diff --git a/00_fetch_data/chembl/export.py b/00_fetch_data/chembl/export.py
deleted file mode 100644
index 24008b3..0000000
--- a/00_fetch_data/chembl/export.py
+++ /dev/null
@@ -1,39 +0,0 @@
-import sqlite3
-import json
-import sys
-
-def export_tables_to_jsonl(sqlite_file):
-    conn = sqlite3.connect(sqlite_file)
-    cursor = conn.cursor()
-    
-    cursor.execute("SELECT name FROM sqlite_master WHERE type='table';")
-    tables = cursor.fetchall()
-
-    for table in tables:
-        table_name = table[0]
-        
-        cursor.execute(f"PRAGMA table_info({table_name});")
-        columns_info = cursor.fetchall()
-        primary_key = None
-        for column_info in columns_info:
-            if column_info[5] == 1:  # PK column
-                primary_key = column_info[1]
-                break
-        
-        cursor.execute(f"SELECT * FROM {table_name};")
-        rows = cursor.fetchall()
-        column_names = [description[0] for description in cursor.description]
-        
-        for row in rows:
-            row_dict = dict(zip(column_names, row))
-            row_dict = {f"chembl:{key}": value for key, value in row_dict.items()}
-            if primary_key:
-                row_dict["id"] = row_dict["chembl:"+primary_key]
-            row_dict["grebi:type"] = f"chembl:{table_name}"
-            print(json.dumps(row_dict))
-    
-    conn.close()
-
-export_tables_to_jsonl('chembl_34/chembl_34_sqlite/chembl_34.db')
-
-
diff --git a/01_ingest/grebi_ingest_gwas/src/main.rs b/01_ingest/grebi_ingest_gwas/src/main.rs
index 32d3707..0bac8a4 100644
--- a/01_ingest/grebi_ingest_gwas/src/main.rs
+++ b/01_ingest/grebi_ingest_gwas/src/main.rs
@@ -38,10 +38,10 @@ fn main() {
         .trim(csv::Trim::All)
         .from_reader(reader);
 
