Merge pull request #86 from AndreaGuarracino/patch-19

corrected the wrong entities

4 files changed, 34 insertions, 8 deletions

diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 7e83564..85d4e8a 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -12,6 +12,9 @@ Armenia,http://www.wikidata.org/entity/Q399
 Australia,http://www.wikidata.org/entity/Q408
 Australia: Queensland,http://www.wikidata.org/entity/Q36074
 Australia: Victoria,http://www.wikidata.org/entity/Q36687
+"Australia: Melbourne, Victoria",http://www.wikidata.org/entity/Q3141
+Australia: Northern Territory,http://www.wikidata.org/entity/Q3235
+Australia: NSW,http://www.wikidata.org/entity/Q3224
 Austria,http://www.wikidata.org/entity/Q40
 Azerbaijan,http://www.wikidata.org/entity/Q227
 Bahrain,http://www.wikidata.org/entity/Q398
@@ -31,8 +34,10 @@ Bulgaria,http://www.wikidata.org/entity/Q219
 Burkina Faso,http://www.wikidata.org/entity/Q965
 Burundi,http://www.wikidata.org/entity/Q967
 Cambodia,http://www.wikidata.org/entity/Q424
+Cambodia:Sihanoukville,http://www.wikidata.org/entity/Q18207676
 Cameroon,http://www.wikidata.org/entity/Q1009
 Canada,http://www.wikidata.org/entity/Q16
+Canada: Toronto,http://www.wikidata.org/entity/Q172
 Cape Verde,http://www.wikidata.org/entity/Q1011
 Central African Republic,http://www.wikidata.org/entity/Q929
 Chad,http://www.wikidata.org/entity/Q657
@@ -65,12 +70,13 @@ China: Jiangxi,http://www.wikidata.org/entity/Q57052
 China: Jilin,http://www.wikidata.org/entity/Q45208
 China: Liaoning,http://www.wikidata.org/entity/Q43934
 China: Macau,http://www.wikidata.org/entity/Q14773
-China: Nanchang,https://www.wikidata.org/wiki/Q171943
+China: Nanchang,http://www.wikidata.org/entity/Q171943
 China: Ningxia Hui Autonomous Region,http://www.wikidata.org/entity/Q57448
 China: Qinghai,http://www.wikidata.org/entity/Q45833
 China: Shaanxi,http://www.wikidata.org/entity/Q47974
 China: Shandong,http://www.wikidata.org/entity/Q43407
 China: Shanghai,http://www.wikidata.org/entity/Q8686
+China:Shanghai,http://www.wikidata.org/entity/Q8686
 China: Shanxi,http://www.wikidata.org/entity/Q46913
 China: Shenzhen,http://www.wikidata.org/entity/Q15174
 China: Sichuan,http://www.wikidata.org/entity/Q19770
@@ -111,11 +117,13 @@ France,http://www.wikidata.org/entity/Q142
 Gabon,http://www.wikidata.org/entity/Q1000
 Georgia,http://www.wikidata.org/entity/Q230
 Germany,http://www.wikidata.org/entity/Q183
-Germany: Bavaria,https://www.wikidata.org/wiki/Q980
-Germany: Dusseldorf,https://www.wikidata.org/wiki/Q1718
+Germany: Bavaria,http://www.wikidata.org/entity/Q980
+Germany: Dusseldorf,http://www.wikidata.org/entity/Q1718
+Germany: Heinsberg,http://www.wikidata.org/entity/Q14833
+Germany: Starnberg,http://www.wikidata.org/entity/Q61936
 Ghana,http://www.wikidata.org/entity/Q117
 Greece,http://www.wikidata.org/entity/Q41
-Greece: Athens,https://www.wikidata.org/wiki/Q1524
+Greece: Athens,http://www.wikidata.org/entity/Q1524
 Grenada,http://www.wikidata.org/entity/Q769
 Guatemala,http://www.wikidata.org/entity/Q774
 Guinea,http://www.wikidata.org/entity/Q1006
@@ -139,8 +147,8 @@ Ireland,http://www.wikidata.org/entity/Q27
 Israel,http://www.wikidata.org/entity/Q801
 Italy,http://www.wikidata.org/entity/Q38
 Italy: Cagliari,http://www.wikidata.org/entity/Q1897
-Italy: Lazio,https://www.wikidata.org/wiki/Q1282
-Italy: Palermo,https://www.wikidata.org/wiki/Q2656
+Italy: Lazio,http://www.wikidata.org/entity/Q1282
+Italy: Palermo,http://www.wikidata.org/entity/Q2656
 Italy: Rome,http://www.wikidata.org/entity/Q220
 Ivory Coast,http://www.wikidata.org/entity/Q1008
 Jamaica,http://www.wikidata.org/entity/Q766
@@ -181,7 +189,7 @@ Mozambique,http://www.wikidata.org/entity/Q1029
 Myanmar,http://www.wikidata.org/entity/Q836
 Namibia,http://www.wikidata.org/entity/Q1030
