#420

build/Snakefile-conversion

@@ -97,6 +97,18 @@ rule ChEMBL_Conversion:
     shell:
         config['PYTHON_COMMAND'] + " {input.code} " + config['MYSQL_CONF'] + " " + config['CHEMBL_MYSQL_DBNAME'] + " {output.nodes} {output.edges} " + config['TEST_ARG'] + " > {log} 2>&1"
 
+rule UNII_Conversion:
+    input:
+        code = config['UNII_CONVERSION_SCRIPT'],
+	real = config['UNII_TSV_FILE'],
+	validation = config['VALIDATION_PLACEHOLDER']
+    output:
+        nodes = config['UNII_OUTPUT_NODES_FILE']
+    log:
+        config['UNII_CONVERSION_LOG']
+    shell:
+        config['PYTHON_COMMAND'] + " {input.code} {input.real} {output.nodes} " + config['TEST_ARG'] + " > {log} 2>&1"
+
 rule NCBIGene_Conversion:
     input:
         code = config['NCBIGENE_CONVERSION_SCRIPT'],

build/Snakefile-post-etl

@@ -41,6 +41,7 @@ rule Merge:
         disgenet_edges = config['DISGENET_OUTPUT_EDGES_FILE'],
         kegg_nodes = config['KEGG_OUTPUT_NODES_FILE'],
         kegg_edges = config['KEGG_OUTPUT_EDGES_FILE'],
+	unii_nodes = config['UNII_OUTPUT_NODES_FILE'],
         clinicaltrialskg_nodes = config['CLINICALTRIALSKG_OUTPUT_NODES_FILE'],
         clinicaltrialskg_edges = config['CLINICALTRIALSKG_OUTPUT_EDGES_FILE']
     output:

build/snakemake-config-var.yaml

@@ -101,6 +101,16 @@ ncbigene_conversion_log: ${BUILD_DIR}/${ncbigene_conversion_base}${version_suffi
 ncbigene_output_nodes_file: ${BUILD_DIR}/${ncbigene_output_base}${nodes_suffix}${test_suffix}.jsonl
 ncbigene_output_edges_file: ${BUILD_DIR}/${ncbigene_output_base}${edges_suffix}${test_suffix}.jsonl
 
+unii_extraction_base: extract-unii
+unii_conversion_base: unii_tsv_to_kg_jsonl
+unii_output_base: kg2-unii
+unii_extraction_script: ${EXTRACT_CODE_DIR}/${unii_extraction_base}.sh
+unii_extraction_log: ${BUILD_DIR}/${unii_extraction_base}${version_suffix}${test_suffix}.log
+unii_tsv_file: ${BUILD_DIR}/unii/unii.tsv
+unii_conversion_script: ${CONVERT_CODE_DIR}/${unii_conversion_base}.py
+unii_conversion_log: ${BUILD_DIR}/${unii_conversion_base}${version_suffix}${test_suffix}.log
+unii_output_nodes_file: ${BUILD_DIR}/${unii_output_base}${nodes_suffix}${test_suffix}.jsonl
+
 dgidb_extraction_base: extract-dgidb
 dgidb_conversion_base: dgidb_tsv_to_kg_jsonl
 dgidb_output_base: kg2-dgidb

kg2_util.py

@@ -125,6 +125,7 @@
 CURIE_PREFIX_UMLS_STY = 'STY'
 CURIE_PREFIX_UMLS_SOURCE = 'umls_source'
 CURIE_PREFIX_UNICHEM_SOURCE = 'UNICHEM_source'
+CURIE_PREFIX_UNII = 'UNII'
 CURIE_PREFIX_UNIPROT = 'UniProtKB'
 CURIE_PREFIX_VANDF = 'VANDF'
 
@@ -178,6 +179,7 @@
 BASE_URL_UMLS = BASE_BASE_URL_IDENTIFIERS_ORG + 'umls:'
 BASE_URL_UMLS_STY = 'http://purl.bioontology.org/ontology/STY/'
 BASE_URL_UNICHEM = 'https://www.ebi.ac.uk/unichem/'
+BASE_URL_UNII = 'https://precision.fda.gov/uniisearch/srs/unii/'
 BASE_URL_UNIPROTKB = 'http://purl.uniprot.org/uniprot/'
 
 BIOLINK_CATEGORY_ANATOMICAL_ENTITY = 'anatomical entity'
@@ -352,14 +354,20 @@ def close_single_jsonlines(info: tuple, output_file_name: str):
     temp_output_file.close()
 
 
-def create_kg2_jsonlines(test_mode: bool = False):
-    return create_single_jsonlines(test_mode), create_single_jsonlines(test_mode)
+def create_kg2_jsonlines(test_mode: bool = False, include_edges = True):
+    jl_nodes = create_single_jsonlines(test_mode)
+    if include_edges:
+        jl_edges = create_single_jsonlines(test_mode)
+    else:
+        jl_edges = None
+    return jl_nodes, jl_edges
 
 
 def close_kg2_jsonlines(nodes_info: tuple, edges_info: tuple,
                         output_nodes_file_name: str, output_edges_file_name: str):
     close_single_jsonlines(nodes_info, output_nodes_file_name)
-    close_single_jsonlines(edges_info, output_edges_file_name)
+    if edges_info is not None:
+        close_single_jsonlines(edges_info, output_edges_file_name)
 
 
 def start_read_jsonlines(file_name: str, type=dict):
@@ -732,4 +740,4 @@ def is_a_valid_http_url(id: str) -> bool:
         valid = id.startswith('http://') or id.startswith('https://')
     except validators.ValidationFailure:
         valid = False
-    return valid
+    return valid

maps/curies-to-urls-map.yaml

@@ -497,6 +497,8 @@ use_for_bidirectional_mapping:
     UMLSSC: http://purl.bioontology.org/ontology/STY/
   -
     UNICHEM_source: "https://www.ebi.ac.uk/unichem/"
+  -
+    UNII: "https://precision.fda.gov/uniisearch/srs/unii/"
   -
     UniProtKB: "http://purl.uniprot.org/uniprot/"
   -

setup/setup-kg2-build.sh

@@ -77,7 +77,8 @@ sudo apt-get install -y \
      automake \
      git \
      libssl-dev \
-     make
+     make \
+     unzip
 
 sudo debconf-set-selections <<< "mysql-server mysql-server/root_password password ${mysql_password}"
 sudo debconf-set-selections <<< "mysql-server mysql-server/root_password_again password ${mysql_password}"
@@ -157,4 +158,4 @@ setup_kg2_build_part2 >> ${setup_log_file} 2>&1
 if [[ "${build_flag}" != "ci" ]]
 then
     ${s3_cp_cmd} ${setup_log_file} s3://${s3_bucket_versioned}/
-fi
+fi