-    if args.filename.starts_with("gwas-catalog-associations") {
+    if args.filename.contains("gwas-catalog-associations") {
         eprintln!("GWAS ingest: writing associations");
         write_associations(&mut csv_reader, &mut output_nodes, &args.datasource_name);
-    } else if args.filename.starts_with("gwas-catalog-studies") {
+    } else if args.filename.contains("gwas-catalog-studies") {
         eprintln!("GWAS ingest: writing studies");
         write_studies(&mut csv_reader, &mut output_nodes, &args.datasource_name);
     } else {
diff --git a/01_ingest/grebi_ingest_sqlite/Cargo.toml b/01_ingest/grebi_ingest_sqlite/Cargo.toml
new file mode 100644
index 0000000..eed8874
--- /dev/null
+++ b/01_ingest/grebi_ingest_sqlite/Cargo.toml
@@ -0,0 +1,13 @@
+[package]
+name = "grebi_ingest_sqlite"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+Inflector = "0.11.4"
+clap = { version = "4.4.11", features = ["derive"] }
+hex = "0.4.3"
+rusqlite = "0.31.0"
+serde_json = { version = "1.0.108", features=["preserve_order"] }
+jemallocator = "0.5.4"
+
diff --git a/01_ingest/grebi_ingest_sqlite/src/main.rs b/01_ingest/grebi_ingest_sqlite/src/main.rs
new file mode 100644
index 0000000..483776e
--- /dev/null
+++ b/01_ingest/grebi_ingest_sqlite/src/main.rs
@@ -0,0 +1,152 @@
+use rusqlite::{params, Connection, Result};
+use serde_json::{json, Value};
+use inflector::Inflector;
+use std::collections::HashMap;
+use clap::Parser;
+
+#[global_allocator]
+static ALLOC: jemallocator::Jemalloc = jemallocator::Jemalloc;
+
+#[derive(clap::Parser, Debug)]
+#[command(author, version, about, long_about = None)]
+struct Args {
+
+    #[arg(long)]
+    datasource_name: String,
+
+    #[arg(long)]
+    filename: String,
+
+}
+
+fn main() -> Result<()> {
+
+    let args = Args::parse();
+    let conn = Connection::open(&args.filename)?;
+    let prefix = args.datasource_name.to_lowercase();
+
+    let schema_info = get_schema_info(&conn)?;
+    let foreign_keys = get_foreign_keys(&conn)?;
+
+    for (table, columns) in &schema_info {
+
+        if table.starts_with("sqlite_") {
+            continue;
+        }
+
+        let grebi_type = format!("{}:{}", prefix, table.to_singular());
+
+        eprintln!("--- Reading table: {} => {}", table, grebi_type);
+
+        let primary_keys = get_primary_keys(&conn, table).unwrap();
+        eprintln!("\tcolumns: {:?}", columns);
+        eprintln!("\tprimary keys: {:?}", primary_keys);
+
+        let mut stmt = conn.prepare(&format!("SELECT * FROM {}", table)).unwrap();
+        let mut rows = stmt.query([])?;
+        while let Some(row) = rows.next()? {
+
+            let mut json_obj = json!({});
+            let mut ids = Vec::new();
+
+            for (idx, column) in columns.iter().enumerate() {
+
+                let value:Option<String> = match row.get(idx)? {
+                    rusqlite::types::Value::Null => None,
+                    rusqlite::types::Value::Integer(i) => Some(i.to_string()),
+                    rusqlite::types::Value::Real(r) => Some(r.to_string()),
+                    rusqlite::types::Value::Text(t) => Some(t.to_string()),
+                    rusqlite::types::Value::Blob(b) => Some(hex::encode(b))
+                };
+
+                if value.is_none() {
+                    continue;
+                }
+
+                let v = value.unwrap();
+
+                let col_name = format!("{}:{}", prefix, column);
+
+                if primary_keys.contains(column) {
+                    ids.push(format!("{}:{}:{}", prefix, table.to_singular(), v.clone()));
+                }
+
+                let fk_info = foreign_keys.get(&(table.clone(), column.clone()));
+
+                if fk_info.is_some() {
+                    json_obj[&col_name] = json!(format!("{}:{}:{}", prefix, fk_info.unwrap().0.to_singular(), v));
+                    ids.push(format!("{}:{}:{}", fk_info.unwrap().0.to_singular(), prefix, v));
+                } else {
+                    json_obj[&col_name] = json!(v);
+                }
+            }
+
+            json_obj["grebi:type"] = json!(grebi_type);
+            json_obj["id"] = json!(ids);
+
+            println!("{}", serde_json::to_string(&json_obj).unwrap());
+        }
+    }
+    Ok(())
+}
+
+fn get_schema_info(conn: &Connection) -> Result<HashMap<String, Vec<String>>> {
+    let mut schema_info = HashMap::new();
+    let mut stmt = conn.prepare("SELECT name FROM sqlite_master WHERE type='table'")?;
+    let tables = stmt.query_map(params![], |row| row.get(0))?;
+
+    for table in tables {
+        let table: String = table?;
+        let mut columns = Vec::new();
+        let mut col_stmt = conn.prepare(&format!("PRAGMA table_info({})", table))?;
+        let col_info = col_stmt.query_map(params![], |row| row.get(1))?;
+
+        for col in col_info {
+            columns.push(col?);
+        }
+        schema_info.insert(table, columns);
+    }
+    Ok(schema_info)
+}
+
+fn get_primary_keys(conn: &Connection, table: &str) -> Result<Vec<String>> {
+    let mut primary_keys = Vec::new();
+    let mut stmt = conn.prepare(&format!("PRAGMA table_info({})", table))?;
+    let col_info = stmt.query_map(params![], |row| {
+        let name: String = row.get(1)?;
+        let is_pk: bool = row.get(5)?;
+        Ok((name, is_pk))
+    })?;
+
+    for col in col_info {
+        let (name, is_pk) = col?;
+        if is_pk {
+            primary_keys.push(name);
+        }
+    }
+    Ok(primary_keys)
+}
+
+fn get_foreign_keys(conn: &Connection) -> Result<HashMap<(String, String), (String, String)>> {
+    let mut foreign_keys = HashMap::new();
+    let mut stmt = conn.prepare("SELECT name FROM sqlite_master WHERE type='table'")?;
+    let tables = stmt.query_map(params![], |row| row.get(0))?;
+
+    for table in tables {
+        let table: String = table?;
+        let mut fk_stmt = conn.prepare(&format!("PRAGMA foreign_key_list({})", table))?;
+        let fk_info = fk_stmt.query_map(params![], |row| {
+            let from: String = row.get(3)?;
+            let to_table: String = row.get(2)?;
+            let to: String = row.get(4)?;
+            Ok((from, to_table, to))
+        })?;
+
+        for fk in fk_info {
+            let (from, to_table, to) = fk?;
+            foreign_keys.insert((table.clone(), from), (to_table, to));
+        }
+    }
+    Ok(foreign_keys)
+}
+
diff --git a/02_assign_ids/grebi_assign_ids/Cargo.toml b/02_assign_ids/grebi_assign_ids/Cargo.toml
index 88bddd0..af59944 100644
--- a/02_assign_ids/grebi_assign_ids/Cargo.toml
+++ b/02_assign_ids/grebi_assign_ids/Cargo.toml
@@ -8,7 +8,6 @@ serde_json = { version = "1.0.108", features=["preserve_order"] }
 grebi_shared = { path = "../../grebi_shared" }
 csv = "1.3.0"
 fasthash = "0.4.0"
-rusqlite = "0.30.0"
 lmdb-zero = "0.4.4"
 bloomfilter = "1.0.13"
 jemallocator = "0.5.4"
diff --git a/02_assign_ids/grebi_identifiers2groups/Cargo.toml b/02_assign_ids/grebi_identifiers2groups/Cargo.toml
index ec77587..f2b322f 100644
--- a/02_assign_ids/grebi_identifiers2groups/Cargo.toml
+++ b/02_assign_ids/grebi_identifiers2groups/Cargo.toml
@@ -8,7 +8,6 @@ serde_json = { version = "1.0.108", features=["preserve_order"] }
 grebi_shared = { path = "../../grebi_shared" }
 csv = "1.3.0"
 fasthash = "0.4.0"
-rusqlite = "0.30.0"
 lmdb-zero = "0.4.4"
 bloomfilter = "1.0.13"
 clap = { version = "4.4.11", features = ["derive"] }
diff --git a/02_assign_ids/grebi_identifiers2groups/src/main.rs b/02_assign_ids/grebi_identifiers2groups/src/main.rs
index c991bdb..c83bcc2 100644
--- a/02_assign_ids/grebi_identifiers2groups/src/main.rs
+++ b/02_assign_ids/grebi_identifiers2groups/src/main.rs
@@ -2,7 +2,6 @@
 use std::collections::{HashSet, HashMap, BTreeMap};
 use std::{env, io};
 use csv;
-use rusqlite::Connection;
 use bloomfilter::Bloom;
 use clap::Parser;
 use std::io::{BufRead, BufReader };
diff --git a/Cargo.lock b/Cargo.lock
index befd238..db0422f 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2,6 +2,16 @@
 # It is not intended for manual editing.
 version = 3
 
