diff --git a/.dockerignore b/.dockerignore
index 83110aa..cf15798 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1 +1,3 @@
 nedrex_files
+neo4j
+tests
\ No newline at end of file
diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
index 78660c6..36c76f6 100644
--- a/.github/workflows/docker-publish.yml
+++ b/.github/workflows/docker-publish.yml
@@ -6,8 +6,8 @@ name: Docker
 # documentation.
 
 on:
-  schedule:
-    - cron: '37 8 * * *'
+#  schedule:
+#    - cron: '37 8 * * *'
   push:
     branches: [ "repo4eu_main", "repo4eu_dev" ]
     # Publish semver tags as releases.
@@ -20,11 +20,11 @@ env:
   REGISTRY: ghcr.io
   # github.repository as <account>/<repo>
   IMAGE_NAME: ${{ github.repository }}
+  NEO4J_IMAGE_NAME: ${{ github.repository }}-neo4j
 
 
 jobs:
-  build:
-
+  build-main:
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -80,3 +80,52 @@ jobs:
           platforms: linux/amd64,linux/arm64
           cache-from: type=gha
           cache-to: type=gha, mode=max
+
+  build-neo4j:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Setup QEMU
+        uses: docker/setup-qemu-action@v2.1.0
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3.0.0
+        with:
+          install: true
+          use: true
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata for Neo4j
+        id: meta-neo4j
+        uses: docker/metadata-action@v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.NEO4J_IMAGE_NAME }}
+
+      - name: Build and push Neo4j Docker image
+        id: build-and-push-neo4j
+        uses: docker/build-push-action@v5.0.0
+        with:
+          context: ./neo4j
+          file: ./neo4j/Dockerfile
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta-neo4j.outputs.tags }}
+          labels: ${{ steps.meta-neo4j.outputs.labels }}
+          #Temporary disabled linux/arm64 because of system library issues
+          # platforms: linux/amd64,linux/arm64
+          platforms: linux/amd64
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
diff --git a/Dockerfile b/Dockerfile
index 4a5984a..02a06ee 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -56,7 +56,8 @@ RUN touch /var/log/nedrexdb.log
 COPY . ./
 RUN rm -rf cron
 RUN pip install .[dependencies]
-RUN mamba install -c conda-forge urllib3=2.3.0 -y
+
+#RUN mamba install -c conda-forge urllib3=2.3.0 -y
 RUN mamba install -c conda-forge openjdk=17 -y
 
 CMD cron && bash build.sh >> /var/log/nedrexdb.log 2>&1 & tail -f /var/log/nedrexdb.log
diff --git a/build.py b/build.py
index 835d652..a9a50bb 100755
--- a/build.py
+++ b/build.py
@@ -1,14 +1,15 @@
 #!/usr/bin/env python
-
 import time
 import pandas as pd
 
 import click
+import os
+import subprocess
 
 import nedrexdb
 from nedrexdb import config, downloaders
-from nedrexdb.control.docker import NeDRexDevInstance, NeDRexLiveInstance
-from nedrexdb.db import MongoInstance, mongo_to_neo, collection_stats, update_db_version
+from nedrexdb.control.docker import NeDRexDevInstance, NeDRexLiveInstance, update_neo4j_image_version
+from nedrexdb.db import MongoInstance, mongo_to_neo, collection_stats
 from nedrexdb.db.parsers import (
     biogrid,
     disgenet,
@@ -39,13 +40,14 @@
     orphanet,
     opentargets,
 )
-from nedrexdb.post_integration import trim_uberon, drop_empty_collections
+from nedrexdb.downloaders import get_versions, update_versions
+from nedrexdb.post_integration import (trim_uberon, drop_empty_collections)
+from nedrexdb.post_integration.neo4j_db_adjustments import create_constraints, create_vector_indices
 
 def parse_method_scores():
     method_scores_file = "./nedrexdb/data/hippie_perplexity_technique_scores.tsv"
     method_scores = pd.read_csv(method_scores_file, sep='\t', usecols=['methods', 'score'])
     method_scores_dict = dict(zip(method_scores['methods'], method_scores['score']))
-    print(method_scores_dict)
     return method_scores_dict
 
 @click.group()
@@ -55,10 +57,14 @@ def cli():
 
