diff options
| -rw-r--r-- | .gitignore | 2 | ||||
| -rw-r--r-- | example/esr_example.yaml | 41 | ||||
| -rw-r--r-- | example/uthsc_example.yaml | 39 |
3 files changed, 82 insertions, 0 deletions
@@ -22,3 +22,5 @@ venv/ ENV/ env.bak/ venv.bak/ + +relabeledSeqs* diff --git a/example/esr_example.yaml b/example/esr_example.yaml new file mode 100644 index 0000000..48b11e4 --- /dev/null +++ b/example/esr_example.yaml @@ -0,0 +1,41 @@ +id: placeholder + +license: + license_type: http://creativecommons.org/licenses/by/4.0/ + title: "SARS-CoV-2 New Zealand" + attribution_name: "ESR" + attribution_url: https://www.esr.cri.nz/ + +host: + host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 + additional_host_information: Optional free text field for additional information + +sample: + sample_id: "20VR0174" + collection_date: "2020-02-26" + collection_location: https://www.wikidata.org/wiki/Q37100 + specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831] + source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence] ?? + additional_collection_information: Optional free text field for additional information + +virus: + virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 + virus_strain: SARS-CoV-2/human/CHN/HS_8/2020 + +technology: + sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION + sequence_assembly_method: https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics + additional_technology_information: "Artic V3 workflow" + +submitter: + authors: [Jemma L Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Sue Huang, Jordan Douglas, Fabio K Mendes, Andrew Sporle, Michael G Baker, David R Murdoch, Nigel French, Colin R Simpson, David Welch, Alexei J Drummond, Edward C Holmes, Sebastian Duchene, Joep de Ligt] + submitter_name: [Joep de Ligt] + submitter_address: "PO Box 50348, Porirua 5240, New Zealand" + originating_lab: ESR + provider_sample_id: "20VR0174" + submitter_sample_id: "PRJNA648792" + submitted_to: https://www.ncbi.nlm.nih.gov/biosample + publication: https://doi.org/10.1101/2020.08.05.20168930 + public_date: "2020-08-20" + submitter_orcid: [https://orcid.org/0000-0003-0970-0153] + additional_submitter_information: Optional free text field for additional information diff --git a/example/uthsc_example.yaml b/example/uthsc_example.yaml new file mode 100644 index 0000000..18188dc --- /dev/null +++ b/example/uthsc_example.yaml @@ -0,0 +1,39 @@ +id: placeholder + +license: + license_type: http://creativecommons.org/licenses/by/4.0/ + title: "Sample" + attribution_name: "Mariah Taylor, Colleen Jonsson" + attribution_url: https://www.uthsc.edu/rbl/ + +host: + host_id: TN_UT2 + host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 + additional_host_information: Optional free text field for additional information + +sample: + sample_id: TN_UT2 + specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831] + collection_date: "2020-04-26" + collection_location: https://www.wikidata.org/wiki/Q3289517 + additional_collection_information: Optional free text field for additional information + +virus: + virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 + virus_strain: SARS-CoV-2/human/USA/AL_UT14/2020 + +technology: + sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION + sequence_assembly_method: guppy + additional_technology_information: Optional free text field for additional information + +submitter: + authors: [Mariah Taylor, Colleen Jonsson] + submitter_name: [Mariah Taylor] + submitter_address: UTHSC, Memphis, Tennessee 38163, USA + originating_lab: Regional Biocontainment Laboratory + provider_sample_id: XXX1 + submitter_sample_id: XXX2 + publication: PMID00001113 + submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] + additional_submitter_information: Optional free text field for additional information |