+[[package]]
+name = "Inflector"
+version = "0.11.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fe438c63458706e03479442743baae6c88256498e6431708f6dfc520a26515d3"
+dependencies = [
+ "lazy_static",
+ "regex",
+]
+
 [[package]]
 name = "adler"
 version = "1.0.2"
@@ -29,12 +39,6 @@ dependencies = [
  "memchr",
 ]
 
-[[package]]
-name = "allocator-api2"
-version = "0.2.16"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5"
-
 [[package]]
 name = "anstream"
 version = "0.6.5"
@@ -95,7 +99,7 @@ version = "0.69.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a00dc851838a2120612785d195287475a3ac45514741da670b735818822129a0"
 dependencies = [
- "bitflags 2.4.1",
+ "bitflags 2.6.0",
  "cexpr",
  "clang-sys",
  "itertools",
@@ -123,9 +127,9 @@ checksum = "4efd02e230a02e18f92fc2735f44597385ed02ad8f831e7c1c1156ee5e1ab3a5"
 
 [[package]]
 name = "bitflags"
-version = "2.4.1"
+version = "2.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07"
+checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
 
 [[package]]
 name = "block-buffer"
@@ -458,7 +462,6 @@ dependencies = [
  "grebi_shared",
  "jemallocator",
  "lmdb-zero",
- "rusqlite",
  "serde_json",
 ]
 
@@ -485,7 +488,6 @@ dependencies = [
  "fasthash",
  "grebi_shared",
  "lmdb-zero",
- "rusqlite",
  "serde_json",
 ]
 
@@ -567,6 +569,18 @@ dependencies = [
  "serde_json",
 ]
 
+[[package]]
+name = "grebi_ingest_sqlite"
+version = "0.1.0"
+dependencies = [
+ "Inflector",
+ "clap",
+ "hex",
+ "jemallocator",
+ "rusqlite",
+ "serde_json",
+]
+
 [[package]]
 name = "grebi_ingest_sssom"
 version = "0.1.0"
@@ -667,14 +681,13 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604"
 dependencies = [
  "ahash",
- "allocator-api2",
 ]
 