 @click.option("--conf", required=True, type=click.Path(exists=True))
 @click.option("--download", is_flag=True, default=False)
+@click.option("--version_update", is_flag=False, default="")
+@click.option("--create_embeddings", is_flag=True, default=False)
 @cli.command()
-def update(conf, download):
+def update(conf, download, version_update, create_embeddings):
     print(f"Config file: {conf}")
     print(f"Download updates: {download}")
+    print(f"Update DB versions: {version_update}")
+    print(f"Create embeddings: {create_embeddings}")
 
     nedrexdb.parse_config(conf)
 
@@ -67,69 +73,125 @@ def update(conf, download):
     if version not in ["open", "licensed"]:
         raise Exception(f"invalid version {version!r}")
 
+    version_update_skip = set()
+    prev_metadata = {}
+
+    update_neo4j_image_version()
+
+# check for metadata of the current live version before fetching new data
+    if download:
+        try:
+            MongoInstance.connect("live")
+            prev_metadata = list(MongoInstance.DB["metadata"].find())
+            prev_metadata = {} if prev_metadata is None else prev_metadata[0]["source_databases"]
+            # log printing
+            print("PREVIOUS METADATA")
+            for source in prev_metadata:
+                print(f"{source}:\t{prev_metadata[source]['version']}"
+                      f" [{prev_metadata[source]['date']}]")
+        except:
+            print("No previous metadata found")
+
     dev_instance = NeDRexDevInstance()
     dev_instance.remove()
     dev_instance.set_up(use_existing_volume=False, neo4j_mode="import")
     MongoInstance.connect("dev")
     MongoInstance.set_indexes()
 
-    if download:
-        downloaders.download_all()
+    if os.environ.get("TEST_MINIMUM", 0) == '1':
+        parse_dev(version=version, download=download, version_update=version_update, prev_metadata=prev_metadata)
+    else:
+        if download:
+            # update metadata
+            # fallback version is rarely needed. Do not change that file, only use the config!
+            default_version = None
+            if os.path.exists("/data/nedrex_files/nedrex_data/fallback_version"):
+                with open("/data/nedrex_files/nedrex_data/fallback_version") as fallback_file:
+                    default_version = fallback_file.readline().rstrip()
+            nedrex_versions = update_versions(version_update_skip, default_version=default_version)
+            with open("/data/nedrex_files/nedrex_data/fallback_version", "w") as fallback_file:
+                fallback_file.write(f"{nedrex_versions['version']}")
 
-    # Parse sources contributing only nodes (and edges amongst those nodes)
-    methods_scores = parse_method_scores()
-    
-    go.parse_go()
-    mondo.parse_mondo_json()
-    ncbi.parse_gene_info()
-    uberon.parse()
-    uniprot.parse_proteins()
-    # Sources that add node type but require existing nodes, too
-    cosmic.parse_gene_disease_associations()
-    clinvar.parse()
+            # do the download
+            print("Download: ON")
+            current_metadata = nedrex_versions["source_databases"]
+            subprocess.run(["./setup_data.sh", "/data/nedrex_files"])
+            downloaders.download_all(prev_metadata=prev_metadata, current_metadata=current_metadata)
 
-    if version == "licensed":
-        drugbank._parse_drugbank()  # requires proteins to be parsed first
-    elif version == "open":
-        drugbank.parse_drugbank()
-        chembl.parse_chembl()
-    uniprot_signatures.parse()  # requires proteins to be parsed first
-    hpo.parse()  # requires disorders to be parsed first
-    reactome.parse()  # requires protein to be parsed first
-    bioontology.parse()  # requires phenotype to be parsed
-    #
-    # Sources that add data to existing nodes
-    drug_central.parse_drug_central()
-    unichem.parse()
-    repotrial.parse()
-    #
-    # Sources adding edges.
-    biogrid.parse_ppis(methods_scores)
-    ctd.parse()
-    #disgenet.parse_gene_disease_associations()
-    go.parse_goa()
-    hpa.parse_hpa()
-    iid.parse_ppis(methods_scores)
-    intact.parse(methods_scores)
-    
+        if version_update:
+            get_versions(version_update)
 
