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-rw-r--r--example/maximum_metadata_example.yaml46
-rw-r--r--example/metadata.yaml43
-rw-r--r--example/minimal_metadata_example.yaml (renamed from example/minimal_example.yaml)6
3 files changed, 49 insertions, 46 deletions
diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
new file mode 100644
index 0000000..1bc70d7
--- /dev/null
+++ b/example/maximum_metadata_example.yaml
@@ -0,0 +1,46 @@
+id: placeholder
+
+host:
+ host_id: XX1
+ host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
+ host_sex: http://purl.obolibrary.org/obo/PATO_0000384
+ host_age: 20
+ host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
+ host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269
+ host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
+ host_vaccination: [vaccines1,vaccine2]
+ ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010
+ additional_host_information: Optional free text field for addtional information
+
+sample:
+ 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 sampling
+ specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835]
+ collection_date: "2020-01-01"
+ collection_location: http://www.wikidata.org/entity/Q148
+ sample_storage_conditions: frozen specimen
+ source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence]
+ additional_collection_information: Optional free text field for addtional information
+
+virus:
+ virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
+ virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
+
+technology:
+ sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
+ sequence_assembly_method: Protocol used for assembly
+ sequencing_coverage: [70.0, 100.0]
+ additional_technology_information: Optional free text field for addtional information
+
+submitter:
+ authors: [John Doe, Joe Boe, Jonny Oe]
+ submitter_name: [John Doe]
+ submitter_address: John Doe's adress
+ originating_lab: John Doe kitchen
+ lab_address: John Doe's address
+ provider_sample_id: XXX1
+ submitter_sample_id: XXX2
+ publication: PMID00001113
+ submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
+ additional_submitter_information: Optional free text field for addtional information \ No newline at end of file
diff --git a/example/metadata.yaml b/example/metadata.yaml
deleted file mode 100644
index a76616c..0000000
--- a/example/metadata.yaml
+++ /dev/null
@@ -1,43 +0,0 @@
-id: placeholder
-
-host:
- host_id: XX1
- host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
- 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: http://purl.obolibrary.org/obo/NCIT_C25269
- host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
- host_vaccination: List of vaccines given to the host (RRIDs?)
- additional_host_information: Field for additional host information
-
-sample:
- 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 sampling
- specimen_source: http://purl.obolibrary.org/obo/NCIT_C155831
- specimen_source2: http://purl.obolibrary.org/obo/NCIT_C155835
- collection_date: "2020-01-01"
- 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: SARS-CoV-2/human/CHN/HS_8/2020
-
-technology:
- 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: John Doe
- submitter_address: John Doe's adress
- originating_lab: John Doe kitchen
- lab_address: John Doe's address
- provider_sample_id: HmX
- submitter_sample_id: xXx
- authors: John Doe et all
- submitter_orcid: https://orcid.org/0000-0000-0000-0000 \ No newline at end of file
diff --git a/example/minimal_example.yaml b/example/minimal_metadata_example.yaml
index 0e36a25..51f8a87 100644
--- a/example/minimal_example.yaml
+++ b/example/minimal_metadata_example.yaml
@@ -5,14 +5,14 @@ host:
sample:
sample_id: XX
- collection_date: 2020-01
+ collection_date: "2020-01-01"
collection_location: http://www.wikidata.org/entity/Q148
virus:
virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
technology:
- sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0008632
+ sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]
submitter:
- authors: John Doe \ No newline at end of file
+ authors: [John Doe] \ No newline at end of file