diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 60 | ||||
| -rw-r--r-- | example/metadata.yaml | 49 | ||||
| -rw-r--r-- | example/minimal_example.yaml | 14 |
3 files changed, 91 insertions, 32 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 6e0973a..38cfb48 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,36 +1,60 @@ $graph: -- name: sampleInformationSchema +- name: hostSchema type: record fields: - location: string - host: string - sequenceTechnology: string - assemblyMethod: string + host_id: string + host_species: string + host_common_name: string? + host_sex: string? + host_age: int? + host_age_unit: string? + host_health_status: string? + host_treatment: string? + additional_host_information: string? -- name: InstituteInformationSchema +- name: sampleSchema type: record fields: - OriginatingLab: string - SubmittingLab: string + collector_name: string + collecting_institution: string + specimen_source: string? + collection_date: string? + collection_location: string? + sample_storage_conditions: string? + additional_collection_information: string? -- name: SubmitterInformationSchema +- name: virusSchema type: record fields: - Submitter: string - submissionDate: string + virus_species: string? + virus_strain: string? -- name: VirusDetailSchema +- name: technologySchema type: record fields: - VirusName: string - AccessionId: string + sample_sequencing_technology: string + sequence_assembly_method: string? + sequencing_coverage: string? + +- name: submitterSchema + type: record + fields: + submitter_name: string + submitter_address: string? + originating_lab: string + lab_address: string? + provider_sample_id: string? + submitter_sample_id: string? + authors: string? + submitter_id: string? - name: MainSchema type: record documentRoot: true fields: - sampleInformation: sampleInformationSchema - InstituteInformation: InstituteInformationSchema - SubmitterInformation: SubmitterInformationSchema - VirusDetail: VirusDetailSchema + host: hostSchema + sample: sampleSchema + virus: virusSchema? + technology: technologySchema + submitter: submitterSchema \ No newline at end of file diff --git a/example/metadata.yaml b/example/metadata.yaml index 587d0be..8a93379 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -1,17 +1,38 @@ -sampleInformation: - location: "USA" - host : "Homo Sapiens" - sequenceTechnology: "Sanger" - assemblyMethod: "CLC Genomics" +host: + host_id: XX1 + host_species: string + host_common_name: string + host_sex: string + host_age: 20 + host_age_unit: string + host_health_status: string + host_treatment: string + additional_host_information: string -InstituteInformation: - OriginatingLab: "Erik's kitchen" - SubmittingLab: "National Institute for Viral Disease Control and Prevention, China CDC" +sample: + collector_name: XXX + collecting_institution: XXX + specimen_source: XXX + collection_date: XXX + collection_location: XXX + sample_storage_conditions: XXX + additional_collection_information: XXX -SubmitterInformation: - Submitter: "National Institute for Viral Disease Control and Prevention, China CDC" - submissionDate: "04-04-2020" +virus: + virus_species: XX + virus_strain: XX -VirusDetail: - VirusName: "hCoV-19/USA/identifer/2020" - AccessionId: "EPI_ISL_Random" +technology: + sample_sequencing_technology: XX + sequence_assembly_method: XX + sequencing_coverage: 70x + +submitter: + submitter_name: tester + submitter_address: testerAdd + originating_lab: testLab + lab_address: labAdd + provider_sample_id: string + submitter_sample_id: string + authors: testAuthor + submitter_id: X12 \ No newline at end of file diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml new file mode 100644 index 0000000..201b080 --- /dev/null +++ b/example/minimal_example.yaml @@ -0,0 +1,14 @@ +host: + host_id: XX + host_species: string + +sample: + collector_name: XXX + collecting_institution: XXX + +technology: + sample_sequencing_technology: XX + +submitter: + submitter_name: tester + originating_lab: testLab \ No newline at end of file |