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| author | LLTommy | 2020-06-24 08:45:07 +0200 |
|---|---|---|
| committer | GitHub | 2020-06-24 08:45:07 +0200 |
| commit | 73ac4b91a44779a54c77e29ba1e8ee52291e390e (patch) | |
| tree | b90d3576b3f54e19c0d07156f7b69abb0e12fba4 /scripts/dict_ontology_standardization | |
| parent | b188fa4d896e1159ae424ab1c9bcfb21eb8ac67b (diff) | |
| parent | 2d822c049f2b7f3e62a3ac4c19c827428b6f73e2 (diff) | |
| download | bh20-seq-resource-73ac4b91a44779a54c77e29ba1e8ee52291e390e.tar.gz bh20-seq-resource-73ac4b91a44779a54c77e29ba1e8ee52291e390e.tar.lz bh20-seq-resource-73ac4b91a44779a54c77e29ba1e8ee52291e390e.zip | |
Merge pull request #87 from AndreaGuarracino/patch-20
added script to crete metadata for SRA data; new dictionary entries; little directory changes
Diffstat (limited to 'scripts/dict_ontology_standardization')
3 files changed, 12 insertions, 0 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index 85d4e8a..204f7f2 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -239,6 +239,7 @@ 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 African Republic,http://www.wikidata.org/entity/Q550374 South Korea,http://www.wikidata.org/entity/Q884 South Sudan,http://www.wikidata.org/entity/Q958 @@ -279,6 +280,7 @@ 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: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 @@ -299,6 +301,7 @@ 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:Los Angeles,http://www.wikidata.org/entity/Q65 "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 @@ -330,6 +333,7 @@ USA: PA,http://www.wikidata.org/entity/Q1400 USA: RI,http://www.wikidata.org/entity/Q1387 "USA: San Francisco, CA",http://www.wikidata.org/entity/Q62 USA: SC,http://www.wikidata.org/entity/Q1456 +USA: South Carolina,http://www.wikidata.org/entity/Q1456 USA: SD,http://www.wikidata.org/entity/Q1211 "USA: Snohomish County, WA",http://www.wikidata.org/entity/Q110403 USA: TN,http://www.wikidata.org/entity/Q1509 diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv index 102d458..bc6ac04 100644 --- a/scripts/dict_ontology_standardization/ncbi_host_species.csv +++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv @@ -1,6 +1,7 @@ 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 +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 110e90b..964cbf3 100644 --- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv +++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -1,3 +1,9 @@ +Illumina HiSeq 1000,http://www.ebi.ac.uk/efo/EFO_0004204 +Illumina HiSeq 2000,http://www.ebi.ac.uk/efo/EFO_0004203 +Illumina HiSeq 2500,http://www.ebi.ac.uk/efo/EFO_0008565 +Illumina HiSeq 3000,http://www.ebi.ac.uk/efo/EFO_0008564 +Illumina HiSeq 4000,http://www.ebi.ac.uk/efo/EFO_0008563 +Illumina iSeq 100,http://www.ebi.ac.uk/efo/EFO_0008635 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 @@ -14,6 +20,7 @@ ONT (Oxford Nanopore Technologies),http://purl.obolibrary.org/obo/NCIT_C146818 Oxford Nanopore Technology,http://purl.obolibrary.org/obo/NCIT_C146818 Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632 MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632 +MinION,http://www.ebi.ac.uk/efo/EFO_0008632 Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818 Illumina MiSeq,http://www.ebi.ac.uk/efo/EFO_0004205 Illumina,http://purl.obolibrary.org/obo/OBI_0000759 |