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-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv32
-rw-r--r--scripts/dict_ontology_standardization/ncbi_host_species.csv2
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv7
-rw-r--r--scripts/dict_ontology_standardization/ncbi_speciesman_source.csv1
-rw-r--r--scripts/docker/Dockerfile4
5 files changed, 36 insertions, 10 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
diff --git a/scripts/docker/Dockerfile b/scripts/docker/Dockerfile
index 5bd38dd..9fb33d5 100644
--- a/scripts/docker/Dockerfile
+++ b/scripts/docker/Dockerfile
@@ -4,7 +4,7 @@ RUN apt-get update && \
apt-get -yq --no-install-recommends -o Acquire::Retries=6 install \
python3 python3-pip python3-setuptools python3-dev python-pycurl \
clustalw python3-biopython libcurl4-openssl-dev build-essential \
- libssl-dev && \
+ libssl-dev libmagic-dev python3-magic && \
apt-get clean
-RUN pip3 install bh20-seq-uploader \ No newline at end of file
+RUN pip3 install bh20-seq-uploader