-    if version == "licensed":
-        omim.parse_gene_disease_associations()
+        methods_scores = parse_method_scores()
+
+        # Parse sources contributing only nodes (and edges amongst those nodes)
+        go.parse_go()
+        mondo.parse_mondo_json()
+        ncbi.parse_gene_info()
+        uberon.parse()
+        uniprot.parse_proteins()
+
+        # Sources that add node type but require existing nodes, too
+        cosmic.parse_gene_disease_associations()
+        clinvar.parse()
+
+        if version == "licensed":
+            drugbank._parse_drugbank()  # requires proteins to be parsed first
+        elif version == "open":
+            drugbank.parse_drugbank()
+            chembl.parse_chembl()
+        uniprot_signatures.parse()  # requires proteins to be parsed first
+        hpo.parse()  # requires disorders to be parsed first
+        reactome.parse()  # requires protein to be parsed first
+        bioontology.parse()  # requires phenotype to be parsed
+
+        # Sources that add data to existing nodes
+        drug_central.parse_drug_central()
+        unichem.parse()
+        repotrial.parse()
+
+        # Sources adding edges.
+        biogrid.parse_ppis(methods_scores)
+        ctd.parse()
+        disgenet.parse_gene_disease_associations()
+        intogen.parse_gene_disease_associations()
+        orphanet.parse_gene_disease_associations()
+        opentargets.parse_gene_disease_associations()    
+        ncg.parse_gene_disease_associations()
+        go.parse_goa()
+        hpa.parse_hpa()
+        iid.parse_ppis(methods_scores)
+        intact.parse(methods_scores)
+
+        if version == "licensed":
+            omim.parse_gene_disease_associations()
+            version_update_skip.add("omim")
+
+        sider.parse()
+        uniprot.parse_idmap()
+
+        from nedrexdb.analyses import molecule_similarity
+        molecule_similarity.run()
+
+        # Post-processing
+        trim_uberon.trim_uberon()
+        
+        #if download:
+            # fallback version is rarely needed. Do not change that file, only use the config!
+         #   default_version = None
+         #   if os.path.exists("/data/nedrex_files/nedrex_data/fallback_version"):
+         #       with open("/data/nedrex_files/nedrex_data/fallback_version") as fallback_file:
+         #           default_version = fallback_file.readline().rstrip()
+         #   nedrex_version = update_versions(version_update_skip, default_version=default_version)
+         #   with open("/data/nedrex_files/nedrex_data/fallback_version", "w") as fallback_file:
+         #       fallback_file.write(f"{nedrex_version}")
+        #if version_update:
+         #   get_versions(version_update)
 
-    sider.parse()
-    uniprot.parse_idmap()
 
-    intogen.parse_gene_disease_associations()
-    orphanet.parse_gene_disease_associations()
-    opentargets.parse_gene_disease_associations()    
-    ncg.parse_gene_disease_associations()
 
-    from nedrexdb.analyses import molecule_similarity
 
-    molecule_similarity.run()
 
-    # Post-processing
-    trim_uberon.trim_uberon()
+    # clean up for export
     drop_empty_collections.drop_empty_collections()
 
     # export to Neo4j
@@ -137,22 +199,118 @@ def update(conf, download):
 
     # Profile the collections
     collection_stats.profile_collections(MongoInstance.DB)
-    update_db_version.update_db_version(default_version="2.0.0")
-    time.sleep(60)
+
+    collection_stats.verify_collections_after_profiling(MongoInstance.DB)
+
 
     # remove dev instance and set up live instance
+    dev_instance.remove(neo4j_mode="import")
+
+    dev_instance = NeDRexDevInstance()
+    dev_instance.set_up(use_existing_volume=True, neo4j_mode="db-write")
+    create_constraints()
+
+    if create_embeddings:
+        # dev_instance = NeDRexDevInstance()
+        # dev_instance.set_up(use_existing_volume=True, neo4j_mode="db-write")
+
+        # create embeddings
+        try:
+            create_vector_indices()
+            # time.sleep(10)
+        except Exception as e:
+            print(e)
+            print("Failed to create vector indices")
+
     dev_instance.remove()
     live_instance = NeDRexLiveInstance()
     live_instance.remove()
     live_instance.set_up(use_existing_volume=True, neo4j_mode="db")
 
