Merge branch 'master' of github.com:arvados/bh20-seq-resource

4 files changed, 45 insertions, 11 deletions

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 8a22db1..81a7f22 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -13,41 +13,52 @@ $graph:
   type: record
   fields:
     host_species:
+        ## autocomplete # NCBITAXON
+        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
     host_id:
+        doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples
         type: string
         jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000115
     host_common_name:
+        doc: Text label for the host species (e.g. homo sapiens)
         type: string?
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NOMEN_0000037
     host_sex:
+        doc: Sex of the host as define in NCIT, IRI expected (http://purl.obolibrary.org/obo/C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female) or unkown (http://purl.obolibrary.org/obo/NCIT_C17998))
         type: string
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/PATO_0000047
     host_age:
+        doc: Age of the host as number (e.g. 50)
         type: int?
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/PATO_0000011
     host_age_unit:
+        doc: Unit of host age.... this field is unstable as of now (might be removed)
         type: string?
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/UO_0000036
     host_health_status:
+        doc: A condition or state at a particular time
         type: string?
         jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
     host_treatment:
+      doc: Process in which the act is intended to modify or alter
       type: string?
       jsonldPredicate:
           _id: http://www.ebi.ac.uk/efo/EFO_0000727
     host_vaccination:
+      doc: Field is unstable
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/VO_0000001
     additional_host_information:
+      doc: Field for additional host information
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_001167
@@ -56,38 +67,47 @@ $graph:
   type: record
   fields:
     collector_name:
+      doc: Name of the person that took the sample
       type: string
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0001895
     collecting_institution:
+      doc: Institute that was responsible of sampeling
       type: string
       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
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0001479
     collection_date:
+      doc: Date when the sample was taken
       type: string?
       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)
       type: string?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/GAZ_00000448
     sample_storage_conditions:
+      doc: Information aboout storage of a specified type, e.g.  frozen specimen, paraffin, fresh ....
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0001472
     additional_collection_information:
+      doc: Add additional comment about the circumstances that a sample was taken
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_001167
     sample_id:
+      doc: Id of the sample as defined by the submitter
       type: string
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000115
     source_database_accession:
+      doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here
       type: string?
       jsonldPredicate:
           _id: http://edamontology.org/data_2091
@@ -96,10 +116,12 @@ $graph:
   type: record
   fields:
     virus_species:
+      doc: The name of a taxon from the NCBI taxonomy database
       type: string?
       jsonldPredicate:
           _id: http://edamontology.org/data_1875
     virus_strain:
+      doc: Name of the virus strain
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_010055
@@ -108,14 +130,17 @@ $graph:
   type: record
   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
     sequence_assembly_method:
+      doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome
       type: string?
       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: string?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/FLU_0000848
@@ -124,22 +149,22 @@ $graph:
   type: record
   fields:
     submitter_name:
+      doc: Name of the submitter
       type: string
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000116
-    submitter_date:
-      type: string
-      jsonldPredicate:
-          _id: http://purl.obolibrary.org/obo/NCIT_C94162
     submitter_address:
+      doc: Address of the submitter
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000172
     originating_lab:
+      doc: Name of the laboratory that took the sample
       type: string
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C37984
     lab_address:
+      doc: Address of the laboratory where the sample was taken
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0600047
@@ -152,10 +177,17 @@ $graph:
       jsonldPredicate:
           _id: http://www.ebi.ac.uk/efo/EFO_0001741
     authors:
+      doc: Name of the author(s)
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C42781
-    submitter_id:
+    publication:
+      doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...)
+      type: string?
+      jsonldPredicate:
+        _id: http://purl.obolibrary.org/obo/NCIT_C19026
+    submitter_orchid:
+      doc: ORCHID of the submitter
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000115
@@ -171,7 +203,8 @@ $graph:
     submitter: submitterSchema
     id:
       doc: The subject (eg the fasta/fastq file) that the metadata describes
-      type: string?
+      type: string
       jsonldPredicate:
         _id: "@id"
         _type: "@id"
+        noLinkCheck: true
diff --git a/bh20sequploader/rdf-mappings.ttl b/bh20sequploader/rdf-mappings.ttl
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/bh20sequploader/rdf-mappings.ttl
diff --git a/example/metadata.yaml b/example/metadata.yaml
index c780921..d9e8e92 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -1,3 +1,5 @@
+id: placeholder
+
 host:
     host_id: XX1
     host_species: string
@@ -36,5 +38,4 @@ submitter:
     provider_sample_id: string
     submitter_sample_id: string
     authors: testAuthor
-    submitter_id: X12
-    submitter_date: Subdate
+    submitter_orchid: X12
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
index f312ab7..160d1d4 100644
--- a/example/minimal_example.yaml
+++ b/example/minimal_example.yaml
@@ -1,8 +1,9 @@
-submission: publicSequenceResource
+id: placeholder
 
 host:
     host_id: XX
     host_species: string
+    host_sex: string
 
 sample:
     sample_id: XXX
@@ -14,5 +15,4 @@ technology:
 
 submitter:
     submitter_name: tester
-    originating_lab: testLab
-    submitter_date: Subdate
\ No newline at end of file
+    originating_lab: testLab
\ No newline at end of file