small updates to the yaml schema, updating the example files

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