| layout |
id |
title |
contact |
status |
fail_mode |
implementations |
rule |
GORULE:0000010 |
PubMed reference formatting must be correct |
|
Proposed |
soft |
| code |
language |
source |
SELECT gene_product.symbol,
CONCAT(gpx.xref_dbname, ':', gpx.xref_key) AS gpxref,
IF(association.is_not=1,"NOT","") AS 'not',
term.acc,
term.name,
evidence.code,
CONCAT(dbxref.xref_dbname, ':', dbxref.xref_key) AS evxref,
db.name AS assigned_by
FROM association
INNER JOIN evidence
ON association.id = evidence.association_id
INNER JOIN gene_product
ON association.gene_product_id = gene_product.id
INNER JOIN term
ON association.term_id = term.id
INNER JOIN dbxref
ON evidence.dbxref_id = dbxref.id
INNER JOIN dbxref AS gpx
ON gene_product.dbxref_id = gpx.id
INNER JOIN db
ON association.source_db_id=db.id
WHERE dbxref.xref_dbname = 'PMID'
AND dbxref.xref_key REGEXP '^[^0-9]' |
SQL |
|
|
| code |
language |
source |
/^(.*?\t){5}([^\t]\|)*PMID:(?!\d+)/ |
regex |
|
|
|
References in the GAF (Column 6) should be of the format
db_name:db_key|PMID:12345678, e.g. SGD_REF:S000047763|PMID:2676709.
No other format is acceptable for PubMed references; the following
examples are invalid:
- PMID:PMID:14561399
- PMID:unpublished
- PMID:.
- PMID:0
This is proposed as a HARD QC check: incorrectly formatted references
will be removed.