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| author | lltommy | 2020-04-13 02:36:18 +0200 |
|---|---|---|
| committer | lltommy | 2020-04-13 02:36:18 +0200 |
| commit | bc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab (patch) | |
| tree | 45087b43c880dc459ea05793005ae8377306d98e | |
| parent | 31686ba2e1b2edec29229ab5adb28b366893f17b (diff) | |
| download | bh20-seq-resource-bc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab.tar.gz bh20-seq-resource-bc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab.tar.lz bh20-seq-resource-bc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab.zip | |
Starting to turn values into IRIs ...
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 10 | ||||
| -rw-r--r-- | example/metadata.yaml | 10 | ||||
| -rw-r--r-- | example/minimal_example.yaml | 4 |
3 files changed, 14 insertions, 10 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 81a7f22..2d2e4c9 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -13,11 +13,11 @@ $graph: type: record fields: host_species: - ## autocomplete # NCBITAXON doc: Host species as defined in NCBITaxon (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens) type: string jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000532 + _type: "@id" host_id: doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples type: string @@ -33,16 +33,18 @@ $graph: type: string jsonldPredicate: _id: http://purl.obolibrary.org/obo/PATO_0000047 + _type: "@id" host_age: doc: Age of the host as number (e.g. 50) type: int? jsonldPredicate: _id: http://purl.obolibrary.org/obo/PATO_0000011 host_age_unit: - doc: Unit of host age.... this field is unstable as of now (might be removed) + doc: Unit of host age e.g. http://purl.obolibrary.org/obo/UO_0000036 type: string? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/UO_0000036 + _id: http://purl.obolibrary.org/obo/NCIT_C42574 + _type: "@id" host_health_status: doc: A condition or state at a particular time type: string? @@ -91,6 +93,7 @@ $graph: type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/GAZ_00000448 + _type: "@id" sample_storage_conditions: doc: Information aboout storage of a specified type, e.g. frozen specimen, paraffin, fresh .... type: string? @@ -120,6 +123,7 @@ $graph: type: string? jsonldPredicate: _id: http://edamontology.org/data_1875 + _type: "@id" virus_strain: doc: Name of the virus strain type: string? diff --git a/example/metadata.yaml b/example/metadata.yaml index d9e8e92..15e4e44 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -2,11 +2,11 @@ id: placeholder host: host_id: XX1 - host_species: string + host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 host_common_name: string - host_sex: string + host_sex: http://purl.obolibrary.org/obo/NCIT_C27993 host_age: 20 - host_age_unit: string + host_age_unit: http://purl.obolibrary.org/obo/UO_0000036 host_health_status: string host_treatment: string additional_host_information: string @@ -17,12 +17,12 @@ sample: collecting_institution: XXX specimen_source: XXX collection_date: XXX - collection_location: XXX + collection_location: http://purl.obolibrary.org/obo/NCIT_C16428 sample_storage_conditions: XXX additional_collection_information: XXX virus: - virus_species: XX + virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 virus_strain: XX technology: diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml index 160d1d4..43adfa8 100644 --- a/example/minimal_example.yaml +++ b/example/minimal_example.yaml @@ -2,8 +2,8 @@ id: placeholder host: host_id: XX - host_species: string - host_sex: string + host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 + host_sex: http://purl.obolibrary.org/obo/NCIT_C20197 sample: sample_id: XXX |