diff options
6 files changed, 537 insertions, 185 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 352a30e..0e1215e 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -23,14 +23,19 @@ term_to_uri_dict = {} for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]: print('Read {}'.format(path_dict_xxx_csv)) - with open(path_dict_xxx_csv, 'r') as f: + with open(path_dict_xxx_csv) as f: for line in f: if len(line.split(',')) > 2: term, uri = line.strip('\n').split('",') - term = term.strip('"') else: term, uri = line.strip('\n').split(',') + term = term.strip('"') + + if term in term_to_uri_dict: + print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term)) + continue + term_to_uri_dict[term] = uri def is_integer(string_to_check): @@ -123,10 +128,12 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if VALUE_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[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']: + 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']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['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']: + 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'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] + elif VALUE_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']: + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] elif VALUE_text.lower() in ['nasal swab and throat swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']] elif VALUE_text.lower() in ['nasal-swab and oro-pharyngeal swab']: @@ -178,6 +185,9 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): else: info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(VALUE_text) elif TAG_text == 'geo_loc_name': + if ': ' in VALUE_text: + VALUE_text = VALUE_text.replace(': ', ':') + if VALUE_text in term_to_uri_dict: info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[VALUE_text] elif VALUE_text.lower() not in ['na', 'not applicable']: diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index 4bea3ec..618e3e1 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -1,6 +1,20 @@ 30.59 N 114.3 E,http://www.wikidata.org/entity/Q11746 35.92 N 74.33 E,http://www.wikidata.org/entity/Q609024 39.54 N 116.23 E,http://www.wikidata.org/entity/Q198244 +22.3039019 N 73.1680977 E,http://www.wikidata.org/entity/Q11909 +22.3394 N 114.166 E,http://www.wikidata.org/entity/Q8646 +22.6813385 N 72.8771793 E,http://www.wikidata.org/entity/Q219039 +23.052214 N 72.603157 E,http://www.wikidata.org/entity/Q1070 +23.0524508 N 72.600668 E,http://www.wikidata.org/entity/Q1070 +24.5046286 N 72.0209126 E,http://www.wikidata.org/entity/Q1266017 +40.71 N 74.00 W,http://www.wikidata.org/entity/Q11253 +41.31 N 72.92 W,http://www.wikidata.org/entity/Q49145 +43.0731 N 89.4012 W,http://www.wikidata.org/entity/Q43788 +44.3148 N 85.6024 W,http://www.wikidata.org/entity/Q22086086 +51.06 N 6.12 E,http://www.wikidata.org/entity/Q14833 +51.22 N 6.77 E,http://www.wikidata.org/entity/Q1718 +22.3137564 N 73.1465874 E,http://www.wikidata.org/entity/Q11909 +"22.8197678 N 72.7573375 E",http://www.wikidata.org/entity/Q2233469 Afghanistan,http://www.wikidata.org/entity/Q889 Albania,http://www.wikidata.org/entity/Q222 Algeria,http://www.wikidata.org/entity/Q262 @@ -10,15 +24,23 @@ Antigua and Barbuda,http://www.wikidata.org/entity/Q781 Argentina,http://www.wikidata.org/entity/Q414 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 +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 +Australia:South Australia,http://www.wikidata.org/entity/Q35715 Austria,http://www.wikidata.org/entity/Q40 Azerbaijan,http://www.wikidata.org/entity/Q227 Bahrain,http://www.wikidata.org/entity/Q398 