Updates to jsonld context for the DCC schemas.

Also I added a comment for what their prefix NTR means.

diff --git a/htsworkflow/submission/encoded.py b/htsworkflow/submission/encoded.py
index 58eb59eb157ed6ffff72d2b8ea845a4b32107d18..04aff707166e20956d18e69add164b7e3c989f99 100644 (file)
--- a/htsworkflow/submission/encoded.py
+++ b/htsworkflow/submission/encoded.py
@@ -20,13 +20,17 @@ ENCODED_CONTEXT = {
     # provide common defaults.
     None: {
         # terms in multiple encoded objects
     # provide common defaults.
     None: {
         # terms in multiple encoded objects

+        'award': { '@type': '@id' },
+        'dataset': {'@type': '@id'},

         'description': 'rdf:description',
         'description': 'rdf:description',

+        'documents': { '@type': '@id' },

         'experiment': {'@type': '@id'},
         'href': { '@type': '@id' },
         'lab': { '@type': '@id' },
         'library': {'@type': '@id' },
         'pi': { '@type': '@id' },
         'platform': { '@type': '@id' },
         'experiment': {'@type': '@id'},
         'href': { '@type': '@id' },
         'lab': { '@type': '@id' },
         'library': {'@type': '@id' },
         'pi': { '@type': '@id' },
         'platform': { '@type': '@id' },

+        'replicates': { '@type': '@id' },

         'submitted_by': { '@type': '@id' },
         'url': { '@type': '@id' },
     },
         'submitted_by': { '@type': '@id' },
         'url': { '@type': '@id' },
     },


@@ -39,9 +43,8 @@ ENCODED_CONTEXT = {
     },
     'experiment': {
         "assay_term_id": { "@type": "@id" },
     },
     'experiment': {
         "assay_term_id": { "@type": "@id" },

-    },
-    'file': {
-        'dataset': {'@type': '@id'},
+        "files": { "@type": "@id" },
+        "original_files": { "@type": "@id"},

     },
     # I tried to use the JSON-LD mapping capabilities to convert the lab
     # contact information into a vcard record, but the encoded model
     },
     # I tried to use the JSON-LD mapping capabilities to convert the lab
     # contact information into a vcard record, but the encoded model


@@ -53,11 +56,7 @@ ENCODED_CONTEXT = {
     #    "state": "vcard:region",
     #    "country": "vcard:country"
     #},
     #    "state": "vcard:region",
     #    "country": "vcard:country"
     #},

-    'human_donor': {
-        'award': { '@type': '@id' },
-    },

     'library': {
     'library': {

-        'award': { '@type': '@id' },

         'nucleic_acid_term_id': { '@type': '@id' }
     }
 }
         'nucleic_acid_term_id': { '@type': '@id' }
     }
 }


@@ -81,6 +80,7 @@ ENCODED_NAMESPACES = {
     # OBI: available from http://svn.code.sf.net/p/obi/code/releases/2012-07-01/merged/merged-obi-comments.owl
     'SO': 'http://purl.obolibrary.org/obo/SO_', # Sequence ontology
     # SO: available from http://www.berkeleybop.org/ontologies/so.owl
     # OBI: available from http://svn.code.sf.net/p/obi/code/releases/2012-07-01/merged/merged-obi-comments.owl
     'SO': 'http://purl.obolibrary.org/obo/SO_', # Sequence ontology
     # SO: available from http://www.berkeleybop.org/ontologies/so.owl

+    # NTR: New Term Request space for DCC to implement new ontology terms

 
 }
 
 
 }