file
diff --git a/models/chebi_allstar/properties.yml b/models/chebi_allstar/properties.yml
index dbefa999f9ee8ebbcacfac019fbf170bf20257c8..6268090a41f6545dc714cec47d9322213a88825b 100644
--- a/models/chebi_allstar/properties.yml
+++ b/models/chebi_allstar/properties.yml
@@ -293,7 +293,31 @@ models:
data_type: text
constraints:
- type: not_null
-
+
+ # relation_type table
+ - name: relation_type
+ description: Relation types can have an entity
+ config:
+ contract:
+ enforced: true
+ columns:
+ - name: id
+ data_type: bigint
+ constraints:
+ - type: not_null
+ - type: primary_key
+ - type: check
+ expression: "id > 0"
+ - name: code
+ data_type: varchar
+ constraints:
+ - type: not_null
+ - name: allow_cycles
+ data_type: bool
+ constraints:
+ - type: not_null
+ - name: description
+ data_type: varchar
# relation table
- name: relation
@@ -313,6 +337,8 @@ models:
data_type: bigint
constraints:
- type: not_null
+ - type: foreign_key
+ expression: "chebi_allstar.relation_type(id)"
- name: init_id
data_type: bigint
constraints:
diff --git a/models/chebi_allstar/relation.sql b/models/chebi_allstar/relation.sql
index d332172ea4166961c0e4e2600caecf081b3d6fd9..a8f4174d29d8c6d81a535fdbcd14e2218a7a0c24 100644
--- a/models/chebi_allstar/relation.sql
+++ b/models/chebi_allstar/relation.sql
@@ -7,11 +7,11 @@ WITH relation AS (
r.status_id,
r.evidence_dbaccid
FROM {{ source('chebi_production', 'relation') }} AS r
+ INNER JOIN {{ source('chebi_production', 'relation_type') }} AS rt ON rt.id = r.relation_type_id
INNER JOIN (SELECT id, stars FROM {{ ref('compounds') }}) AS c ON r.init_id = c.id
INNER JOIN (SELECT id, stars FROM {{ ref('compounds') }}) AS c2 ON r.final_id = c2.id
WHERE
- {{ dumps_data_condition('r') }}
- OR {{ dumps_data_condition('r', 'c2') }}
+ r.status_id IN (SELECT s.id FROM {{ ref('status') }} AS s)
)
SELECT * FROM relation
diff --git a/models/chebi_allstar/relation_type.sql b/models/chebi_allstar/relation_type.sql
new file mode 100644
index 0000000000000000000000000000000000000000..cb01c45f662502825542e2dc5a078daf66b8a21d
--- /dev/null
+++ b/models/chebi_allstar/relation_type.sql
@@ -0,0 +1,10 @@
+WITH cte_relation_type AS (
+ SELECT
+ rt.id,
+ rt.code,
+ rt.allow_cycles,
+ rt.description
+ FROM {{ source('chebi_production', 'relation_type') }} AS rt
+)
+
+SELECT * FROM cte_relation_type
diff --git a/models/chebi_ontology/axioms_exact_synonyms.sql b/models/chebi_ontology/axioms_exact_synonyms.sql
index 62482746be14bb012768c0f4ed7c6837f2a6e726..5783e2a9f12ea7f70c76ccebc08f4a0fec4a5df6 100644
--- a/models/chebi_ontology/axioms_exact_synonyms.sql
+++ b/models/chebi_ontology/axioms_exact_synonyms.sql
@@ -18,12 +18,11 @@ WITH cte_exact_synonym_disperse AS (
n.name,
s.name AS axiom,
CONCAT('chebi', ':', REPLACE(n."type", ' ', '_')) AS axiom_type -- convert IUPAC NAME TO IUPAC_NAME
- FROM {{ source('chebi_production', 'compounds') }} AS c
- INNER JOIN {{ source('chebi_production', 'names') }} AS n ON c.id = n.compound_id
- INNER JOIN {{ source('chebi_production', 'source') }} AS s ON n.source_id = s.id
+ FROM {{ ref('compounds') }} AS c
+ INNER JOIN {{ ref('names') }} AS n ON c.id = n.compound_id
+ INNER JOIN {{ ref('source') }} AS s ON n.source_id = s.id
WHERE
n."type" = 'IUPAC NAME'
- AND ({{ ontology_data_condition('n') }})
AND c.parent_id IS NULL
UNION
SELECT
@@ -35,13 +34,12 @@ WITH cte_exact_synonym_disperse AS (
CASE
WHEN n."type" = 'IUPAC NAME' THEN CONCAT('chebi', ':', REPLACE(n."type", ' ', '_'))
END AS axiom_type -- convert IUPAC NAME TO IUPAC_NAME
