From 7c5c91000661f268c4fc8bc2001918c5e86a9aee Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Sat, 18 Apr 2020 22:16:13 +0200 Subject: ncbi_speciesman_source mapping --- scripts/dict_ontology_standardization | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 scripts/dict_ontology_standardization diff --git a/scripts/dict_ontology_standardization b/scripts/dict_ontology_standardization new file mode 100644 index 0000000..fcd6c94 --- /dev/null +++ b/scripts/dict_ontology_standardization @@ -0,0 +1,22 @@ +nasopharyngeal swab, http://purl.obolibrary.org/obo/NCIT_C155831 +nasopharyngeal exudate,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 +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 +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 +oro-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835 +buccal swab,http://purl.obolibrary.org/obo/NCIT_C155835 +throat washing,http://purl.obolibrary.org/obo/NCIT_C155835 +Throat Swab,http://purl.obolibrary.org/obo/NCIT_C155835 +throat (oropharyngeal) swab,http://purl.obolibrary.org/obo/NCIT_C155835 +bronchoalveolar lavage fluid,http://purl.obolibrary.org/obo/NCIT_C13195 +swab,http://purl.obolibrary.org/obo/NCIT_C13195 +oral swab,http://purl.obolibrary.org/obo/NCIT_C13195 +bronchoalveolar lavage,http://purl.obolibrary.org/obo/NCIT_C13195 +sputum,http://purl.obolibrary.org/obo/NCIT_C13278 -- cgit v1.2.3 From d0aae0bbaa1ba3a6f25bc5bb02a37af5ad1d54fc Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Sat, 18 Apr 2020 22:17:32 +0200 Subject: Delete dict_ontology_standardization --- scripts/dict_ontology_standardization | 22 ---------------------- 1 file changed, 22 deletions(-) delete mode 100644 scripts/dict_ontology_standardization diff --git a/scripts/dict_ontology_standardization b/scripts/dict_ontology_standardization deleted file mode 100644 index fcd6c94..0000000 --- a/scripts/dict_ontology_standardization +++ /dev/null @@ -1,22 +0,0 @@ -nasopharyngeal swab, http://purl.obolibrary.org/obo/NCIT_C155831 -nasopharyngeal exudate,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 -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 -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 -oro-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835 -buccal swab,http://purl.obolibrary.org/obo/NCIT_C155835 -throat washing,http://purl.obolibrary.org/obo/NCIT_C155835 -Throat Swab,http://purl.obolibrary.org/obo/NCIT_C155835 -throat (oropharyngeal) swab,http://purl.obolibrary.org/obo/NCIT_C155835 -bronchoalveolar lavage fluid,http://purl.obolibrary.org/obo/NCIT_C13195 -swab,http://purl.obolibrary.org/obo/NCIT_C13195 -oral swab,http://purl.obolibrary.org/obo/NCIT_C13195 -bronchoalveolar lavage,http://purl.obolibrary.org/obo/NCIT_C13195 -sputum,http://purl.obolibrary.org/obo/NCIT_C13278 -- cgit v1.2.3 From 4a7f822a502ca213d405c93cea9b330b3d32ba20 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Sat, 18 Apr 2020 22:18:11 +0200 Subject: ncbi_speciesman_source mapping --- .../ncbi_speciesman_source.csv | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 scripts/dict_ontology_standardization/ncbi_speciesman_source.csv diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv new file mode 100644 index 0000000..fcd6c94 --- /dev/null +++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv @@ -0,0 +1,22 @@ +nasopharyngeal swab, http://purl.obolibrary.org/obo/NCIT_C155831 +nasopharyngeal exudate,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 +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 +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 +oro-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835 +buccal swab,http://purl.obolibrary.org/obo/NCIT_C155835 +throat washing,http://purl.obolibrary.org/obo/NCIT_C155835 +Throat Swab,http://purl.obolibrary.org/obo/NCIT_C155835 +throat (oropharyngeal) swab,http://purl.obolibrary.org/obo/NCIT_C155835 +bronchoalveolar lavage fluid,http://purl.obolibrary.org/obo/NCIT_C13195 +swab,http://purl.obolibrary.org/obo/NCIT_C13195 +oral swab,http://purl.obolibrary.org/obo/NCIT_C13195 +bronchoalveolar lavage,http://purl.obolibrary.org/obo/NCIT_C13195 +sputum,http://purl.obolibrary.org/obo/NCIT_C13278 -- cgit v1.2.3 From 96409bac49eafa1f797a667e662efeb0431383f7 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Sat, 18 Apr 2020 22:18:30 +0200 Subject: dictionaries for mapping --- .../ncbi_countries.csv | 243 +++++++++++++++++++++ .../ncbi_sequencing_technology.csv | 15 ++ 2 files changed, 258 insertions(+) create mode 100644 scripts/dict_ontology_standardization/ncbi_countries.csv create mode 100644 scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv new file mode 100644 index 0000000..9813f52 --- /dev/null +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -0,0 +1,243 @@ +USA,http://www.wikidata.org/entity/Q30 +USA: CA,http://www.wikidata.org/entity/Q99 +USA: ME,http://www.wikidata.org/entity/Q724 +USA: NH,http://www.wikidata.org/entity/Q759 +USA: 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b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -0,0 +1,15 @@ +Illumian NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173 +Illumina NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173 +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://www.ebi.ac.uk/efo/EFO_0008632 +Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632 +MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632 +Illumina MiSeq,http://www.ebi.ac.uk/efo/EFO_0004205 +Illumina,http://purl.obolibrary.org/obo/OBI_0000759 +Oxford Nanopore technology,http://purl.obolibrary.org/obo/NCIT_C146818 +Oxford Nanopore Technologies,http://purl.obolibrary.org/obo/NCIT_C146818 +Oxford Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818 +IonTorrent,http://purl.obolibrary.org/obo/NCIT_C125894 +Ion Torrent X5Plus,http://purl.obolibrary.org/obo/NCIT_C125894 +Sanger dideoxy sequencing,http://purl.obolibrary.org/obo/NCIT_C19641 -- cgit v1.2.3