Bangladesh,http://www.wikidata.org/entity/Q902 +Bangladesh:Barishal,http://www.wikidata.org/entity/Q747840 +Bangladesh:Chattogram,http://www.wikidata.org/entity/Q376749 +Bangladesh:Chittagong,http://www.wikidata.org/entity/Q376749 +Bangladesh:Dhaka,http://www.wikidata.org/entity/Q1354 +Bangladesh:Khulna,http://www.wikidata.org/entity/Q243325 +Bangladesh:Narayanganj,http://www.wikidata.org/entity/Q1990163 +Bangladesh:Rangpur,http://www.wikidata.org/entity/Q994514 Barbados,http://www.wikidata.org/entity/Q244 Belarus,http://www.wikidata.org/entity/Q184 Belgium,http://www.wikidata.org/entity/Q31 @@ -29,6 +51,7 @@ Bolivia,http://www.wikidata.org/entity/Q750 Bosnia and Herzegovina,http://www.wikidata.org/entity/Q225 Botswana,http://www.wikidata.org/entity/Q963 Brazil,http://www.wikidata.org/entity/Q155 +"Brazil:Feira de Santana, BA",http://www.wikidata.org/entity/Q194343 Brunei,http://www.wikidata.org/entity/Q921 Bulgaria,http://www.wikidata.org/entity/Q219 Burkina Faso,http://www.wikidata.org/entity/Q965 @@ -37,59 +60,59 @@ 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 +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 Chile,http://www.wikidata.org/entity/Q298 China,http://www.wikidata.org/entity/Q148 -China: Anhui,http://www.wikidata.org/entity/Q40956 -"China: Anhui, Fuyang":http://www.wikidata.org/entity/Q360584 -China: Beijing,http://www.wikidata.org/entity/Q956 -China: Chongqing,http://www.wikidata.org/entity/Q11725 -China: Fujian,http://www.wikidata.org/entity/Q41705 -China: Gansu,http://www.wikidata.org/entity/Q42392 -China: Guangdong,http://www.wikidata.org/entity/Q15175 -"China: Guangdong, Guangzhou",http://www.wikidata.org/entity/Q16572 -China: Guangxi Zhuang Autonomous Region,http://www.wikidata.org/entity/Q15176 -China: Guangzhou,http://www.wikidata.org/entity/Q16572 -China: Guizhou,http://www.wikidata.org/entity/Q47097 -China: Hangzhou,http://www.wikidata.org/entity/Q4970 -China: Hainan,http://www.wikidata.org/entity/Q42200 -China: Hebei,http://www.wikidata.org/entity/Q21208 -China: Heilongjiang,http://www.wikidata.org/entity/Q19206 -China: Henan,http://www.wikidata.org/entity/Q43684 -China: Hong Kong,http://www.wikidata.org/entity/Q8646 -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: Inner Mongolia,http://www.wikidata.org/entity/Q41079 -China: Jiangsu,http://www.wikidata.org/entity/Q16963 -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,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:Anhui,http://www.wikidata.org/entity/Q40956 +"China:Anhui, Fuyang",http://www.wikidata.org/entity/Q360584 +China:Beijing,http://www.wikidata.org/entity/Q956 +China:Chongqing,http://www.wikidata.org/entity/Q11725 +China:Chengdu,http://www.wikidata.org/entity/Q30002 +China:Fujian,http://www.wikidata.org/entity/Q41705 +China:Gansu,http://www.wikidata.org/entity/Q42392 +China:Guangdong,http://www.wikidata.org/entity/Q15175 +"China:Guangdong, Guangzhou",http://www.wikidata.org/entity/Q16572 +China:Guangxi Zhuang Autonomous Region,http://www.wikidata.org/entity/Q15176 +China:Guangzhou,http://www.wikidata.org/entity/Q16572 +China:Guizhou,http://www.wikidata.org/entity/Q47097 +China:Hangzhou,http://www.wikidata.org/entity/Q4970 +China:Hainan,http://www.wikidata.org/entity/Q42200 +China:Hebei,http://www.wikidata.org/entity/Q21208 +China:Heilongjiang,http://www.wikidata.org/entity/Q19206 +China:Henan,http://www.wikidata.org/entity/Q43684 +China:Hong Kong,http://www.wikidata.org/entity/Q8646 +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: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 +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,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: