Synthetic / drug derivatives identification

[vcnainala]

Goal:
Approach: Device a filter criteria based on NPLikeness score and Annotation score

Analysis:

• SureChEMBL entries should be checked closely
• SN3 overlap with other data
• SN3 annotation score
• Filter compounds without organism info
• Filter the about compounds if their parent has organism info
• Check the compound for citations if not, update it, even if it is from commercial vendor catalogues
• Check for the presence of non-naturally occurring functional groups or rare natural functional groups and flag them

Proposed filtering:

[vcnainala]

Molecules ~ Organism associations analysis

SELECT count(*)
FROM molecules m
WHERE organism_count > 0
AND m.active = TRUE
AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE);

To account for the scenario where a molecule without organism associations (organism_count = 0) may still be considered associated if its parent has an association

SELECT COUNT(*) AS count_with_parent_associations
FROM molecules m
LEFT JOIN molecule_organism mo ON m.id = mo.molecule_id
LEFT JOIN (
    SELECT DISTINCT parent.id AS parent_id
    FROM molecules parent
    JOIN molecule_organism mo_parent ON parent.id = mo_parent.molecule_id
) parents_with_associations ON m.parent_id = parents_with_associations.parent_id
WHERE mo.organism_id IS NULL
  AND (parents_with_associations.parent_id IS NOT NULL)
  AND m.active = TRUE
  AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE);

To account for the scenario where a molecule without organism associations (organism_count = 0) may still be considered associated if it has citation associations and in cases where both associations are not present check if the parent has an association

SELECT COUNT(*) AS total_associated_molecules
FROM molecules m
LEFT JOIN (
    SELECT DISTINCT parent.id AS parent_id
    FROM molecules parent
    WHERE parent.organism_count > 0 OR parent.citation_count > 0
) parents_with_associations ON m.parent_id = parents_with_associations.parent_id
WHERE (m.organism_count > 0 OR m.citation_count > 0)
   OR parents_with_associations.parent_id IS NOT NULL;