Merge pull request #68 from biothings/semmed-sentences

semmed sentence edge attributes

data/jq/pair/semmed.jq

@@ -0,0 +1,23 @@
+if $edge.query.method == "post" then
+  # if response is not an array, then use response.hits
+  if (.response | type) == "array" then .response else .response.hits end |
+  reduce .[] as $item ({};
+    # if the item is notfound, then proceed to next item & keep current object
+    if ($item | keys | contains(["notfound"])) then
+      .
+    else
+      generateCurieWithInputs(
+        $edge.input.id;
+        $item.query; 
+        $edge.input.curies
+        | toArray
+        | map(. | split(":") | last)
+      ) as $curie | .[$curie] += [$item]
+    end
+  )
+else
+  .response as $res | generateCurie(
+    $edge.input.id;
+    ($edge.input.curies | toArray | map(. | split(":") | last) | first)
+  ) as $curie | {} | .[$curie] = [$res]
+end

data/jq/wrap/semmed.jq

@@ -0,0 +1,29 @@
+# finds start/end index of sub in main string
+# ie. "ab" in "12abcd" will return "2|3"
+def index_text(main; sub): (main|index(sub)|tostring)+"|"+((main|index(sub)) + (sub|length) | tostring);
+
+
+.["edge-attributes"] = ([.predication | group_by(.pmid) | .[] | .[0] |
+# create edge attributes for each publication
+{
+  "attribute_type_id": "biolink:has_supporting_study_result",
+  "attributes": [
+    {
+      "attribute_type_id": "biolink:supporting_text",
+      "value": .sentence,
+    },
+    {
+      "attribute_type_id": "biolink:publications",
+      "value": ( "PMID:"+(.pmid|tostring) ),
+    },
+    {
+      "attribute_type_id": "biolink:subject_location_in_text",
+      "value": ( .subject_text as $text | index_text(.sentence; $text) ),
+    },
+    {
+      "attribute_type_id": "biolink:object_location_in_text",
+      "value": ( .object_text as $text | index_text(.sentence; $text) ),
+    }
+  ],
+  "value": ( .predication_id | tostring ),
+}] | .[:50])

src/index.ts

@@ -50,6 +50,8 @@ export default class Transformer {
     } else if (api === "EBI Proteins API") {
       // this.tf = new EBIProteinTransformer(this.data, this.config)
       this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" });
+    } else if (api === "BioThings SEMMEDDB API") {
+      this.tf = new JQTransformer(this.data, { ...this.config, type: "semmed" });
     } else if (tags.includes("biothings")) {
       this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" });
     } else if (tags.includes("ctd")) {