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authorLLTommy2020-04-23 20:18:36 +0200
committerGitHub2020-04-23 20:18:36 +0200
commit7049cd5d29acd601ccbbc9d04f001b84a51e9bd5 (patch)
tree34a1254d81c2e526427fedb1deaa9f8441e8b260 /bh20sequploader/bh20seq-schema.yml
parentf38b9c6f22b82327df9648938a5a4bcf863d8c41 (diff)
parentc7612e7eda5cd38bfbb2d293bebf732893a41b6c (diff)
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Merge branch 'master' into patch-3
Diffstat (limited to 'bh20sequploader/bh20seq-schema.yml')
-rw-r--r--bh20sequploader/bh20seq-schema.yml76
1 files changed, 43 insertions, 33 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index bbcafc8..9a89979 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -18,17 +18,19 @@ $graph:
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000532
_type: "@id"
+ noLinkCheck: true
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
+ type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
host_sex:
- doc: Sex of the host, IRI expected
+ doc: Sex of the host as defined in PATO, expect male () or female ()
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000047
_type: "@id"
+ noLinkCheck: true
host_age:
doc: Age of the host as number (e.g. 50)
type: int?
@@ -40,10 +42,12 @@ $graph:
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42574
_type: "@id"
+ noLinkCheck: true
host_health_status:
- doc: A condition or state at a particular time
+ doc: A condition or state at a particular time, must be one of the following (obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987)
type: string?
- jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NCIT_C25688
host_treatment:
doc: Process in which the act is intended to modify or alter host status
type: string?
@@ -63,39 +67,47 @@ $graph:
- name: sampleSchema
type: record
fields:
+ sample_id:
+ doc: Id of the sample as defined by the submitter
+ type: string
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_000115
+ collection_date:
+ doc: Date when the sample was taken
+ type: string
+ jsonldPredicate:
+ _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
+ collection_location:
+ doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China)
+ type: string
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/GAZ_00000448
+ _type: "@id"
+ noLinkCheck: true
collector_name:
doc: Name of the person that took the sample
- type: string
+ type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001895
collecting_institution:
doc: Institute that was responsible of sampeling
- type: string
+ type: string?
jsonldPredicate:
- _id: http://semanticscience.org/resource/SIO_001167
+ _id: http://purl.obolibrary.org/obo/NCIT_C41206
specimen_source:
doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155831 (=nasopharyngeal swab)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001479
_type: "@id"
+ noLinkCheck: true
specimen_source2:
doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155835 (=throat swabb)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001479
_type: "@id"
- collection_date:
- doc: Date when the sample was taken
- type: string
- jsonldPredicate:
- _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
- collection_location:
- doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China)
- type: string
- jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/GAZ_00000448
- _type: "@id"
+ noLinkCheck: true
sample_storage_conditions:
doc: Information about storage of a specified type, e.g. frozen specimen, paraffin, fresh ....
type: string?
@@ -106,11 +118,6 @@ $graph:
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
- sample_id:
- doc: Id of the sample as defined by the submitter
- type: string
- jsonldPredicate:
- _id: http://semanticscience.org/resource/SIO_000115
source_database_accession:
doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here
type: string?
@@ -126,6 +133,7 @@ $graph:
jsonldPredicate:
_id: http://edamontology.org/data_1875
_type: "@id"
+ noLinkCheck: true
virus_strain:
doc: Name of the virus strain
type: string?
@@ -137,16 +145,18 @@ $graph:
fields:
sample_sequencing_technology:
doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
- type: string
+ type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0600047
_type: "@id"
+ noLinkCheck: true
sample_sequencing_technology2:
doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0600047
_type: "@id"
+ noLinkCheck: true
sequence_assembly_method:
doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome
type: string?
@@ -158,7 +168,7 @@ $graph:
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
sequencing_coverage2:
- doc: If a second sequence technology was use you can submit its coverage here
+ doc: If a second sequence technology was used you can submit its coverage here
type: float?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
@@ -171,9 +181,14 @@ $graph:
- name: submitterSchema
type: record
fields:
+ authors:
+ doc: Name of the author(s)
+ type: string
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NCIT_C42781
submitter_name:
doc: Name of the submitter
- type: string
+ type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000116
submitter_address:
@@ -183,7 +198,7 @@ $graph:
_id: http://semanticscience.org/resource/SIO_000172
originating_lab:
doc: Name of the laboratory that took the sample
- type: string
+ type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C37984
lab_address:
@@ -199,11 +214,6 @@ $graph:
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0001741
- authors:
- doc: Name of the author(s)
- type: string?
- jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/NCIT_C42781
publication:
doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...)
type: string?
@@ -223,7 +233,7 @@ $graph:
fields:
host: hostSchema
sample: sampleSchema
- virus: virusSchema?
+ virus: virusSchema
technology: technologySchema
submitter: submitterSchema
id: