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-rw-r--r--bh20sequploader/bh20seq-schema.yml65
1 files changed, 25 insertions, 40 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index ea813a0..99e1a11 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -48,6 +48,8 @@ $graph:
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C25688
+ _type: "@id"
+ noLinkCheck: true
host_treatment:
doc: Process in which the act is intended to modify or alter host status
type: string?
@@ -55,9 +57,16 @@ $graph:
_id: http://www.ebi.ac.uk/efo/EFO_0000727
host_vaccination:
doc: List of vaccines given to the host
- type: string?
+ type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/VO_0000002
+ ethnicity:
+ doc: Ethinicity of the host e.g. http://purl.obolibrary.org/obo/HANCESTRO_0010
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_001014
+ _type: "@id"
+ noLinkCheck: true
additional_host_information:
doc: Field for additional host information
type: string?
@@ -90,20 +99,13 @@ $graph:
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001895
collecting_institution:
- doc: Institute that was responsible of sampeling
+ doc: Institute that was responsible for sampeling
type: string?
jsonldPredicate:
_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?
+ type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001479
_type: "@id"
@@ -119,16 +121,18 @@ $graph:
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
source_database_accession:
- doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here
- type: string?
+ doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here. Please use a resolveable URL (e.g. http://identifiers.org/insdc/LC522350.1#sequence)
+ type: string[]?
jsonldPredicate:
_id: http://edamontology.org/data_2091
+ _type: "@id"
+ noLinkCheck: true
- name: virusSchema
type: record
fields:
virus_species:
- doc: The name of a taxon from the NCBI taxonomy database
+ doc: The name of virus species from the NCBI taxonomy database, e.g. http://purl.obolibrary.org/obo/NCBITaxon_2697049 for Severe acute respiratory syndrome coronavirus 2
type: string
jsonldPredicate:
_id: http://edamontology.org/data_1875
@@ -145,21 +149,7 @@ $graph:
fields:
sample_sequencing_technology:
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
- 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
- sample_sequencing_technology3:
- 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"
@@ -170,13 +160,8 @@ $graph:
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0002699
sequencing_coverage:
- doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x)
- type: float?
- jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/FLU_0000848
- sequencing_coverage2:
- doc: If a second sequence technology was used you can submit its coverage here
- type: float?
+ doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20]
+ type: double[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
additional_technology_information:
@@ -189,13 +174,13 @@ $graph:
type: record
fields:
authors:
- doc: Name of the author(s)
- type: string
+ doc: Name(s) of the author(s)
+ type: string[]
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42781
submitter_name:
- doc: Name of the submitter
- type: string?
+ doc: Name of the submitter(s)
+ type: string[]?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000116
submitter_address:
@@ -228,7 +213,7 @@ $graph:
_id: http://purl.obolibrary.org/obo/NCIT_C19026
submitter_orcid:
doc: ORCID of the submitter as a full URI, e.g. https://orcid.org/0000-0002-1825-0097
- type: string?
+ type: string[]?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
_type: "@id"