 [[package]]
 name = "hashlink"
-version = "0.8.4"
+version = "0.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e8094feaf31ff591f651a2664fb9cfd92bba7a60ce3197265e9482ebe753c8f7"
+checksum = "6ba4ff7128dee98c7dc9794b6a411377e1404dba1c97deb8d1a55297bd25d8af"
 dependencies = [
  "hashbrown",
 ]
@@ -819,9 +832,9 @@ dependencies = [
 
 [[package]]
 name = "libsqlite3-sys"
-version = "0.27.0"
+version = "0.28.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cf4e226dcd58b4be396f7bd3c20da8fdee2911400705297ba7d2d7cc2c30f716"
+checksum = "0c10584274047cb335c23d3e61bcef8e323adae7c5c8c760540f73610177fc3f"
 dependencies = [
  "pkg-config",
  "vcpkg",
@@ -1115,11 +1128,11 @@ dependencies = [
 
 [[package]]
 name = "rusqlite"
-version = "0.30.0"
+version = "0.31.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a78046161564f5e7cd9008aff3b2990b3850dc8e0349119b98e8f251e099f24d"
+checksum = "b838eba278d213a8beaf485bd313fd580ca4505a00d5871caeb1457c55322cae"
 dependencies = [
- "bitflags 2.4.1",
+ "bitflags 2.6.0",
  "fallible-iterator",
  "fallible-streaming-iterator",
  "hashlink",
diff --git a/Cargo.toml b/Cargo.toml
index f4a0ca1..4f782bd 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -10,6 +10,7 @@ members = [
 	"01_ingest/grebi_ingest_json",
 	"01_ingest/grebi_ingest_reactome",
 	"01_ingest/grebi_ingest_kgx_edges",
+	"01_ingest/grebi_ingest_sqlite",
 	"01_ingest/grebi_normalise_prefixes",
 	"02_assign_ids/grebi_extract_identifiers",
 	"02_assign_ids/grebi_identifiers2groups",
diff --git a/configs/datasource_configs/chembl.json b/configs/datasource_configs/chembl.json
new file mode 100644
index 0000000..344b106
--- /dev/null
+++ b/configs/datasource_configs/chembl.json
@@ -0,0 +1,13 @@
+{
+    "name": "ChEMBL",
+    "enabled": true,
+    "ingests": [
+        {
+            "ingest_files": ["./00_fetch_data/chembl/chembl_34/chembl_34_sqlite/chembl_34.db"],
+            "ingest_script": "./target/release/grebi_ingest_sqlite",
+            "stdin": false,
+            "ingest_args": [
+            ]
+        }
+    ]
+}
\ No newline at end of file
diff --git a/configs/subgraph_configs/ebi_full_monarch.json b/configs/subgraph_configs/ebi_full_monarch.json
index 013b10d..b724b22 100644
--- a/configs/subgraph_configs/ebi_full_monarch.json
+++ b/configs/subgraph_configs/ebi_full_monarch.json
@@ -49,6 +49,7 @@
         "./configs/datasource_configs/mondo_efo.json",
         "./configs/datasource_configs/hett_pesticides_appril.json",
         "./configs/datasource_configs/hett_pesticides_eu.json",
-        "./configs/datasource_configs/hett_pesticides_gb.json"
+        "./configs/datasource_configs/hett_pesticides_gb.json",
+        "./configs/datasource_configs/chembl.json"
     ]
 }
diff --git a/configs/subgraph_configs/hett.json b/configs/subgraph_configs/hett.json
index 7e24e2d..af52bd1 100644
--- a/configs/subgraph_configs/hett.json
+++ b/configs/subgraph_configs/hett.json
@@ -38,6 +38,7 @@
     "datasource_configs": [
         "./configs/datasource_configs/hett_pesticides_appril.json",
         "./configs/datasource_configs/hett_pesticides_eu.json",
-        "./configs/datasource_configs/hett_pesticides_gb.json"
+        "./configs/datasource_configs/hett_pesticides_gb.json",
+        "./configs/datasource_configs/chembl.json"
     ]
 }
diff --git a/nextflow/01_create_subgraph.nf b/nextflow/01_create_subgraph.nf
index 400e461..20167ba 100644
--- a/nextflow/01_create_subgraph.nf
+++ b/nextflow/01_create_subgraph.nf
@@ -8,6 +8,7 @@ params.tmp = "$GREBI_TMP"
 params.home = "$GREBI_HOME"
 params.config = "$GREBI_CONFIG"
 params.subgraph = "$GREBI_SUBGRAPH"
+params.timestamp = "$GREBI_TIMESTAMP"
 params.is_ebi = "$GREBI_IS_EBI"
 
