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authorAndreaGuarracino2020-06-22 23:23:03 +0200
committerAndreaGuarracino2020-06-22 23:23:03 +0200
commit5bd991fe5f048b2c4b2c23c6149c1bd789d3bdbc (patch)
tree799eb4037771736cbc5c2ba34f62ac82426595ef /scripts/dict_ontology_standardization
parent21ac66de2f92b7a433c6677d7526ee8d9639d999 (diff)
downloadbh20-seq-resource-5bd991fe5f048b2c4b2c23c6149c1bd789d3bdbc.tar.gz
bh20-seq-resource-5bd991fe5f048b2c4b2c23c6149c1bd789d3bdbc.tar.lz
bh20-seq-resource-5bd991fe5f048b2c4b2c23c6149c1bd789d3bdbc.zip
added new dictionary entries
Diffstat (limited to 'scripts/dict_ontology_standardization')
-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv4
-rw-r--r--scripts/dict_ontology_standardization/ncbi_host_species.csv1
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv7
3 files changed, 12 insertions, 0 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 85d4e8a..204f7f2 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -239,6 +239,7 @@ Solomon Islands,http://www.wikidata.org/entity/Q685
Somalia,http://www.wikidata.org/entity/Q1045
South Africa,http://www.wikidata.org/entity/Q258
South Africa: KwaZulu-Natal,http://www.wikidata.org/entity/Q81725
+South Africa: KZN,http://www.wikidata.org/entity/Q81725
South African Republic,http://www.wikidata.org/entity/Q550374
South Korea,http://www.wikidata.org/entity/Q884
South Sudan,http://www.wikidata.org/entity/Q958
@@ -279,6 +280,7 @@ USA: AR,http://www.wikidata.org/entity/Q1612
USA: AZ,http://www.wikidata.org/entity/Q816
USA: Arizona,http://www.wikidata.org/entity/Q816
USA: CA,http://www.wikidata.org/entity/Q99
+USA:CA,http://www.wikidata.org/entity/Q99
USA: California,http://www.wikidata.org/entity/Q99
USA:California,http://www.wikidata.org/entity/Q99
"USA: CA, San Diego County",http://www.wikidata.org/entity/Q108143
@@ -299,6 +301,7 @@ USA: IN,http://www.wikidata.org/entity/Q1415
USA: KS,http://www.wikidata.org/entity/Q1558
USA: KY,http://www.wikidata.org/entity/Q1603
USA: LA,http://www.wikidata.org/entity/Q1588
+USA:Los Angeles,http://www.wikidata.org/entity/Q65
"USA: New Orleans, LA",http://www.wikidata.org/entity/Q34404
USA: MA,http://www.wikidata.org/entity/Q771
USA: Massachusetts,http://www.wikidata.org/entity/Q771
@@ -330,6 +333,7 @@ USA: PA,http://www.wikidata.org/entity/Q1400
USA: RI,http://www.wikidata.org/entity/Q1387
"USA: San Francisco, CA",http://www.wikidata.org/entity/Q62
USA: SC,http://www.wikidata.org/entity/Q1456
+USA: South Carolina,http://www.wikidata.org/entity/Q1456
USA: SD,http://www.wikidata.org/entity/Q1211
"USA: Snohomish County, WA",http://www.wikidata.org/entity/Q110403
USA: TN,http://www.wikidata.org/entity/Q1509
diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv
index 102d458..bc6ac04 100644
--- a/scripts/dict_ontology_standardization/ncbi_host_species.csv
+++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv
@@ -1,6 +1,7 @@
Homo sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606
human,http://purl.obolibrary.org/obo/NCBITaxon_9606
Human,http://purl.obolibrary.org/obo/NCBITaxon_9606
+sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606
Mustela lutreola,http://purl.obolibrary.org/obo/NCBITaxon_9666
Manis javanica,http://purl.obolibrary.org/obo/NCBITaxon_9974
Felis catus,http://purl.obolibrary.org/obo/NCBITaxon_9685
diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
index 110e90b..964cbf3 100644
--- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -1,3 +1,9 @@
+Illumina HiSeq 1000,http://www.ebi.ac.uk/efo/EFO_0004204
+Illumina HiSeq 2000,http://www.ebi.ac.uk/efo/EFO_0004203
+Illumina HiSeq 2500,http://www.ebi.ac.uk/efo/EFO_0008565
+Illumina HiSeq 3000,http://www.ebi.ac.uk/efo/EFO_0008564
+Illumina HiSeq 4000,http://www.ebi.ac.uk/efo/EFO_0008563
+Illumina iSeq 100,http://www.ebi.ac.uk/efo/EFO_0008635
Illumian NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
Illumina NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
NextSeq500,http://www.ebi.ac.uk/efo/EFO_0009173
@@ -14,6 +20,7 @@ ONT (Oxford Nanopore Technologies),http://purl.obolibrary.org/obo/NCIT_C146818
Oxford Nanopore Technology,http://purl.obolibrary.org/obo/NCIT_C146818
Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632
MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632
+MinION,http://www.ebi.ac.uk/efo/EFO_0008632
Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818
Illumina MiSeq,http://www.ebi.ac.uk/efo/EFO_0004205
Illumina,http://purl.obolibrary.org/obo/OBI_0000759