diff options
Diffstat (limited to 'scripts')
3 files changed, 38 insertions, 2 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index d94093e..59218e9 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -155,7 +155,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if VALUE_text in field_to_term_to_uri_dict['ncbi_speciesman_source']: info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][VALUE_text]] else: - if VALUE_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: + if VALUE_text.lower() in ['np/op', 'np-op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']] elif VALUE_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']: info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index c466474..90d9af3 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -30,6 +30,7 @@ Australia:Victoria,http://www.wikidata.org/entity/Q36687 Australia:Northern Territory,http://www.wikidata.org/entity/Q3235 Australia:NSW,http://www.wikidata.org/entity/Q3224 Australia:South Australia,http://www.wikidata.org/entity/Q35715 +Australia:Tasmania,http://www.wikidata.org/entity/Q34366 Austria,http://www.wikidata.org/entity/Q40 Azerbaijan,http://www.wikidata.org/entity/Q227 Bahrain,http://www.wikidata.org/entity/Q398 @@ -88,6 +89,7 @@ China:HuaShang,http://www.wikidata.org/entity/Q148 China:Hubei,http://www.wikidata.org/entity/Q46862 "China:Hubei, Wuhan",http://www.wikidata.org/entity/Q11746 China:Hunan,http://www.wikidata.org/entity/Q45761 +"China:Hunan,Huaihua",http://www.wikidata.org/entity/Q416922 China:Inner Mongolia,http://www.wikidata.org/entity/Q41079 China:Jiangsu,http://www.wikidata.org/entity/Q16963 "China:Jiangsu, Changzhou",http://www.wikidata.org/entity/Q16963 @@ -126,6 +128,7 @@ Dominican Republic,http://www.wikidata.org/entity/Q786 East Timor,http://www.wikidata.org/entity/Q574 Ecuador,http://www.wikidata.org/entity/Q736 Egypt,http://www.wikidata.org/entity/Q79 +Egypt:Cairo,http://www.wikidata.org/entity/Q85 El Salvador,http://www.wikidata.org/entity/Q792 Equatorial Guinea,http://www.wikidata.org/entity/Q983 Eritrea,http://www.wikidata.org/entity/Q986 @@ -137,6 +140,7 @@ Federated States of Micronesia,http://www.wikidata.org/entity/Q702 Fiji,http://www.wikidata.org/entity/Q712 Finland,http://www.wikidata.org/entity/Q33 France,http://www.wikidata.org/entity/Q142 +France:Charente-Maritime,http://www.wikidata.org/entity/Q3278 Gabon,http://www.wikidata.org/entity/Q1000 Georgia,http://www.wikidata.org/entity/Q230 Germany,http://www.wikidata.org/entity/Q183 @@ -160,9 +164,17 @@ Hong Kong,http://www.wikidata.org/entity/Q8646 Iceland,http://www.wikidata.org/entity/Q189 Icelandic Commonwealth,http://www.wikidata.org/entity/Q62389 India,http://www.wikidata.org/entity/Q668 +India:Adajan,http://www.wikidata.org/entity/Q2722074 "India:Assam, Golaghat",http://www.wikidata.org/entity/Q1708160 India:Kerala State,http://www.wikidata.org/entity/Q1186 "India:Ahmedabad",http://www.wikidata.org/entity/Q1070 +India:Dhandhuka,http://www.wikidata.org/entity/Q1259584 +India:Khambhaliya,http://www.wikidata.org/entity/Q2120093 +India:Mehsana,http://www.wikidata.org/entity/Q1922283 +India:Patan,http://www.wikidata.org/entity/Q579702 +India:Siddhpur,http://www.wikidata.org/entity/Q2572203 +India:Uttar Pradesh,http://www.wikidata.org/entity/Q1498 +India:Telangana,http://www.wikidata.org/entity/Q677037 "India:Gujarat, Ahmedabad",http://www.wikidata.org/entity/Q1070 "India:Bardoli",http://www.wikidata.org/entity/Q712003 "India:Gujarat, Bardoli",http://www.wikidata.org/entity/Q712003 @@ -264,11 +276,14 @@ Iraq,http://www.wikidata.org/entity/Q796 Ireland,http://www.wikidata.org/entity/Q27 Israel,http://www.wikidata.org/entity/Q801 Italy,http://www.wikidata.org/entity/Q38 +Italy:Bologna,http://www.wikidata.org/entity/Q1891 Italy:Cagliari,http://www.wikidata.org/entity/Q1897 Italy:Lazio,http://www.wikidata.org/entity/Q1282 Italy:Milan,http://www.wikidata.org/entity/Q490 +Italy:Lombardia, Milan,http://www.wikidata.org/entity/Q490 Italy:Palermo,http://www.wikidata.org/entity/Q2656 Italy:Rome,http://www.wikidata.org/entity/Q220 +Italy:Turin,http://www.wikidata.org/entity/Q495 Ivory Coast,http://www.wikidata.org/entity/Q1008 Jamaica,http://www.wikidata.org/entity/Q766 Japan,http://www.wikidata.org/entity/Q17 @@ -301,6 +316,7 @@ Malawi,http://www.wikidata.org/entity/Q1020 Malaysia,http://www.wikidata.org/entity/Q833 