Shanxi,http://www.wikidata.org/entity/Q46913 -China: Shenzhen,http://www.wikidata.org/entity/Q15174 -China: Sichuan,http://www.wikidata.org/entity/Q19770 -China: Tianjin,http://www.wikidata.org/entity/Q11736 -China: Tibet Autonomous Region,http://www.wikidata.org/entity/Q17269 -China: Wuhan,http://www.wikidata.org/entity/Q11746 +China:Shanxi,http://www.wikidata.org/entity/Q46913 +China:Shenzhen,http://www.wikidata.org/entity/Q15174 +China:Sichuan,http://www.wikidata.org/entity/Q19770 +China:Tianjin,http://www.wikidata.org/entity/Q11736 +China:Tibet Autonomous Region,http://www.wikidata.org/entity/Q17269 China:Wuhan,http://www.wikidata.org/entity/Q11746 -China: Xinjiang,http://www.wikidata.org/entity/Q34800 -China: Yunnan,http://www.wikidata.org/entity/Q43194 -China: Zhejiang,http://www.wikidata.org/entity/Q16967 -"China: Zhejiang, Hangzhou",http://www.wikidata.org/entity/Q4970 +China:Xinjiang,http://www.wikidata.org/entity/Q34800 +China:Yunnan,http://www.wikidata.org/entity/Q43194 +China:Zhejiang,http://www.wikidata.org/entity/Q16967 +"China:Zhejiang, Hangzhou",http://www.wikidata.org/entity/Q4970 Colombia,http://www.wikidata.org/entity/Q739 -Colombia: Antioquia,http://www.wikidata.org/entity/Q123304 +Colombia:Antioquia,http://www.wikidata.org/entity/Q123304 Comoros,http://www.wikidata.org/entity/Q970 Costa Rica,http://www.wikidata.org/entity/Q800 Croatia,http://www.wikidata.org/entity/Q224 @@ -117,43 +140,146 @@ 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,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 +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,http://www.wikidata.org/entity/Q1524 +Greece:Athens,http://www.wikidata.org/entity/Q1524 Grenada,http://www.wikidata.org/entity/Q769 Guatemala,http://www.wikidata.org/entity/Q774 +Guam,http://www.wikidata.org/entity/Q16635 Guinea,http://www.wikidata.org/entity/Q1006 Guinea-Bissau,http://www.wikidata.org/entity/Q1007 Guyana,http://www.wikidata.org/entity/Q734 Haiti,http://www.wikidata.org/entity/Q790 Honduras,http://www.wikidata.org/entity/Q783 Hungary,http://www.wikidata.org/entity/Q28 +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: Ahmedabad,http://www.wikidata.org/entity/Q1070 -India: Kerala State,http://www.wikidata.org/entity/Q1186 -India: Rajkot,http://www.wikidata.org/entity/Q1815245 +"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: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 +"India:Bayad",http://www.wikidata.org/entity/Q25622187 +"India:Gujarat, Bayad",http://www.wikidata.org/entity/Q25622187 +"India:Bharuch",http://www.wikidata.org/entity/Q760153 +"India:Gujarat, Bharuch",http://www.wikidata.org/entity/Q760153 +"India:Bhavnagar",http://www.wikidata.org/entity/Q242992 +"India:Gujarat, Bhavnagar",http://www.wikidata.org/entity/Q242992 +"India:Bhuj",http://www.wikidata.org/entity/Q15244505 +"India:Gujarat, Bhuj",http://www.wikidata.org/entity/Q15244505 +"India:Botad",http://www.wikidata.org/entity/Q858162 +"India:Gujarat, Botad",http://www.wikidata.org/entity/Q858162 +"India:Choryasi",http://www.wikidata.org/entity/Q2757125 +"India:Gujarat, Choryasi",http://www.wikidata.org/entity/Q2757125 +"India:Chuda",http://www.wikidata.org/entity/Q724951 +"India:Gujarat, Chuda",http://www.wikidata.org/entity/Q724951 +"India:Dahegam",http://www.wikidata.org/entity/Q582485 +"India:Gujarat, Dahegam",http://www.wikidata.org/entity/Q582485 +"India:Dahod",http://www.wikidata.org/entity/Q186518 +"India:Gujarat, Dahod",http://www.wikidata.org/entity/Q186518 +"India:Daskroi",http://www.wikidata.org/entity/Q27684996 +"India:Gujarat, Daskroi",http://www.wikidata.org/entity/Q27684996 +"India:Dhanera",http://www.wikidata.org/entity/Q1266017 +"India:Gujarat, Dhanera",http://www.wikidata.org/entity/Q1266017 +"India:Dhansura",http://www.wikidata.org/entity/Q5269024 +"India:Gujarat, Dhansura",http://www.wikidata.org/entity/Q5269024 +"India:Dholka",http://www.wikidata.org/entity/Q1263568 +"India:Gujarat, Dholka",http://www.wikidata.org/entity/Q1263568 +"India:Gandhinagar",http://www.wikidata.org/entity/Q11910 +"India:Gujarat, Gandhinagar",http://www.wikidata.org/entity/Q11910 +"India:Ghogha",http://www.wikidata.org/entity/Q1707463 +"India:Gujarat, Ghogha",http://www.wikidata.org/entity/Q1707463 +"India:Gondal",http://www.wikidata.org/entity/Q1536978 +"India:Gujarat, Gondal",http://www.wikidata.org/entity/Q1536978 +"India:Himatnagar",http://www.wikidata.org/entity/Q1708155 +"India:Gujarat, Himatnagar",http://www.wikidata.org/entity/Q1708155 +"India:Jamnagar",http://www.wikidata.org/entity/Q1154 +"India:Gujarat, Jamnagar",http://www.wikidata.org/entity/Q1154 +"India:Jetpur",http://www.wikidata.org/entity/Q968713 +"India:Gujarat, Jetpur",http://www.wikidata.org/entity/Q968713 +"India:Junagadh",http://www.wikidata.org/entity/Q11864 +"India:Gujarat, Junagadh",http://www.wikidata.org/entity/Q11864 +"India:Kadi",http://www.wikidata.org/entity/Q2726621 +"India:Gujarat, Kadi",http://www.wikidata.org/entity/Q2726621 +"India:Kalol",http://www.wikidata.org/entity/Q2724740 +"India:Gujarat, Kalol",http://www.wikidata.org/entity/Q2724740 +"India:Kamrej",http://www.wikidata.org/entity/Q6359640 +"India:Gujarat, Kamrej",http://www.wikidata.org/entity/Q6359640 +"India:Kapadvanj",http://www.wikidata.org/entity/Q2341421 +"India:Gujarat, Kapadvanj",http://www.wikidata.org/entity/Q2341421 +"India:Kheda",http://www.wikidata.org/entity/Q775759 +"India:Gujarat, Kheda",http://www.wikidata.org/entity/Q775759 +"India:Khedbrahma",http://www.wikidata.org/entity/Q9461 +"India:Gujarat, Khedbrahma",http://www.wikidata.org/entity/Q9461 +"India:Kodinar",http://www.wikidata.org/entity/Q2239007 +"India:Gujarat, Kodinar",http://www.wikidata.org/entity/Q2239007 +"India:Mahemdavad",http://www.wikidata.org/entity/Q2233469 +"India:Gujarat, Mahemdavad",http://www.wikidata.org/entity/Q2233469 +"India:Mahuva",http://www.wikidata.org/entity/Q1924998 +"India:Gujarat, Mahuva",http://www.wikidata.org/entity/Q1924998 +"India:Mandvi",http://www.wikidata.org/entity/Q2570689 +"India:Gujarat, Mandvi",http://www.wikidata.org/entity/Q2570689 +"India:Mansa",http://www.wikidata.org/entity/Q720211 +"India:Gujarat, Mansa",http://www.wikidata.org/entity/Q720211 +"India:Modasa",http://www.wikidata.org/entity/Q2320097 +"India:Gujarat, Modasa",http://www.wikidata.org/entity/Q2320097 +"India:Nadiad",http://www.wikidata.org/entity/Q219039 +"India:Gujarat, Nadiad",http://www.wikidata.org/entity/Q219039 +"India:Olpad",http://www.wikidata.org/entity/Q2726258 +"India:Gujarat, Olpad",http://www.wikidata.org/entity/Q2726258 +"India:Palanpur",http://www.wikidata.org/entity/Q949907 +"India:Gujarat, Palanpur",http://www.wikidata.org/entity/Q949907 +"India:Prantij",http://www.wikidata.org/entity/Q2724388 +"India:Gujarat, Prantij",http://www.wikidata.org/entity/Q2724388 +"India:Rajkot",http://www.wikidata.org/entity/Q1815245 +"India:Gujarat, Rajkot",http://www.wikidata.org/entity/Q1815245 +"India:Savli",http://www.wikidata.org/entity/Q7428379 +"India:Gujarat, Savli",http://www.wikidata.org/entity/Q7428379 +"India:Surat",http://www.wikidata.org/entity/Q4629 +"India:Gujarat, Surat",http://www.wikidata.org/entity/Q4629 +"India:Talod",http://www.wikidata.org/entity/Q2570216 +"India:Gujarat, Talod",http://www.wikidata.org/entity/Q2570216 +"India:Una",http://www.wikidata.org/entity/Q1622928 +"India:Gujarat, Una",http://www.wikidata.org/entity/Q1622928 +"India:Vadodara",http://www.wikidata.org/entity/Q11909 +"India:Gujarat, Vadodara",http://www.wikidata.org/entity/Q11909 +"India:Hyderabad",http://www.wikidata.org/entity/Q1361 +"Iran:hamadan",http://www.wikidata.org/entity/Q1361 +"Iran:Hamadan",http://www.wikidata.org/entity/Q28587 +"Iraq:Erbil",http://www.wikidata.org/entity/Q132754 +"Iraq:Kurdistan region, Erbil",http://www.wikidata.org/entity/Q132754 +"Iraq:Kuedistan region, Erbil",http://www.wikidata.org/entity/Q132754 Indonesia,http://www.wikidata.org/entity/Q252 Iran,http://www.wikidata.org/entity/Q794 -Iran: Qum,http://www.wikidata.org/entity/Q131664 -Iran: Tehran,http://www.wikidata.org/entity/Q3616 +Iran:Qum,http://www.wikidata.org/entity/Q131664 +Iran:Tehran,http://www.wikidata.org/entity/Q3616 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: Cagliari,http://www.wikidata.org/entity/Q1897 -Italy: Lazio,http://www.wikidata.org/entity/Q1282 -Italy: Palermo,http://www.wikidata.org/entity/Q2656 -Italy: Rome,http://www.wikidata.org/entity/Q220 +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: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 Japan,http://www.wikidata.org/entity/Q17 +Japan:Chiba,http://www.wikidata.org/entity/Q170616 +Japan:Ishikawa,http://www.wikidata.org/entity/Q1205335 +Japan:Kochi,http://www.wikidata.org/entity/Q200251 +Japan:Saitama,http://www.wikidata.org/entity/Q134635 +Japan:Tokyo,http://www.wikidata.org/entity/Q1490 Jordan,http://www.wikidata.org/entity/Q810 +Jordan:Amman,http://www.wikidata.org/entity/Q3805 +Jordan:Irbid,http://www.wikidata.org/entity/Q194165 Kazakhstan,http://www.wikidata.org/entity/Q232 Kenya,http://www.wikidata.org/entity/Q114 Kingdom of Denmark,http://www.wikidata.org/entity/Q756617 @@ -174,42 +300,61 @@ Madagascar,http://www.wikidata.org/entity/Q1019 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 Mali,http://www.wikidata.org/entity/Q912 Malta,http://www.wikidata.org/entity/Q233 Marshall Islands,http://www.wikidata.org/entity/Q709 Mauritania,http://www.wikidata.org/entity/Q1025 Mauritius,http://www.wikidata.org/entity/Q1027 Mexico,http://www.wikidata.org/entity/Q96 +Mexico:Baja California Sur,http://www.wikidata.org/entity/Q46508 +"Mexico:Tijuana, BajaCalifornia",http://www.wikidata.org/entity/Q124739 +Mexico:Hidalgo,http://www.wikidata.org/entity/Q80903 +Mexico:Mexico City,http://www.wikidata.org/entity/Q1489 +Mexico:Mexico State,http://www.wikidata.org/entity/Q82112 +Mexico:Michoacan,http://www.wikidata.org/entity/Q79861 +Mexico:Morelos,http://www.wikidata.org/entity/Q66117 +Mexico:Oaxaca,http://www.wikidata.org/entity/Q34110 +Mexico:Puebla,http://www.wikidata.org/entity/Q79923 +Mexico:Queretaro,http://www.wikidata.org/entity/Q79754 Moldova,http://www.wikidata.org/entity/Q217 Monaco,http://www.wikidata.org/entity/Q235 Mongolia,http://www.wikidata.org/entity/Q711 Montenegro,http://www.wikidata.org/entity/Q236 Morocco,http://www.wikidata.org/entity/Q1028 +Morocco:Casablanca,http://www.wikidata.org/entity/Q7903 +Morocco:casablanca,http://www.wikidata.org/entity/Q7903 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,http://www.wikidata.org/entity/Q3314115 +Netherlands:Milheeze,http://www.wikidata.org/entity/Q3314115 +Netherlands,http://www.wikidata.org/entity/Q55 +Netherlands:Leiden,http://www.wikidata.org/entity/Q33456378 Nepal,http://www.wikidata.org/entity/Q837 +Nepal:Kathmandu,http://www.wikidata.org/entity/Q3037 New Zealand,http://www.wikidata.org/entity/Q664 +New Zealand:Auckland,http://www.wikidata.org/entity/Q37100 Nicaragua,http://www.wikidata.org/entity/Q811 Niger,http://www.wikidata.org/entity/Q1032 