diff --git a/data/jq/pair/biothings.jq b/data/jq/pair/biothings.jq
index cf57f40..9430656 100644
--- a/data/jq/pair/biothings.jq
+++ b/data/jq/pair/biothings.jq
@@ -1,4 +1,4 @@
-if $edge.query_operation._method == "post" then
+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 ({};
@@ -6,17 +6,18 @@ if $edge.query_operation._method == "post" then
     if ($item | keys | contains(["notfound"])) then
       .
     else
-      if $edge.input | type == "object" then
-        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
-      else
-        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input | toArray) as $curie | .[$curie] = .[$curie] + [$item]
-      end
+      generateCurieWithInputs(
+        $edge.input.id;
+        $item.query; 
+        $edge.input.curies
+          | toArray
+          | map(. | split(":"))[0]
+      ) as $curie | .[$curie] = .[$curie] + [$item]
     end
   )
 else
-  if ($edge.input | type) == "object" then
-    .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
-  else
-    .response as $res | generateCurie($edge.association.input_id; ($edge.input | toArray)[0]) as $curie | {} | .[$curie] = [$res]
-  end
+  .response as $res | generateCurie(
+    $edge.input.id;
+    ($edge.input.curies | toArray | map(. | split(":"))[0])[0]
+  ) as $curie | {} | .[$curie] = [$res]
 end
diff --git a/data/jq/pair/ctd.jq b/data/jq/pair/ctd.jq
index a912f1f..2f03503 100644
--- a/data/jq/pair/ctd.jq
+++ b/data/jq/pair/ctd.jq
@@ -1,23 +1,11 @@
 reduce .response[] as $item (
-  {}; .[(
-      if ($edge.input | type) == "object" then
-        ($edge.input.queryInputs | toArray)[]
-      else
-        ($edge.input | toArray)[]
-      end
-    ) 
+  {}; .[$edge.input.curies 
     | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase))
-    | generateCurie($edge.association.input_id; .)
+    | generateCurie($edge.input.id; .)
   ] = [] 
-  + .[(
-      if ($edge.input | type) == "object" then
-        ($edge.input.queryInputs | toArray)[]
-      else
-        ($edge.input | toArray)[]
-      end
-    )
+  + .[$edge.input.curies
     | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase))
-    | generateCurie($edge.association.input_id; .)
+    | generateCurie($edge.input.id; .)
   ] 
   + [$item]
 ) | map_values([.])
diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index d6c4d7b..aadcbf2 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -1,8 +1,12 @@
 import { JQVariable, BTEKGOperationObject } from "./types";
 import Path from "path";
 import fs from "fs";
+import { toArray } from "./utils";
 
-const functions = fs.readFileSync(Path.resolve(`${__dirname}/../data/jq/utils.jq`), { encoding: "utf8" });
+const functions = fs.readFileSync(
+  Path.resolve(`${__dirname}/../data/jq/utils.jq`),
+  { encoding: "utf8" },
+);
 
 function generateVariables(variables: JQVariable[]) {
   let variableString = "";
@@ -12,12 +16,6 @@ function generateVariables(variables: JQVariable[]) {
   return variableString;
 }
 
-export function generateFilterString(filterString: string, edge: BTEKGOperationObject) {
-  const variables = [
-    {
-      name: "$edge",
-      value: JSON.stringify(edge),
-    },
-  ];
-  return `${functions}\n${generateVariables(variables)}${filterString}`;
+export function generateFilterString(filterString: string) {
+  return `${functions}\n${filterString}`;
 }
diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts
index 1489fde..d690b03 100644
--- a/src/transformers/jq_transformer.ts
+++ b/src/transformers/jq_transformer.ts
@@ -5,52 +5,73 @@ import Path from "path";
 
 import * as jq from "node-jq"; // If converted to import, ts compile breaks it (imports default as undefined)
 import { JSONDoc, PairedResponse } from "../json_transform/types";
+import { toArray } from "../utils";
 
 // Get prefab JQ strings from data/jq
 const filterStringsWrap = Object.fromEntries(
   fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/wrap`)).map(file => {
     const filePath = Path.resolve(`${__dirname}/../../data/jq/wrap/${file}`);
-    return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })];
+    return [
+      Path.parse(filePath).name,
+      fs.readFileSync(filePath, { encoding: "utf8" }),
+    ];
   }),
 );
 
 const filterStringsPair = Object.fromEntries(
   fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/pair`)).map(file => {
     const filePath = Path.resolve(`${__dirname}/../../data/jq/pair/${file}`);
-    return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })];
+    return [
+      Path.parse(filePath).name,
+      fs.readFileSync(filePath, { encoding: "utf8" }),
+    ];
   }),
 );
 
 export default class JQTransformer extends BaseTransformer {
   // TODO more specific typing?
   async wrap(res: JSONDoc | JSONDoc[]): Promise<JSONDoc> {
-    if (this.config.wrap)
-      res = JSON.parse(
-        (await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: "json" })) as string,
-      );
-    else if (filterStringsWrap[this.config.type])
-      res = JSON.parse(
-        (await jq.run(generateFilterString(filterStringsWrap[this.config.type], this.edge), res, {
-          input: "json",
-        })) as string,
-      );
-    else res = super.wrap(res);
-
-    return res;
+    const filterString: string | undefined =
+      this.config.wrap ?? filterStringsWrap[this.config.type];
+    if (typeof filterString === "undefined") return super.wrap(res);
+    return JSON.parse(
+      (await jq.run(generateFilterString(filterString), res, {
+        input: "json",
+      })) as string,
+    );
   }
 
   async pairCurieWithAPIResponse(): Promise<PairedResponse> {
-    if (this.config.pair)
-      return JSON.parse(
-        (await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: "json" })) as string,
-      );
-    else if (filterStringsPair[this.config.type])
-      return JSON.parse(
-        (await jq.run(generateFilterString(filterStringsPair[this.config.type], this.edge), this.data, {
-          input: "json",
-        })) as string,
-      );
-
-    return super.pairCurieWithAPIResponse();
+    let filterString: string | undefined =
+      this.config.pair ?? filterStringsPair[this.config.type];
+    if (typeof filterString === "undefined")
+      return super.pairCurieWithAPIResponse();
+    const data = {
+      response: this.data.response,
+      edge: {
+        query: {
+          method: this.edge.query_operation.method,
+        },
+        input: {
+          id: this.edge.association.input_id,
+          type: this.edge.association.input_type,
+          // input is array or is object with queryInputs
+          curies:
+            Array.isArray(this.edge.input) ||
+              typeof this.edge.input === "string"
+              ? toArray(this.edge.input)
+              : this.edge.input.queryInputs,
+        },
+        predicate: this.edge.association.predicate,
+        output: {
+          id: this.edge.association.output_id,
+          type: this.edge.association.output_type,
+        },
+      },
+    };
+    filterString = `.edge as $edge | ${generateFilterString(filterString)}`;
+    return JSON.parse(
+      (await jq.run(filterString, data, { input: "json" })) as string,
+    );
   }
 }