From 07bc4c65535437b8e9e0744f08da8cea541d0116 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 7 Apr 2020 15:28:42 -0400 Subject: Add metadata validation with schema-salad --- bh20sequploader/bh20seq-schema.yml | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 bh20sequploader/bh20seq-schema.yml (limited to 'bh20sequploader/bh20seq-schema.yml') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml new file mode 100644 index 0000000..6e0973a --- /dev/null +++ b/bh20sequploader/bh20seq-schema.yml @@ -0,0 +1,36 @@ +$graph: + +- name: sampleInformationSchema + type: record + fields: + location: string + host: string + sequenceTechnology: string + assemblyMethod: string + +- name: InstituteInformationSchema + type: record + fields: + OriginatingLab: string + SubmittingLab: string + +- name: SubmitterInformationSchema + type: record + fields: + Submitter: string + submissionDate: string + +- name: VirusDetailSchema + type: record + fields: + VirusName: string + AccessionId: string + +- name: MainSchema + type: record + documentRoot: true + fields: + sampleInformation: sampleInformationSchema + InstituteInformation: InstituteInformationSchema + SubmitterInformation: SubmitterInformationSchema + VirusDetail: VirusDetailSchema -- cgit v1.2.3 From d7498093d0f5e0db052ef88815d57c2648d09425 Mon Sep 17 00:00:00 2001 From: lltommy Date: Thu, 9 Apr 2020 14:34:54 +0200 Subject: Updating schema and examples. This is still work in progress but we get there --- bh20sequploader/bh20seq-schema.yml | 60 ++++++++++++++++++++++++++------------ example/metadata.yaml | 49 ++++++++++++++++++++++--------- example/minimal_example.yaml | 14 +++++++++ 3 files changed, 91 insertions(+), 32 deletions(-) create mode 100644 example/minimal_example.yaml (limited to 'bh20sequploader/bh20seq-schema.yml') 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 -- cgit v1.2.3 From deedb2ed7046bbe81136b8d9d1edc353984d356b Mon Sep 17 00:00:00 2001 From: lltommy Date: Thu, 9 Apr 2020 20:38:55 +0200 Subject: Adding functionality of turning keys into ontology terms (URI). This is work in progress - of course! --- bh20sequploader/bh20seq-schema.yml | 30 ++++++++++++++++++++++++------ 1 file changed, 24 insertions(+), 6 deletions(-) (limited to 'bh20sequploader/bh20seq-schema.yml') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 38cfb48..fd9e854 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -3,14 +3,20 @@ $graph: - name: hostSchema type: record fields: + host_species: + type: string + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000532 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? + host_treatment: + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000727 additional_host_information: string? - name: sampleSchema @@ -20,7 +26,10 @@ $graph: collecting_institution: string specimen_source: string? collection_date: string? - collection_location: string? + collection_location: + type: string? + jsonldPredicate: + _id: https://schema.org/fromLocation sample_storage_conditions: string? additional_collection_information: string? @@ -33,9 +42,18 @@ $graph: - name: technologySchema type: record fields: - sample_sequencing_technology: string - sequence_assembly_method: string? - sequencing_coverage: string? + sample_sequencing_technology: + type: string + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000532 + sequence_assembly_method: + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0002699 + sequencing_coverage: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/FLU_0000848 - name: submitterSchema type: record -- cgit v1.2.3 From dbe094a150d6c969b3d69f112b3538e6a87a74a2 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 9 Apr 2020 15:59:46 -0400 Subject: Add "sequencefile" for the metadata subject. --- bh20sequploader/bh20seq-schema.yml | 13 ++++++++++++- example/metadata.yaml | 2 +- 2 files changed, 13 insertions(+), 2 deletions(-) (limited to 'bh20sequploader/bh20seq-schema.yml') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index fd9e854..5c962d1 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,3 +1,8 @@ +$base: http://biohackathon.org/bh20-seq-schema +$namespaces: + sch: https://schema.org/ + efo: http://www.ebi.ac.uk/efo/ + obo: http://purl.obolibrary.org/obo/ $graph: - name: hostSchema @@ -75,4 +80,10 @@ $graph: sample: sampleSchema virus: virusSchema? technology: technologySchema - submitter: submitterSchema \ No newline at end of file + submitter: submitterSchema + sequencefile: + doc: The subject (eg the fasta/fastq file) that this metadata describes + type: string? + jsonldPredicate: + _id: "@id" + _type: "@id" diff --git a/example/metadata.yaml b/example/metadata.yaml index 8a93379..41ff93e 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -35,4 +35,4 @@ submitter: provider_sample_id: string submitter_sample_id: string authors: testAuthor - submitter_id: X12 \ No newline at end of file + submitter_id: X12 -- cgit v1.2.3