Nigeria,http://www.wikidata.org/entity/Q1033 -Nigeria: Lagos,http://www.wikidata.org/entity/Q8673 +Nigeria:Lagos,http://www.wikidata.org/entity/Q8673 North Korea,http://www.wikidata.org/entity/Q423 North Macedonia,http://www.wikidata.org/entity/Q221 Norway,http://www.wikidata.org/entity/Q20 Oman,http://www.wikidata.org/entity/Q842 Ottoman Empire,http://www.wikidata.org/entity/Q12560 Pakistan,http://www.wikidata.org/entity/Q843 -Pakistan: Gilgit,http://www.wikidata.org/entity/Q609024 -Pakistan: KPK,http://www.wikidata.org/entity/Q183314 +Pakistan:Gilgit,http://www.wikidata.org/entity/Q609024 +Pakistan:Karachi,http://www.wikidata.org/entity/Q8660 +Pakistan:KPK,http://www.wikidata.org/entity/Q183314 Palau,http://www.wikidata.org/entity/Q695 Panama,http://www.wikidata.org/entity/Q804 Papua New Guinea,http://www.wikidata.org/entity/Q691 Paraguay,http://www.wikidata.org/entity/Q733 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 Poland,http://www.wikidata.org/entity/Q36 Portugal,http://www.wikidata.org/entity/Q45 @@ -220,6 +365,12 @@ Republic of Geneva,http://www.wikidata.org/entity/Q23366230 Republic of the Congo,http://www.wikidata.org/entity/Q971 Romania,http://www.wikidata.org/entity/Q218 Russia,http://www.wikidata.org/entity/Q159 +Russia:Saint Petersburg,http://www.wikidata.org/entity/Q656 +"Russia:Saint Petersburg, Krasnoye Selo",http://www.wikidata.org/entity/Q155587 +"Russia:Leningrad region,Kipen",http://www.wikidata.org/entity/Q4221032 +"Russia:Moscow",http://www.wikidata.org/entity/Q649 +"Russia:Moscow region",http://www.wikidata.org/entity/Q649 +"Russia:Republic of Buryatia,Ulan-Ude",http://www.wikidata.org/entity/Q6816 Rwanda,http://www.wikidata.org/entity/Q1037 Saint Kitts and Nevis,http://www.wikidata.org/entity/Q763 Saint Lucia,http://www.wikidata.org/entity/Q760 @@ -228,23 +379,33 @@ Samoa,http://www.wikidata.org/entity/Q683 San Marino,http://www.wikidata.org/entity/Q238 São Tomé and Príncipe,http://www.wikidata.org/entity/Q1039 Saudi Arabia,http://www.wikidata.org/entity/Q851 +Saudi Arabia:Jeddah,http://www.wikidata.org/entity/Q374365 Senegal,http://www.wikidata.org/entity/Q1041 Serbia,http://www.wikidata.org/entity/Q403 +Serbia:Kraljevo,http://www.wikidata.org/entity/Q206317 +Serbia:Novi Pazar,http://www.wikidata.org/entity/Q202453 +Serbia:Novi Sad,http://www.wikidata.org/entity/Q55630 +Serbia:Uzice,http://www.wikidata.org/entity/Q59473 Seychelles,http://www.wikidata.org/entity/Q1042 Sierra Leone,http://www.wikidata.org/entity/Q1044 +Sierra Leone:Bonthe,http://www.wikidata.org/entity/Q892886 +Sierra Leone:Freetown,http://www.wikidata.org/entity/Q3780 Singapore,http://www.wikidata.org/entity/Q334 Slovakia,http://www.wikidata.org/entity/Q214 Slovenia,http://www.wikidata.org/entity/Q215 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 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 Spain,http://www.wikidata.org/entity/Q29 -Spain: Valencia,http://www.wikidata.org/entity/Q8818 +Spain:ASTURIAS,http://www.wikidata.org/entity/Q3934 +Spain:Asturias,http://www.wikidata.org/entity/Q3934 +Spain:Donostia-San Sebatian,http://www.wikidata.org/entity/Q10313 +Spain:Valencia,http://www.wikidata.org/entity/Q8818 Sri Lanka,http://www.wikidata.org/entity/Q854 State of Los Altos,http://www.wikidata.org/entity/Q738264 Sudan,http://www.wikidata.org/entity/Q1049 @@ -262,7 +423,9 @@ Togo,http://www.wikidata.org/entity/Q945 Tonga,http://www.wikidata.org/entity/Q678 Trinidad and Tobago,http://www.wikidata.org/entity/Q754 Tunisia,http://www.wikidata.org/entity/Q948 -Tunisia: Tunis,http://www.wikidata.org/entity/Q3572 +Tunisia:Tunis,http://www.wikidata.org/entity/Q3572 +Tunisia:Ben