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c2 ON c.id = c2.parent_id
- INNER JOIN {{ source('chebi_production', 'names') }} AS n ON c2.id = n.compound_id
- INNER JOIN {{ source('chebi_production', 'source') }} AS s ON n.source_id = s.id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('compounds') }} AS c2 ON c.id = c2.parent_id
+ INNER JOIN {{ ref('names') }} AS n ON c2.id = n.compound_id
+ INNER JOIN {{ ref('source') }} AS s ON n.source_id = s.id
WHERE
- LOWER(n.ascii_name) IN (SELECT LOWER(n.ascii_name) FROM {{ source('chebi_production', 'names') }} AS n WHERE n."type" = 'IUPAC NAME')
- AND ({{ ontology_data_condition('n') }})
+ LOWER(n.ascii_name) IN (SELECT LOWER(n.ascii_name) FROM {{ ref('names') }} AS n WHERE n."type" = 'IUPAC NAME')
AND c.parent_id IS NULL
),
diff --git a/models/chebi_ontology/axioms_related_synonyms.sql b/models/chebi_ontology/axioms_related_synonyms.sql
index 7a673aa3a380d8e1245bbe1429c7630bd4683dba..99be361e9cf98f2fd5ca88d2cf500798002816cd 100644
--- a/models/chebi_ontology/axioms_related_synonyms.sql
+++ b/models/chebi_ontology/axioms_related_synonyms.sql
@@ -20,13 +20,12 @@ WITH cte_related_synonym_disperse AS (
WHEN n."type" = 'BRAND NAME' THEN CONCAT('chebi', ':', REPLACE(n."type", ' ', '_'))
WHEN n."type" = 'INN' THEN CONCAT('chebi', ':', n."type")
END AS axiom_type
- FROM {{ source('chebi_production', 'compounds') }} AS c
- INNER JOIN {{ source('chebi_production', 'names') }} AS n ON c.id = n.compound_id
- INNER JOIN {{ source('chebi_production', 'source') }} AS s ON n.source_id = s.id
+ FROM {{ ref('compounds') }} AS c
+ INNER JOIN {{ ref('names') }} AS n ON c.id = n.compound_id
+ INNER JOIN {{ ref('source') }} AS s ON n.source_id = s.id
LEFT JOIN {{ ref('axioms_exact_synonyms') }} AS es ON n.ascii_name = es.ascii_name
WHERE
- ({{ ontology_data_condition('n') }})
- AND es.ascii_name IS NULL
+ es.ascii_name IS NULL
AND c.parent_id IS NULL
UNION
SELECT
@@ -40,14 +39,13 @@ WITH cte_related_synonym_disperse AS (
WHEN n."type" = 'BRAND NAME' THEN CONCAT('chebi', ':', REPLACE(n."type", ' ', '_'))
WHEN n."type" = 'INN' THEN CONCAT('chebi', ':', n."type")
END AS axiom_type
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c2 ON c.id = c2.parent_id
- INNER JOIN {{ source('chebi_production', 'names') }} AS n ON c2.id = n.compound_id
- INNER JOIN {{ source('chebi_production', 'source') }} AS s ON n.source_id = s.id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('compounds') }} AS c2 ON c.id = c2.parent_id
+ INNER JOIN {{ ref('names') }} AS n ON c2.id = n.compound_id
+ INNER JOIN {{ ref('source') }} AS s ON n.source_id = s.id
LEFT JOIN {{ ref('axioms_exact_synonyms') }} AS es ON n.ascii_name = es.ascii_name
WHERE
- ({{ ontology_data_condition('n') }})
- AND es.ascii_name IS NULL
+ es.ascii_name IS NULL
AND c.parent_id IS NULL
),
diff --git a/models/chebi_ontology/compound_base_information.sql b/models/chebi_ontology/compound_base_information.sql
index 50ad421e939796c92746976325f9f35d653198e1..e3f70256ef830ad0f4d0e0cff80a9adfb29001a7 100644
--- a/models/chebi_ontology/compound_base_information.sql
+++ b/models/chebi_ontology/compound_base_information.sql
@@ -3,8 +3,8 @@ WITH cte_alternative_ids AS (
SELECT
c.id, --parent_id
STRING_AGG(c2.chebi_accession, '|') AS alternative_ids --children ids
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c2 ON c.id = c2.parent_id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('compounds') }} AS c2 ON c.id = c2.parent_id
GROUP BY c.id
