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authorlltommy2020-04-19 20:12:21 +0200
committerlltommy2020-04-19 20:12:21 +0200
commit8f97a0e0d8d2d7e32c396d3b9881d770e58ab832 (patch)
treeb71a2a1d17ea90338a22b2fff4cd2a4cdbda7d3b
parent47666ab547da0c2fbdc2026f955d7d7b615d11fb (diff)
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small updates to the yaml schema, updating the example files
-rw-r--r--bh20sequploader/bh20seq-schema.yml10
-rw-r--r--example/metadata.yaml43
-rw-r--r--example/minimal_example.yaml15
3 files changed, 35 insertions, 33 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index fc80080..c48ebce 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -13,7 +13,7 @@ $graph:
type: record
fields:
host_species:
- doc: Host species as defined in NCBITaxon (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens)
+ 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
@@ -45,7 +45,7 @@ $graph:
type: string?
jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
host_treatment:
- doc: Process in which the act is intended to modify or alter
+ doc: Process in which the act is intended to modify or alter host status
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000727
@@ -74,12 +74,12 @@ $graph:
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
specimen_source:
- doc: A specimen that derives from an anatomical part or substance arising from an organism, e.g. tissue, organ
+ 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
specimen_source2:
- doc: A specimen that derives from an anatomical part or substance arising from an organism, e.g. tissue, organ
+ 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
@@ -89,7 +89,7 @@ $graph:
jsonldPredicate:
_id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
collection_location:
- doc: Geographical location where the sample was collected as Gazetteer (https://www.ebi.ac.uk/ols/ontologies/gaz) reference, e.g. http://purl.obolibrary.org/obo/GAZ_00002845 (China)
+ 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
diff --git a/example/metadata.yaml b/example/metadata.yaml
index bbd3e36..5e1be0a 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -6,35 +6,38 @@ host:
host_sex: http://purl.obolibrary.org/obo/NCIT_C27993
host_age: 20
host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
- host_health_status: string
- host_treatment: string
- additional_host_information: string
+ host_health_status: A condition or state at a particular time
+ host_treatment: Process in which the act is intended to modify or alter host status
+ host_vaccination: List of vaccines given to the host
+ additional_host_information: Field for additional host information
sample:
- sample_id: XXX
- collector_name: XXX
- collecting_institution: XXX
- specimen_source: XXX
- collection_date: 2020-01
- collection_location: http://purl.obolibrary.org/obo/GAZ_00002459
+ sample_id: Id of the sample as defined by the submitter
+ collector_name: Name of the person that took the sample
+ collecting_institution: Institute that was responsible of sampeling
+ specimen_source: Method how specimen was derived
+ specimen_source2: Method how specimen was derived if two methods were used
+ collection_date: Date when the sample was taken
+ collection_location: http://www.wikidata.org/entity/Q148
sample_storage_conditions: XXX
additional_collection_information: XXX
virus:
virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
- virus_strain: XX
+ virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
technology:
- sample_sequencing_technology: XX
- sequence_assembly_method: XX
+ sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0009173
+ sample_sequencing_technology2: http://www.ebi.ac.uk/efo/EFO_0009173
+ sequence_assembly_method: Protocol used for assembly
sequencing_coverage: 70
submitter:
- submitter_name: tester
- submitter_address: testerAdd
- originating_lab: testLab
- lab_address: labAdd
- provider_sample_id: string
- submitter_sample_id: string
- authors: testAuthor
- submitter_orcid: https://orcid.org/0000-0002-1825-0097
+ submitter_name: John Doe
+ submitter_address: John Doe's adress
+ originating_lab: John Doe kitchen
+ lab_address: John Doe's adress
+ provider_sample_id: HmX
+ submitter_sample_id: xXx
+ authors: John Doe et all
+ submitter_orcid: https://orcid.org/0000-0000-0000-0000
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
index 0080c6d..f4118d1 100644
--- a/example/minimal_example.yaml
+++ b/example/minimal_example.yaml
@@ -1,21 +1,20 @@
id: placeholder
host:
- host_id: XX
+ host_id: XX1
host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
- host_sex: http://purl.obolibrary.org/obo/NCIT_C20197
sample:
- sample_id: XXX
- collector_name: XXX
- collecting_institution: XXX
+ sample_id: XX
+ collector_name: John Doe
+ collecting_institution: Doe university
virus:
virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
technology:
- sample_sequencing_technology: XX
+ sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0008632
submitter:
- submitter_name: tester
- originating_lab: testLab \ No newline at end of file
+ submitter_name: John Doe
+ originating_lab: John Doe's kitchen \ No newline at end of file