Arous,http://www.wikidata.org/entity/Q816443 +Tunisia:Bizerte,http://www.wikidata.org/entity/Q189546 Turkey,http://www.wikidata.org/entity/Q43 Turkmenistan,http://www.wikidata.org/entity/Q874 Tuvalu,http://www.wikidata.org/entity/Q672 @@ -273,122 +436,282 @@ United Arab Republic,http://www.wikidata.org/entity/Q170468 United Kingdom,http://www.wikidata.org/entity/Q145 United States of America,http://www.wikidata.org/entity/Q30 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+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: Washington,Yakima County",http://www.wikidata.org/entity/Q156629 -"USA: Washington, Yakima County",http://www.wikidata.org/entity/Q156629 -"USA: Washington,Whatcom County",http://www.wikidata.org/entity/Q156623 -"USA: Dane County, Wisconsin",http://www.wikidata.org/entity/Q502200 -USA: WV,http://www.wikidata.org/entity/Q1371 -USA: WY,http://www.wikidata.org/entity/Q1214 +"USA:Washington, Yakima County",http://www.wikidata.org/entity/Q156629 +"USA:Washington,Whatcom County",http://www.wikidata.org/entity/Q156623 +"USA:Dane County, Wisconsin",http://www.wikidata.org/entity/Q502200 +USA:WV,http://www.wikidata.org/entity/Q1371 +USA:WY,http://www.wikidata.org/entity/Q1214 +"USA:WI,Madison",http://www.wikidata.org/entity/Q43788 +"USA:Madison, Wisconsin",http://www.wikidata.org/entity/Q43788 Uzbekistan,http://www.wikidata.org/entity/Q265 Vanuatu,http://www.wikidata.org/entity/Q686 Vatican City,http://www.wikidata.org/entity/Q237 Venezuela,http://www.wikidata.org/entity/Q717 Viet nam,http://www.wikidata.org/entity/Q881 Viet Nam,http://www.wikidata.org/entity/Q881 -Viet Nam: Ho Chi Minh city,http://www.wikidata.org/entity/Q1854 +Viet Nam:Ho Chi Minh city,http://www.wikidata.org/entity/Q1854 Vietnam,http://www.wikidata.org/entity/Q881 Yemen,http://www.wikidata.org/entity/Q805 Zambia,http://www.wikidata.org/entity/Q953 diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv index 0bfc455..2add179 100644 --- a/scripts/dict_ontology_standardization/ncbi_host_species.csv +++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv @@ -3,6 +3,7 @@ human,http://purl.obolibrary.org/obo/NCBITaxon_9606 Human,http://purl.obolibrary.org/obo/NCBITaxon_9606 sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606 homosapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606 +howo 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 59c4800..0a3f926 100644 --- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv +++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -38,6 +38,7 @@ MGISEQ2000,http://virtual-bh/MGISEQ2000 Illumina HiSeq X,http://www.ebi.ac.uk/efo/EFO_0008567 ONT GridION X5,http://www.ebi.ac.uk/efo/EFO_0008633 ONT PremethION,http://www.ebi.ac.uk/efo/EFO_0008634 +PromethION,http://www.ebi.ac.uk/efo/EFO_0008634 PacBio RS II,http://www.ebi.ac.uk/efo/EFO_0008631 PacBio Sequel System,http://www.ebi.ac.uk/efo/EFO_0008630 Illumina Genome Analyzer,http://www.ebi.ac.uk/efo/EFO_0004200 diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv index 0fa2219..42168e6 100644 --- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv +++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv @@ -1,14 +1,23 @@ nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831 +Nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831 +NPS,http://purl.obolibrary.org/obo/NCIT_C155831 +NasopharyngealSwab,http://purl.obolibrary.org/obo/NCIT_C155831 +Naso-pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831 +nasopharingeal swab,http://purl.obolibrary.org/obo/NCIT_C155831 +Nasopharyngeal (NP) Swab,http://purl.obolibrary.org/obo/NCIT_C155831 nasopharyngeal swabs,http://purl.obolibrary.org/obo/NCIT_C155831 nasopharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831 nasopharyngeal,http://purl.obolibrary.org/obo/NCIT_C155831 +Nasopharyngeal,http://purl.obolibrary.org/obo/NCIT_C155831 respiratory swab,http://purl.obolibrary.org/obo/NCIT_C155831 naso-pharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831 nasopharyngeal aspirate,http://purl.obolibrary.org/obo/NCIT_C155831 nasal swab specimen,http://purl.obolibrary.org/obo/NCIT_C155831 +nasal swal,http://purl.obolibrary.org/obo/NCIT_C155831 pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831 respiratory secretion,http://purl.obolibrary.org/obo/NCIT_C155831 mid-nasal swab,http://purl.obolibrary.org/obo/NCIT_C155831 +Mid-nasal swab,http://purl.obolibrary.org/obo/NCIT_C155831 nasopharyngeal (throat) washings,http://purl.obolibrary.org/obo/NCIT_C155831 oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835 throat swab,http://purl.obolibrary.org/obo/NCIT_C155835 @@ -16,7 +25,10 @@ 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 +oral-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835 +oro-pharngyl swab,http://purl.obolibrary.org/obo/NCIT_C155835 Oro-pharyngeal swab,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 oro pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835 buccal swab,http://purl.obolibrary.org/obo/NCIT_C155835 @@ -33,4 +45,5 @@ aspirate,http://purl.obolibrary.org/obo/NCIT_C13347 stool,http://purl.obolibrary.org/obo/NCIT_C13234 serum,http://purl.obolibrary.org/obo/NCIT_C13325 saliva,http://purl.obolibrary.org/obo/NCIT_C13275 +Deep throat saliva,http://purl.obolibrary.org/obo/NCIT_C13275 nasal swab,http://purl.obolibrary.org/obo/NCIT_C132119 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 dbebfbb..f314a1d 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 @@ -121,10 +121,11 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x for line in f: if len(line.split(',')) > 2: term, uri = line.strip('\n').split('",') - term = term.strip('"') else: term, uri = line.strip('\n').split(',') + term = term.strip('"') + if term in term_to_uri_dict: print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term)) continue @@ -243,6 +244,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text if GBQualifier_name_text == 'host': + GBQualifier_value_text = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female if GBQualifier_value_text in term_to_uri_dict: # Cases like 'Felis catus; Domestic Shorthair' info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text] @@ -314,10 +316,12 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_value_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[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']: + 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']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['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']: + 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'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] + elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']: + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']] elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']: @@ -353,8 +357,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) info_for_yaml_dict['sample']['collection_date'] = date_to_write elif GBQualifier_name_text in ['lat_lon', 'country']: - if GBQualifier_value_text == 'Hong Kong': - GBQualifier_value_text = 'China: Hong Kong' + if GBQualifier_name_text == 'country' and ': ' in GBQualifier_value_text: + GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':') if GBQualifier_value_text in term_to_uri_dict: info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[GBQualifier_value_text] |