Search ontology tree by relationships in MySQL - mysql

Question

i am working on a MySQL database with the following schema:
In which we save information from different ontologies (exmp). Some of the terms have relationships (exmp: MS:1000004, sample mass) which are indicated by relationship: or is_a:. For the sake of this question let's focus on the is_a relationships.
We now want to provide an option to search along these is_a relationships. So a function which we give MS:1000004/sample mass as input and get in return all Terms which are connected to it by an is_a relationship. But not only all terms directly connected to MS:1000004, but also all terms which are connected to the children and so on. This image describes this a bit better, where thing would be MS:1000004/sample mass and everything below is what i want as result.
Currently we are using a rather unoptimized recursive function as a stored procedure to do this:
DELIMITER $$
CREATE DEFINER=`root`#`localhost` PROCEDURE `getAllTermsByParentTerm`(IN `parentOntology` varchar(512))
BEGIN
WITH RECURSIVE previous (accession, FK_OntologyName, name, definition, xrefvaluetype, isobsolete, fk_termAccession, relationshiptype, fk_termAccession_related, depth_level) AS (
SELECT
t.accession,
t.FK_OntologyName,
t.name,
t.definition,
t.xrefvaluetype,
t.isobsolete,
trt.fk_termAccession,
trt.relationshiptype,
trt.fk_termAccession_related,
0 depth_level
FROM Term t
INNER JOIN (TermRelationship AS trt, Term AS ref) ON(
t.Accession = trt.FK_TermAccession
AND trt.FK_TermAccession_Related = ref.Accession
AND (trt.RelationshipType = `is_a` OR trt.RelationshipType = `part_of`)
AND
(
trt.FK_TermAccession_Related = ref.Accession
AND ref.Name = parentOntology
)
)
UNION All
SELECT
t2.accession,
t2.FK_OntologyName,
t2.name,
t2.definition,
t2.xrefvaluetype,
t2.isobsolete,
trt2.fk_termAccession,
trt2.relationshiptype,
trt2.fk_termAccession_related,
(previous.depth_level+1) depth_level
FROM Term t2
INNER JOIN (TermRelationship AS trt2, previous) ON(
t2.Accession = trt2.FK_TermAccession
AND trt2.FK_TermAccession_Related = previous.Accession
)
)
SELECT
t.Accession,
t.FK_OntologyName,
t.Name,
t.Definition,
t.xRefValueType,
t.IsObsolete,
p.depth_level
FROM previous p
Inner JOIN Term AS t ON (
p.Accession = t.Accession
);
END$$
DELIMITER ;
To the question: i am not that experienced with MySQL so are there any options to optimize this function, or is MySQL the wrong tool overall?
Example rows:
Term
| Accession | FK_OntologyName | Name | Definition | XRefValueType | IsObsolete |
|------------|-----------------|----------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------|------------|
| TEST:0000000 | TEST | Proteomics Standards Initiative Mass Spectrometry Vocabularies | "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS] | | 0 |
| TEST:1000001 | TEST | sample number | "A reference number relevant to the sample under study." [PSI:MS] | value-type:xsd\:string "The allowed value-type for this CV term." | 0 |
| TEST:1000002 | TEST | sample name | "A reference string relevant to the sample under study." [PSI:MS] | value-type:xsd\:string "The allowed value-type for this CV term." | 0 |
| TEST:1000003 | TEST | sample state | "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS] | | 0 |
| TEST:1000004 | TEST | sample mass | "Total mass of sample used." [PSI:MS] | value-type:xsd\:float "The allowed value-type for this CV term." | 0 |
| TEST:1000005 | TEST | sample volume | "Total volume of solution used." [PSI:MS] | value-type:xsd\:float "The allowed value-type for this CV term." | 0 |
| TEST:1000006 | TEST | sample concentration | "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] | value-type:xsd\:float "The allowed value-type for this CV term." | 0 |
| TEST:1000007 | TEST | inlet type | "The nature of the sample inlet." [PSI:MS] | | 0 |
| TEST:1000008 | TEST | ionization type | "The method by which gas phase ions are generated from the sample." [PSI:MS] | | 0 |
| TEST:1000011 | TEST | mass resolution | "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] | value-type:xsd\:string "The allowed value-type for this CV term." | 0 |
| TEST:1000012 | TEST | resolution measurement method | "Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS] | | 0 |
| TEST:1000014 | TEST | accuracy | "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS] | value-type:xsd\:float "The allowed value-type for this CV term." | 0 |
| TEST:1000015 | TEST | scan rate | "Rate in Th/sec for scanning analyzers." [PSI:MS] | value-type:xsd\:float "The allowed value-type for this CV term." | 0 |
| TEST:1000016 | TEST | scan start time | "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS] | value-type:xsd\:float "The allowed value-type for this CV term." | 0 |
| TEST:1000018 | TEST | scan direction | "Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS] | | 0 |
| TEST:1000019 | TEST | scan law | "Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used." [PSI:MS] | | 0 |
| TEST:1000021 | TEST | reflectron state | "Status of the reflectron, turned on or off." [PSI:MS] | | 0 |
| TEST:1000022 | TEST | TOF Total Path Length | "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS] | value-type:xsd\:float "The allowed value-type for this CV term." | 0 | | value-type:xsd\:int "The allowed value-type for this CV term." | 0 |
TermRelationship
| ID | FK_TermAccession | RelationshipType | FK_TermAccession_Related | FK_OntologyName |
|--------|------------------|------------------|--------------------------|-----------------|
| 0 | TEST:1000001 | is_a | TEST:0000000 | TEST |
| 1 | TEST:1000002 | is_a | TEST:0000000 | TEST |
| 2 | TEST:1000003 | is_a | TEST:1000002 | TEST |
| 3 | TEST:1000004 | is_a | TEST:1000002 | TEST |
| 4 | TEST:1000005 | is_a | TEST:1000002 | TEST |
| 5 | TEST:1000006 | is_a | TEST:1000002 | TEST |
| 6 | TEST:1000007 | is_a | TEST:1000002 | TEST |
| 7 | TEST:1000008 | is_a | TEST:1000007 | TEST |
| 8 | TEST:1000011 | is_a | TEST:1000007 | TEST |
| 9 | TEST:1000022 | is_a | TEST:0000000 | TEST |
Expected outcome is to execute the function for TEST:0000000/Proteomics Standards Initiative Mass Spectrometry Vocabularies and get all the following terms, because they are child/grandchild terms to TEST:0000000.
TEST:1000001
TEST:1000002
TEST:1000003
TEST:1000004
TEST:1000005
TEST:1000006
TEST:1000007
TEST:1000008
TEST:1000011
TEST:1000022

Answer 1

Some of these may help performance:
t: INDEX(Accession)
trt: INDEX(FK_TermAccession_Related, relationshiptype, FK_TermAccession)
trt: INDEX(FK_TermAccession, FK_TermAccession_Related, relationshiptype)
ref: INDEX(Accession, Name)
previous: INDEX(Accession, depth_level)
Please use JOIN...ON instead of (TermRelationship AS trt, Term AS ref)
What table is parentOntology in?
trt.FK_TermAccession_Related = ref.Accession show up redundantly.