),
@@ -73,7 +73,7 @@ SELECT DISTINCT
rs.related_synonym,
c.stars AS star_id,
'chebi:' || c.stars || '_STAR' AS stars
-FROM {{ source('chebi_production', 'compounds') }} AS c
+FROM {{ ref('compounds') }} AS c
INNER JOIN {{ ref('valid_relations') }} AS cr ON c.id = cr.compound_id
LEFT JOIN {{ ref('valid_chemical_data') }} AS cd ON c.id = cd.compound_id
LEFT JOIN {{ ref('valid_structures') }} AS s ON c.id = s.compound_id
diff --git a/models/chebi_ontology/deprecated_compounds.sql b/models/chebi_ontology/deprecated_compounds.sql
index 677fe9cd766781709ecbc82e0eaeae1e2c83bbb8..adf9e4911ec80ff70a3b103a4bcbe6bd41b25be0 100644
--- a/models/chebi_ontology/deprecated_compounds.sql
+++ b/models/chebi_ontology/deprecated_compounds.sql
@@ -1,49 +1,35 @@
--- There are two kind of deprecated compounds:
-- 1. Deprecated because of a merging process. Basically, when a compound c0 is merged with a compound C1, the field parent_id
-- in the c0 compound is populated with the id of C1.
--- 2. Deprecated because of a deleted compound
-
WITH cte_deprecated_for_merging AS (
SELECT
c.id AS compound_id,
c.chebi_accession AS curie,
+ c.stars,
+ c.status_id,
'owl:Class' AS property_type,
1 AS is_deprecated,
- CONCAT('CHEBI:', c.parent_id) AS terms_merged_with,
- 'obo:IAO_0000227' AS terms_merged_definition,
- -- This is a curie to describe the merged process: https://ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000227
- NULL AS namespace,
- NULL AS object_property
- FROM {{ source('chebi_production', 'compounds') }} AS c
+ CASE
+ WHEN c.id NOT IN (27189) THEN CONCAT('CHEBI:', c.parent_id)
+ END AS terms_merged_with,
+ CASE
+ -- This is a curie to describe the merged process: https://ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000227
+ WHEN c.id NOT IN (27189) THEN 'obo:IAO_0000227'
+ END AS terms_merged_definition,
+ CASE
+ WHEN c.id NOT IN (27189) THEN NULL
+ ELSE 'chebi_ontology'
+ END AS namespace,
+ CASE
+ WHEN c.id NOT IN (27189) THEN NULL
+ ELSE c.chebi_accession
+ END AS object_property
+ FROM {{ ref('compounds') }} AS c
WHERE
c.parent_id IS NOT NULL
- AND c.stars > 0
-),
-
-cte_deprecated_for_deleted AS (
- SELECT
- c.id AS compound_id,
- c.chebi_accession AS curie,
- 'owl:Class' AS property_type,
- 1 AS is_deprecated,
- NULL AS terms_merged_with,
- NULL AS terms_merged_definition,
- 'chebi_ontology' AS namespace,
- c.chebi_accession AS object_property
- FROM {{ source('chebi_production', 'compounds') }} AS c
- WHERE (
- (c.status_id = 2 AND c.stars IN (1, 2, 3)) -- Status 2 = Deleted
- OR c.id = 27189
- ) -- We must include the 'unclassified' definition, CHEBI:27189
-),
-
-cte_deprecated_compounds AS (
- SELECT * FROM cte_deprecated_for_merging
- UNION
- SELECT * FROM cte_deprecated_for_deleted
+ OR c.id = 27189 -- We must include the 'unclassified' definition, CHEBI:27189
)
SELECT
ROW_NUMBER() OVER (ORDER BY cdc.compound_id) AS id,
cdc.*
-FROM cte_deprecated_compounds AS cdc
+FROM cte_deprecated_for_merging AS cdc;
diff --git a/models/chebi_ontology/valid_chemical_data.sql b/models/chebi_ontology/valid_chemical_data.sql
index 468417b1221345e015c73897d4c37af9faa762e5..a0ed9c47a0d1ecb58260143109c8e1560f4f32e4 100644
--- a/models/chebi_ontology/valid_chemical_data.sql
+++ b/models/chebi_ontology/valid_chemical_data.sql
@@ -9,11 +9,10 @@ WITH cte_chemical_data_parents AS (
cd.charge::text,
cd.mass::text,
cd.monoisotopic_mass::text
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'chemical_data') }} AS cd ON c.id = cd.compound_id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('chemical_data') }} AS cd ON c.id = cd.compound_id
