aboutsummaryrefslogtreecommitdiff
path: root/example
diff options
context:
space:
mode:
authorPjotr Prins2020-10-26 08:01:13 +0000
committerPjotr Prins2020-10-26 09:00:39 +0000
commit9745e79e71797bc445f193e8d1dafc5b805a7fc4 (patch)
tree68971864c8512bcf09f1bf266a1dbbb26e0863b6 /example
parentbc6abed0303d985036458c3e7fd8a67b3fad1353 (diff)
downloadbh20-seq-resource-9745e79e71797bc445f193e8d1dafc5b805a7fc4.tar.gz
bh20-seq-resource-9745e79e71797bc445f193e8d1dafc5b805a7fc4.tar.lz
bh20-seq-resource-9745e79e71797bc445f193e8d1dafc5b805a7fc4.zip
Adding upload metadata examples
Diffstat (limited to 'example')
-rw-r--r--example/esr_example.yaml41
-rw-r--r--example/uthsc_example.yaml39
2 files changed, 80 insertions, 0 deletions
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