diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 145 | ||||
| -rw-r--r-- | example/metadata.yaml | 4 | ||||
| -rw-r--r-- | example/minimal_example.yaml | 6 |
3 files changed, 128 insertions, 27 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 5c962d1..cf9b015 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -3,6 +3,10 @@ $namespaces: sch: https://schema.org/ efo: http://www.ebi.ac.uk/efo/ obo: http://purl.obolibrary.org/obo/ + sio: http://semanticscience.org/resource/ + edam: http://edamontology.org/ + evs: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# + $graph: - name: hostSchema @@ -12,37 +16,93 @@ $graph: type: string jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000532 - host_id: string - host_common_name: string? - host_sex: string? - host_age: int? - host_age_unit: string? - host_health_status: string? + host_id: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 + host_common_name: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NOMEN_0000037 + host_sex: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/PATO_0000047 + host_age: + type: int? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/PATO_0000011 + host_age_unit: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/UO_0000036 + host_health_status: + type: string? + jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688 host_treatment: type: string? jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000727 - additional_host_information: string? + host_vaccination: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/VO_0000001 + additional_host_information: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 - name: sampleSchema type: record fields: - collector_name: string - collecting_institution: string - specimen_source: string? - collection_date: string? + collector_name: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001895 + collecting_institution: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + specimen_source: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001479 + collection_date: + type: string? + jsonldPredicate: + _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164 collection_location: type: string? jsonldPredicate: - _id: https://schema.org/fromLocation - sample_storage_conditions: string? - additional_collection_information: string? + _id: http://purl.obolibrary.org/obo/GAZ_00000448 + sample_storage_conditions: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001472 + additional_collection_information: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + sample_id: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 + source_database_accession: + type: string? + jsonldPredicate: + _id: http://edamontology.org/data_2091 - name: virusSchema type: record fields: - virus_species: string? - virus_strain: string? + virus_species: + type: string? + jsonldPredicate: + _id: http://edamontology.org/data_1875 + virus_strain: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_010055 - name: technologySchema type: record @@ -50,7 +110,7 @@ $graph: sample_sequencing_technology: type: string jsonldPredicate: - _id: http://www.ebi.ac.uk/efo/EFO_0000532 + _id: http://purl.obolibrary.org/obo/OBI_0600047 sequence_assembly_method: type: string? jsonldPredicate: @@ -63,14 +123,42 @@ $graph: - 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? + submitter_name: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000116 + submitter_date: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C94162 + submitter_address: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000172 + originating_lab: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C37984 + lab_address: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0600047 + provider_sample_id: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C37900 + submitter_sample_id: + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0001741 + authors: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C42781 + submitter_id: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 - name: MainSchema type: record @@ -81,9 +169,14 @@ $graph: virus: virusSchema? technology: technologySchema submitter: submitterSchema + submission: + type: string + jsonldPredicate: + _id: "@id" + #_type: "@id" sequencefile: doc: The subject (eg the fasta/fastq file) that this metadata describes type: string? jsonldPredicate: _id: "@id" - _type: "@id" + _type: "@id" \ No newline at end of file diff --git a/example/metadata.yaml b/example/metadata.yaml index 41ff93e..a2f6e57 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -1,3 +1,5 @@ +submission: publicSequenceResource + host: host_id: XX1 host_species: string @@ -10,6 +12,7 @@ host: additional_host_information: string sample: + sample_id: XXX collector_name: XXX collecting_institution: XXX specimen_source: XXX @@ -36,3 +39,4 @@ submitter: submitter_sample_id: string authors: testAuthor submitter_id: X12 + submitter_date: Subdate diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml index 201b080..f312ab7 100644 --- a/example/minimal_example.yaml +++ b/example/minimal_example.yaml @@ -1,8 +1,11 @@ +submission: publicSequenceResource + host: host_id: XX host_species: string sample: + sample_id: XXX collector_name: XXX collecting_institution: XXX @@ -11,4 +14,5 @@ technology: submitter: submitter_name: tester - originating_lab: testLab \ No newline at end of file + originating_lab: testLab + submitter_date: Subdate \ No newline at end of file |