WHERE
- {{ ontology_data_condition('cd') }}
- AND c.parent_id IS NULL
+ c.parent_id IS NULL
--AND c.id IN (41981, 27427)
),
@@ -25,13 +24,10 @@ cte_chemical_data_children AS (
STRING_AGG(DISTINCT cd.charge::text, ';') AS charge,
STRING_AGG(DISTINCT cd.mass::text, ';') AS mass,
STRING_AGG(DISTINCT cd.monoisotopic_mass::text, ';') AS monoisotopic_mass
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c2 ON c.id = c2.parent_id
- LEFT JOIN {{ source('chebi_production', 'chemical_data') }} AS cd
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('compounds') }} AS c2 ON c.id = c2.parent_id
+ LEFT JOIN {{ ref('chemical_data') }} AS cd
ON c2.id = cd.compound_id
- WHERE
- {{ ontology_data_condition('cd') }}
- --AND c.id IN (41981, 27427)
GROUP BY c.id
),
diff --git a/models/chebi_ontology/valid_database_references.sql b/models/chebi_ontology/valid_database_references.sql
index 6ce885307450e5ac2791056ab77ddbdc46cce335..f66fc4ccd8751cb4a2ebc077672f4e4f516a099f 100644
--- a/models/chebi_ontology/valid_database_references.sql
+++ b/models/chebi_ontology/valid_database_references.sql
@@ -14,12 +14,11 @@ WITH cte_database_references_disperse AS (
END AS prefix,
sr.name AS source_name,
da.source_id
- FROM {{ source('chebi_production', 'compounds') }} AS c
- INNER JOIN {{ source('chebi_production', 'database_accession') }} AS da ON c.id = da.compound_id
- INNER JOIN {{ source('chebi_production', 'source') }} AS sr ON da.source_id = sr.id
+ FROM {{ ref('compounds') }} AS c
+ INNER JOIN {{ ref('database_accession') }} AS da ON c.id = da.compound_id
+ INNER JOIN {{ ref('source') }} AS sr ON da.source_id = sr.id
WHERE
- ({{ ontology_data_condition('da') }})
- AND c.parent_id IS NULL
+ c.parent_id IS NULL
UNION
SELECT
c.id AS compound_id,
@@ -32,13 +31,12 @@ WITH cte_database_references_disperse AS (
END AS prefix,
sr.name AS source_name,
da.source_id
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c2 ON c.id = c2.parent_id
- INNER JOIN {{ source('chebi_production', 'database_accession') }} AS da ON c2.id = da.compound_id
- INNER JOIN {{ source('chebi_production', 'source') }} AS sr ON da.source_id = sr.id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('compounds') }} AS c2 ON c.id = c2.parent_id
+ INNER JOIN {{ ref('database_accession') }} AS da ON c2.id = da.compound_id
+ INNER JOIN {{ ref('source') }} AS sr ON da.source_id = sr.id
WHERE
- ({{ ontology_data_condition('da') }})
- AND c.parent_id IS NULL
+ c.parent_id IS NULL
)
SELECT
diff --git a/models/chebi_ontology/valid_relations.sql b/models/chebi_ontology/valid_relations.sql
index 338c1e0224c51966a369afae38fcbc0a70cfc454..fb05c676cdb96b0bad4e4607ef7d9150ddaaa37c 100644
--- a/models/chebi_ontology/valid_relations.sql
+++ b/models/chebi_ontology/valid_relations.sql
@@ -10,30 +10,28 @@ WITH cte_compounds_relations AS (
c.id AS compound_id,
r.init_id,
r.relation_type_id
- FROM {{ source('chebi_production', 'compounds') }} AS c
- INNER JOIN {{ source('chebi_production', 'relation') }} AS r ON c.id = r.final_id
- INNER JOIN {{ source('chebi_production', 'relation_type') }} AS rt ON r.relation_type_id = rt.id
+ FROM {{ ref('compounds') }} AS c
+ INNER JOIN {{ ref('relation') }} AS r ON c.id = r.final_id
+ INNER JOIN {{ ref('relation_type') }} AS rt ON r.relation_type_id = rt.id
WHERE
- {{ ontology_data_condition('r') }}
- AND r.init_id <> 27189 -- We're NOT showing compounds that have 'unclassified' AS a parent, the chebi_id FOR unclassified IS 27189
