Open mfiume opened 10 years ago
The mapping between HPO IDs and genes has been updated, and the format has changed.
The new format is here: http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes.txt
The old format is here: http://medsavant.com/serve/ontology/phenotype_to_genes.txt
And the SQL format that we require is:
CREATE TABLE ontology ( ontology varchar(10) COLLATE latin1_bin NOT NULL, id varchar(30) COLLATE latin1_bin NOT NULL, name varchar(300) COLLATE latin1_bin NOT NULL, def mediumtext COLLATE latin1_bin, alt_ids varchar(300) COLLATE latin1_bin DEFAULT NULL, parents varchar(120) COLLATE latin1_bin DEFAULT NULL, genes mediumtext COLLATE latin1_bin, PRIMARY KEY (id) ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
ontology
id
name
def
alt_ids
parents
genes
Where genes is a pipe (|) delimited string of genes for the term with name. See the ontology table in any MedSavant database for an example.
The mapping between HPO IDs and genes has been updated, and the format has changed.
The new format is here: http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes.txt
The old format is here: http://medsavant.com/serve/ontology/phenotype_to_genes.txt
And the SQL format that we require is:
CREATE TABLE
ontology(ontologyvarchar(10) COLLATE latin1_bin NOT NULL,idvarchar(30) COLLATE latin1_bin NOT NULL,namevarchar(300) COLLATE latin1_bin NOT NULL,defmediumtext COLLATE latin1_bin,alt_idsvarchar(300) COLLATE latin1_bin DEFAULT NULL,parentsvarchar(120) COLLATE latin1_bin DEFAULT NULL,genesmediumtext COLLATE latin1_bin, PRIMARY KEY (id) ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;Where genes is a pipe (|) delimited string of genes for the term with name. See the ontology table in any MedSavant database for an example.