 Nauru,http://www.wikidata.org/entity/Q697
-Netherlands: Milheeze,https://www.wikidata.org/wiki/Q3314115
+Netherlands: Milheeze,http://www.wikidata.org/entity/Q3314115
 Nepal,http://www.wikidata.org/entity/Q837
 New Zealand,http://www.wikidata.org/entity/Q664
 Nicaragua,http://www.wikidata.org/entity/Q811
@@ -269,10 +277,14 @@ USA: AK,http://www.wikidata.org/entity/Q797
 USA: AL,http://www.wikidata.org/entity/Q173
 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: 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
 USA: CO,http://www.wikidata.org/entity/Q1261
 USA: CT,http://www.wikidata.org/entity/Q779
+USA: Connecticut,http://www.wikidata.org/entity/Q779
 USA: DC,http://www.wikidata.org/entity/Q3551781
 USA: DE,http://www.wikidata.org/entity/Q1393
 USA: FL,http://www.wikidata.org/entity/Q812
@@ -287,7 +299,7 @@ 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: New Orleans, LA",https://www.wikidata.org/wiki/Q34404
+"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
 USA: MD,http://www.wikidata.org/entity/Q1391
@@ -295,6 +307,8 @@ USA: ME,http://www.wikidata.org/entity/Q724
 USA: MI,http://www.wikidata.org/entity/Q1166
 USA: Michigan,http://www.wikidata.org/entity/Q1166
 USA: MN,http://www.wikidata.org/entity/Q1527
+USA:Minnesota,http://www.wikidata.org/entity/Q1527
+USA: Minnesota,http://www.wikidata.org/entity/Q1527
 USA: MO,http://www.wikidata.org/entity/Q1581
 USA: MS,http://www.wikidata.org/entity/Q1494
 USA: MT,http://www.wikidata.org/entity/Q1212
@@ -323,8 +337,10 @@ USA: TX,http://www.wikidata.org/entity/Q1439
 USA: UT,http://www.wikidata.org/entity/Q829
 USA: VA,http://www.wikidata.org/entity/Q1370
 USA: Virginia,http://www.wikidata.org/entity/Q1370
+USA:Virginia,http://www.wikidata.org/entity/Q1370
 USA: VT,http://www.wikidata.org/entity/Q16551
 USA: WA,http://www.wikidata.org/entity/Q1223
+USA: Washington,http://www.wikidata.org/entity/Q1223
 USA: WI,http://www.wikidata.org/entity/Q1537
 USA: Wisconsin,http://www.wikidata.org/entity/Q1537
 USA: WV,http://www.wikidata.org/entity/Q1371
diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv
index 0d2120c..102d458 100644
--- a/scripts/dict_ontology_standardization/ncbi_host_species.csv
+++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv
@@ -1,4 +1,6 @@
 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
 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 49cb6b7..110e90b 100644
--- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -1,6 +1,13 @@
 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
+NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
+Illumian NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566
+Illumina NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566
+NextSeq550,http://www.ebi.ac.uk/efo/EFO_0008566
+NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566
+Illumina MiniSeq,http://www.ebi.ac.uk/efo/EFO_0008636
+Illumina NovaSeq 6000,http://www.ebi.ac.uk/efo/EFO_0008637
 Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 Oxford Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 ONT (Oxford Nanopore Technologies),http://purl.obolibrary.org/obo/NCIT_C146818
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
index 18b986c..0fa2219 100644
--- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -14,6 +14,7 @@ oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
 throat swab,http://purl.obolibrary.org/obo/NCIT_C155835
 oro-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
 Oropharyngal,http://purl.obolibrary.org/obo/NCIT_C155835
+oralpharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
 Oral-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
 Oro-pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
 Oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835