+ r.init_id <> 27189 -- We're NOT showing compounds that have 'unclassified' AS a parent, the chebi_id FOR unclassified IS 27189
UNION
SELECT
c.id AS compound_id,
--c2.id AS alternative_id,
r.init_id,
r.relation_type_id
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c2 ON c.id = c2.parent_id
- INNER JOIN {{ source('chebi_production', 'relation') }} AS r ON c2.id = r.final_id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('compounds') }} AS c2 ON c.id = c2.parent_id
+ INNER JOIN {{ ref('relation') }} AS r ON c2.id = r.final_id
WHERE
- {{ ontology_data_condition('r') }}
- AND r.init_id <> 27189
+ r.init_id <> 27189
UNION
SELECT
c.id AS compound_id,
NULL AS init_id,
NULL AS relation_type_id
- FROM {{ source('chebi_production', 'compounds') }} AS c
+ FROM {{ ref('compounds') }} AS c
-- There ARE 3 chebi ids that are special, they don't have any parents because they are the upper definitions:
-- chemical entity, role and subatomic particle. Anyway, they must appear in the chebi ontology!
WHERE c.id IN (24431, 50906, 36342)
@@ -48,7 +46,7 @@ cte_compound_relations_parents AS (
cr.init_id,
cr.relation_type_id
FROM cte_compounds_relations AS cr -- the previous cte_compounds_relations
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c ON cr.init_id = c.id
+ LEFT JOIN {{ ref('compounds') }} AS c ON cr.init_id = c.id
WHERE c.parent_id IS NULL
UNION
SELECT
@@ -56,7 +54,7 @@ cte_compound_relations_parents AS (
c.parent_id AS init_id,
cr.relation_type_id
FROM cte_compounds_relations AS cr
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c ON cr.init_id = c.id
+ LEFT JOIN {{ ref('compounds') }} AS c ON cr.init_id = c.id
WHERE c.parent_id IS NOT NULL
),
@@ -99,7 +97,7 @@ cte_compounds_by_relations_disperse AS (
END AS compounds_is_tautomer_of
FROM cte_compound_relations_parents AS r
-- left join to take into account the special ones chebi ids: 24431, 50906, 36342,
- LEFT JOIN {{ source('chebi_production', 'relation_type') }} AS rt ON r.relation_type_id = rt.id
+ LEFT JOIN {{ ref('relation_type') }} AS rt ON r.relation_type_id = rt.id
GROUP BY
r.compound_id,
r.relation_type_id
diff --git a/models/chebi_ontology/valid_structures.sql b/models/chebi_ontology/valid_structures.sql
index 87d41cbfddf9b23cdead949f0f540522e76270c7..385b23076ab53da9ccb2222a9ad7e90b92324dc5 100644
--- a/models/chebi_ontology/valid_structures.sql
+++ b/models/chebi_ontology/valid_structures.sql
@@ -7,12 +7,11 @@ WITH cte_structures_parents AS (
s.standard_inchi_key,
s.standard_inchi,
s.smiles
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'structures') }} AS s ON c.id = s.compound_id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('structures') }} AS s ON c.id = s.compound_id
WHERE
s.molfile IS NOT NULL
AND s.default_structure
- AND ({{ ontology_data_condition('s') }})
AND c.parent_id IS NULL
),
@@ -23,13 +22,12 @@ cte_structures_children AS (
s.standard_inchi_key,
s.standard_inchi,
s.smiles
- FROM {{ source('chebi_production', 'compounds') }} AS c
- LEFT JOIN {{ source('chebi_production', 'compounds') }} AS c2 ON c.id = c2.parent_id
- LEFT JOIN {{ source('chebi_production', 'structures') }} AS s ON c2.id = s.compound_id
+ FROM {{ ref('compounds') }} AS c
+ LEFT JOIN {{ ref('compounds') }} AS c2 ON c.id = c2.parent_id
+ LEFT JOIN {{ ref('structures') }} AS s ON c2.id = s.compound_id
WHERE
s.molfile IS NOT NULL
AND s.default_structure
- AND ({{ ontology_data_condition('s') }})
),
cte_structure AS (