From 6032a373003affa641ca1e70a44c29a232b5b3ed Mon Sep 17 00:00:00 2001
From: lltommy
Date: Tue, 28 Apr 2020 20:31:42 +0200
Subject: Changes to the structure - we use lists now instead of strings where
 it makes sense. This allows us to have multiple values where in makes sense

---
 example/maximum_metadata_example.yaml | 44 +++++++++++++++++++++++++++++++++++
 example/metadata.yaml                 | 43 ----------------------------------
 example/minimal_example.yaml          | 18 --------------
 example/minimal_metadata_example.yaml |  0
 4 files changed, 44 insertions(+), 61 deletions(-)
 create mode 100644 example/maximum_metadata_example.yaml
 delete mode 100644 example/metadata.yaml
 delete mode 100644 example/minimal_example.yaml
 create mode 100644 example/minimal_metadata_example.yaml

(limited to 'example')

diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
new file mode 100644
index 0000000..0a6d910
--- /dev/null
+++ b/example/maximum_metadata_example.yaml
@@ -0,0 +1,44 @@
+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]
+    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, 100]
+    additional_technology_information: Optional free text field for addtional information
+
+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: XXX1
+    submitter_sample_id: XXX2
+    authors: [John Doe, Joe Boe, Jonny Oe]
+    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_example.yaml
deleted file mode 100644
index 0e36a25..0000000
--- a/example/minimal_example.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-id: placeholder
-
-host:
-    host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
-
-sample:
-    sample_id: XX
-    collection_date: 2020-01
-    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
-
-submitter:
-    authors: John Doe
\ No newline at end of file
diff --git a/example/minimal_metadata_example.yaml b/example/minimal_metadata_example.yaml
new file mode 100644
index 0000000..e69de29
-- 
cgit v1.2.3


From f795744116a9e86ab2a5c5e78761162e9d4ff7e0 Mon Sep 17 00:00:00 2001
From: lltommy
Date: Tue, 28 Apr 2020 20:43:03 +0200
Subject: Adding field 'publication' to the maximum example

---
 example/maximum_metadata_example.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'example')

diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
index 0a6d910..260e4e4 100644
--- a/example/maximum_metadata_example.yaml
+++ b/example/maximum_metadata_example.yaml
@@ -33,12 +33,13 @@ technology:
     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
-    authors: [John Doe, Joe Boe, Jonny Oe]
+    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
-- 
cgit v1.2.3


From b4ec03398d5e74eeb33a4a2a396fe4518c0c5465 Mon Sep 17 00:00:00 2001
From: lltommy
Date: Tue, 28 Apr 2020 20:48:42 +0200
Subject: Whatever happend to the minimal metadata, I restored it

---
 example/minimal_metadata_example.yaml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

(limited to 'example')

diff --git a/example/minimal_metadata_example.yaml b/example/minimal_metadata_example.yaml
index e69de29..1e8d3f5 100644
--- a/example/minimal_metadata_example.yaml
+++ b/example/minimal_metadata_example.yaml
@@ -0,0 +1,18 @@
+id: placeholder
+
+host:
+    host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
+
+sample:
+    sample_id: XX
+    collection_date: 2020-01
+    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]
+
+submitter:
+    authors: [John Doe]
\ No newline at end of file
-- 
cgit v1.2.3


From ceb34edf0449cca328dfe8cf61277d7f05ea7cf9 Mon Sep 17 00:00:00 2001
From: lltommy
Date: Tue, 28 Apr 2020 22:09:37 +0200
Subject: Decision to settle for float instead of integers for the coverage

---
 bh20sequploader/bh20seq-schema.yml    | 2 +-
 bh20sequploader/bh20seq-shex.rdf      | 2 +-
 example/maximum_metadata_example.yaml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

(limited to 'example')

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index f36a6e6..d3e992a 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -152,7 +152,7 @@ $graph:
         _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. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20]
-      type: int[]?
+      type: float[]?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/FLU_0000848
     additional_technology_information:
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 4ec957d..fe6deee 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -57,7 +57,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
 :technologyShape {
     obo:OBI_0600047 IRI {0,3} ;
     efo:EFO_0002699 xsd:string ?;
-    obo:FLU_0000848 xsd:integer {0,2};
+    obo:FLU_0000848 xsd:float {0,3};
     sio:SIO_001167 xsd:string ?;
 }
 
diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
index 260e4e4..0ba9ada 100644
--- a/example/maximum_metadata_example.yaml
+++ b/example/maximum_metadata_example.yaml
@@ -29,7 +29,7 @@ virus:
 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, 100]
+    sequencing_coverage: [70.0, 100.0]
     additional_technology_information: Optional free text field for addtional information
 
 submitter:
-- 
cgit v1.2.3


From 5c05facbdb1e35556256cd11d6a814822ebb6159 Mon Sep 17 00:00:00 2001
From: lltommy
Date: Thu, 30 Apr 2020 18:00:58 +0200
Subject: Last addition/edits to the meta data schema

---
 bh20sequploader/bh20seq-schema.yml    | 15 ++++++++++++---
 bh20sequploader/bh20seq-shex.rdf      |  5 +++--
 example/maximum_metadata_example.yaml |  1 +
 example/minimal_metadata_example.yaml |  2 +-
 4 files changed, 17 insertions(+), 6 deletions(-)

(limited to 'example')

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index d3e992a..99e1a11 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -49,6 +49,7 @@ $graph:
         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?
@@ -59,6 +60,13 @@ $graph:
       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?
@@ -91,7 +99,7 @@ $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
@@ -118,12 +126,13 @@ $graph:
       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
@@ -152,7 +161,7 @@ $graph:
         _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. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20]
-      type: float[]?
+      type: double[]?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/FLU_0000848
     additional_technology_information:
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index fe6deee..cdf2296 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -27,6 +27,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
     efo:EFO_0000727 xsd:string ?;
     obo:VO_0000002 xsd:string {0,10};
     sio:SIO_001167 xsd:string ?;
+    sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity
 }
 
 :sampleShape  {
@@ -42,7 +43,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
 }
 
 :submitterShape {
-    obo:NCIT_C42781 xsd:string * ;
+    obo:NCIT_C42781 xsd:string + ;
     sio:SIO_000116 xsd:string *;
     sio:SIO_000172 xsd:string ?;
     obo:NCIT_C37984 xsd:string ?;
@@ -57,7 +58,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
 :technologyShape {
     obo:OBI_0600047 IRI {0,3} ;
     efo:EFO_0002699 xsd:string ?;
-    obo:FLU_0000848 xsd:float {0,3};
+    obo:FLU_0000848 xsd:double OR xsd:integer {0,3};
     sio:SIO_001167 xsd:string ?;
 }
 
diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
index 0ba9ada..1bc70d7 100644
--- a/example/maximum_metadata_example.yaml
+++ b/example/maximum_metadata_example.yaml
@@ -9,6 +9,7 @@ host:
     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:
diff --git a/example/minimal_metadata_example.yaml b/example/minimal_metadata_example.yaml
index 1e8d3f5..51f8a87 100644
--- a/example/minimal_metadata_example.yaml
+++ b/example/minimal_metadata_example.yaml
@@ -5,7 +5,7 @@ host:
 
 sample:
     sample_id: XX
-    collection_date: 2020-01
+    collection_date: "2020-01-01"
     collection_location: http://www.wikidata.org/entity/Q148
 
 virus:
-- 
cgit v1.2.3