Maldives,http://www.wikidata.org/entity/Q826 Malaysia:Kuala Lumpur,http://www.wikidata.org/entity/Q1865 +"Malaysia:Crocker Range National Park, Sabah, Malaysia (Borneo)",http://www.wikidata.org/entity/Q1974550 Mali,http://www.wikidata.org/entity/Q912 Malta,http://www.wikidata.org/entity/Q233 Marshall Islands,http://www.wikidata.org/entity/Q709 @@ -364,6 +380,17 @@ People's Republic of China,http://www.wikidata.org/entity/Q148 Peru,http://www.wikidata.org/entity/Q419 Peru:Lima,http://www.wikidata.org/entity/Q2868 Philippines,http://www.wikidata.org/entity/Q928 +"Philippines:National Capital Region, Makati City",http://www.wikidata.org/entity/Q1508 +"Philippines:NCR, Makati City",http://www.wikidata.org/entity/Q1508 +"Philippines:NCR, Caloocan City",http://www.wikidata.org/entity/Q1478 +"Philippines:NCR, Cavite City",http://www.wikidata.org/entity/Q1482 +"Philippines:NCR, Pasay City",http://www.wikidata.org/entity/Q17189 +"Philippines:NCR, Quezon City",http://www.wikidata.org/entity/Q1475 +"Philippines:NCR, San Juan City",http://www.wikidata.org/entity/Q749283 +"Philippines:NCR, Taguig City",http://www.wikidata.org/entity/Q1643 +"Philippines:Region 3 (Bulacan), San Jose del Monte City",http://www.wikidata.org/entity/Q2193 +"Philippines:Region 4A (Laguna), Calamba City",http://www.wikidata.org/entity/Q75978 +"Philippines:Region 4A (Rizal), Rodriguez",http://www.wikidata.org/entity/Q106825 Poland,http://www.wikidata.org/entity/Q36 Portugal,http://www.wikidata.org/entity/Q45 Principality of Turov and Pinsk,http://www.wikidata.org/entity/Q671362 @@ -458,6 +485,12 @@ USA:AL,http://www.wikidata.org/entity/Q173 "USA:Avondale, LA",http://www.wikidata.org/entity/Q79449 "USA:AVONDALE, LA",http://www.wikidata.org/entity/Q79449 "USA:CA, Alameda",http://www.wikidata.org/entity/Q490744 +"USA:CA, Humboldt County",http://www.wikidata.org/entity/Q109651 +"USA:CA, Marin County",http://www.wikidata.org/entity/Q108117 +"USA:CA, Orange County",http://www.wikidata.org/entity/Q5925 +"USA:CA, San Francisco County",http://www.wikidata.org/entity/Q13188841 +"USA:CA, Santa Clara County",http://www.wikidata.org/entity/Q110739 +"USA:CA, Sonoma County",http://www.wikidata.org/entity/Q108067 "USA:California, Los Angeles county",http://www.wikidata.org/entity/Q104994 "USA:California,Los Angeles County",http://www.wikidata.org/entity/Q104994 "USA:California, San Diego county",http://www.wikidata.org/entity/Q108143 @@ -493,6 +526,7 @@ USA:AL,http://www.wikidata.org/entity/Q173 "USA:LOCKPORT, LA",http://www.wikidata.org/entity/Q2194112 "USA:Maringouin, LA",http://www.wikidata.org/entity/Q2673176 "USA:MARINGOUIN, LA",http://www.wikidata.org/entity/Q2673176 +"USA:Maryland",http://www.wikidata.org/entity/Q1391 "USA:Marrero, LA",http://www.wikidata.org/entity/Q1902531 "USA:MARRERO, LA",http://www.wikidata.org/entity/Q1902531 "USA:Massachusetts, Middlesex county",http://www.wikidata.org/entity/Q54073 @@ -506,10 +540,12 @@ USA:New Hampshire,http://www.wikidata.org/entity/Q759 "USA:New Jersey, Bergen county",http://www.wikidata.org/entity/Q112915 "USA:New Jersey, Burlington county",http://www.wikidata.org/entity/Q138141 "USA:New Jersey, Essex county",http://www.wikidata.org/entity/Q128077 +"USA:Pennsylvania, Philadelphia county",http://www.wikidata.org/entity/Q496900 "USA:Raceland, LA",http://www.wikidata.org/entity/Q2154341 "USA:RACELAND, LA",http://www.wikidata.org/entity/Q2154341 "USA:Saint Rose, LA",http://www.wikidata.org/entity/Q7402139 "USA:SAINT ROSE, LA",http://www.wikidata.org/entity/Q7402139 +"USA:SC, HORRY",http://www.wikidata.org/entity/Q502288 "USA:Slidell LA",http://www.wikidata.org/entity/Q988156 "USA:SLIDELL LA",http://www.wikidata.org/entity/Q988156 "USA:Snohomish County,WA",http://www.wikidata.org/entity/Q110403 diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py index 9b8fedc..364090e 100755 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py @@ -305,7 +305,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_speciesman_source']: info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]] else: - if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: + if GBQualifier_value_text.lower() in ['np/op', 'np-op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']] elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']: info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] |