 workflow {
@@ -95,10 +96,10 @@ process ingest {
     """
     #!/usr/bin/env bash
     set -Eeuo pipefail
-    ${getDecompressionCommand(file_listing.filename)} \
-        | ${getIngestCommand(file_listing.ingest.ingest_script)} \
+    ${getStdinCommand(file_listing.ingest, file_listing.filename)} \
+        ${getIngestCommand(file_listing.ingest.ingest_script)} \
             --datasource-name ${file_listing.datasource.name} \
-            --filename "${basename(file_listing.filename)}" \
+            --filename "${file_listing.filename}" \
             ${buildIngestArgs(file_listing.ingest.ingest_args)} \
         | ${params.home}/target/release/grebi_normalise_prefixes ${params.home}/prefix_maps/prefix_map_normalise.json \
         | tee >(${params.home}/target/release/grebi_extract_identifiers \
@@ -201,7 +202,7 @@ process index {
     path("metadata.jsonl"), emit: metadata_jsonl
     path("summary.json"), emit: summary_json
     path("names.txt"), emit: names_txt
-    path("ids.txt"), emit: ids_txt
+    path("ids_${params.subgraph}.txt"), emit: ids_txt
 
     script:
     """
@@ -209,11 +210,11 @@ process index {
     set -Eeuo pipefail
     cat ${merged_filenames.iterator().join(" ")} \
         | ${params.home}/target/release/grebi_index \
-        --subgraph-name {params.subgraph} \
+        --subgraph-name ${params.subgraph} \
         --out-metadata-jsonl-path metadata.jsonl \
         --out-summary-json-path summary.json \
         --out-names-txt names.txt \
-        --out-ids-txt ids.txt
+        --out-ids-txt ids_${params.subgraph}.txt
     """
 }
 
@@ -639,17 +640,20 @@ def parseJson(json) {
     return new JsonSlurper().parseText(json)
 }
 
-def getDecompressionCommand(filename) {
+def getStdinCommand(ingest, filename) {
+    if (ingest.stdin == false) {
+        return ""
+    }
     def f = filename
     if (filename.startsWith(".")) {
         f = new File(params.home, filename).toString()
     }
     if (f.endsWith(".gz")) {
-        return "zcat ${f}"
+        return "zcat ${f} |"
     } else if (f.endsWith(".xz")) {
-        return "xzcat ${f}"
+        return "xzcat ${f} |"
     } else {
-        return "cat ${f}"
+        return "cat ${f} |"
     }
 }
 
diff --git a/nextflow/02_create_dbs.nf b/nextflow/02_create_dbs.nf
index 7aa6d0d..bdfc12d 100644
--- a/nextflow/02_create_dbs.nf
+++ b/nextflow/02_create_dbs.nf
@@ -16,7 +16,7 @@ workflow {
 
     neo_nodes_files = Channel.fromPath("${params.tmp}/${params.config}/*/neo4j_csv/neo_nodes_*.csv").collect()
     neo_edges_files = Channel.fromPath("${params.tmp}/${params.config}/*/neo4j_csv/neo_edges_*.csv").collect()
-    id_txts = Channel.fromPath("${params.tmp}/${params.config}/*/ids.txt").collect()
+    id_txts = Channel.fromPath("${params.tmp}/${params.config}/*/ids_*.txt").collect()
     ids_csv = create_combined_neo_ids_csv(id_txts).collect()
 
     neo_db = create_neo(neo_nodes_files.collect() + neo_edges_files.collect() + ids_csv)
diff --git a/prefix_maps/extra_prefixes.json b/prefix_maps/extra_prefixes.json
index 97bcbe4..cc4f1ef 100644
--- a/prefix_maps/extra_prefixes.json
+++ b/prefix_maps/extra_prefixes.json
@@ -186,5 +186,8 @@
 "rouge:": "http://purl.uniprot.org/rouge/",
 "source:": "http://purl.uniprot.org/source/",
 "swiss-model-workspace:": "http://purl.uniprot.org/swiss-model-workspace/",
-"unipathway:": "http://purl.uniprot.org/unipathway/"
+"unipathway:": "http://purl.uniprot.org/unipathway/",
+"EFO_": "efo:",
+"GO_": "go:",
+"BAO_": "bao:"
 }