+def parse_dev(version, download, version_update, prev_metadata):
+    # control source downloads
+    ignored_sources = {"chembl",
+                       "biogrid",
+                       "go",
+                       "uberon",
+                       "clinvar",
+                       "hpo",
+                       "hpa",
+                       "uniprot",
+                       "reactome",
+                       "bioontology",
+                       "drug_central",
+                       "unichem",
+                       "repotrial",
+                       "iid",
+                       "intact",
+                       "omim",
+                       "sider"}
+    if download:
+        # fallback version is rarely needed. Do not change that file, only use the config!
+        default_version = None
+        if os.path.exists("/data/nedrex_files/nedrex_data/fallback_version"):
+            with open("/data/nedrex_files/nedrex_data/fallback_version") as fallback_file:
+                default_version = fallback_file.readline().rstrip()
+        nedrex_versions = update_versions(ignored_sources=ignored_sources, default_version=default_version)
+        with open("/data/nedrex_files/nedrex_data/fallback_version", "w") as fallback_file:
+            fallback_file.write(f"{nedrex_versions['version']}")
+
+        # do the download
+        print("Download: ON")
+        current_metadata = nedrex_versions["source_databases"]
+        subprocess.run(["./setup_data.sh", "/data/nedrex_files"])
+        downloaders.download_all(ignored_sources=ignored_sources,
+                                 prev_metadata=prev_metadata,
+                                 current_metadata=current_metadata)
+
+    if version_update:
+        get_versions(version_update)
+
+
+    mondo.parse_mondo_json()
+    ncbi.parse_gene_info()
+    if version == "licensed":
+        drugbank._parse_drugbank()
+    elif version == "open":
+        drugbank.parse_drugbank()
+    ctd.parse()
+    disgenet.parse_gene_disease_associations()
+
+
+#    if download:
+#        # fallback version is rarely needed. Do not change that file, only use the config!
+#        default_version = None
+#        if os.path.exists("/data/nedrex_files/nedrex_data/fallback_version"):
+#            with open("/data/nedrex_files/nedrex_data/fallback_version") as fallback_file:
+#                default_version = fallback_file.readline().rstrip()
+#        nedrex_version = update_versions(ignored_sources=ignored_sources, default_version=default_version)
+#        with open("/data/nedrex_files/nedrex_data/fallback_version", "w") as fallback_file:
+#            fallback_file.write(f"{nedrex_version}")
+#    if version_update:
+#        get_versions(version_update)
+
 
 @click.option("--conf", required=True, type=click.Path(exists=True))
+# @click.option("--create_embeddings", is_flag=True, default=False)
 @cli.command()
 def restart_live(conf):
     print(f"Config file: {conf}")
     nedrexdb.parse_config(conf)
-
+    
+    # if create_embeddings:
+    #     dev_instance = NeDRexDevInstance()
+    #     dev_instance.remove(neo4j_mode="import")
+    #     dev_instance.set_up(use_existing_volume=True, neo4j_mode="db-write")
+    #     # create embeddings
+    #     time.sleep(60)
+    #     try:
+    #         create_vector_indices.create_vector_indices()
+    #     except Exception as e:
+    #         print(e)
+    #         print("Failed to create vector indices")
+    #     dev_instance.remove()
+    
     live_instance = NeDRexLiveInstance()
     live_instance.remove()
     live_instance.set_up(use_existing_volume=True, neo4j_mode="db")
diff --git a/build.sh b/build.sh
index de4ca7e..d6fb241 100755
--- a/build.sh
+++ b/build.sh
@@ -1,41 +1,55 @@
 #!/bin/bash
 
-echo "Starting setup of licensed DB"
-if [ "${DOWNLOAD_ON_STARTUP}" == "1" ]; then
-     echo "Download: ON"
-     ./setup_data.sh /data/nedrex_files; ./build.py update --conf .licensed_config.toml --download
-  else
-     echo "Download: OFF"
-     if [ "${SKIP_UPDATE}" == "1" ]; then
-       echo "only restarting"
-       ./build.py restart-live --conf .licensed_config.toml
-     else
-       ./build.py update --conf .licensed_config.toml
-       ./set_metadata.py --config .licensed_config.toml --version live
-     fi
-     if [ "${SKIP_CLEAN}" == "1" ]; then
+setup_db() {
+    local db_type=$1
+    local config_file=".$db_type"_config.toml
+
+    echo "Starting setup of $db_type DB"
+
+    # Handle DB updates
+    if [[ "$SKIP_UPDATE" == "1" ]]; then
+       ./build.py restart-live --conf "$config_file"
+    else
+        local build_args=(update --conf "$config_file")
+
+        if [[ "$DOWNLOAD_ON_STARTUP" == "1" ]]; then
+
+          # update incl. metadata when setting download flag
+          if [[ "$db_type" == "licensed" ]]; then
+              build_args+=(--download)
+
+           # when only building open db, download flag must be set
+          elif [[ "$db_type" == "open" ]]; then
+              if [[ "$SKIP_LICENSED" == "1" ]]; then
+                build_args+=(--download)
+              else
+                build_args+=(--version_update .licensed_config.toml)
+              fi
+
+          fi
+        # set versions anyways when no download
+        else
+          build_args+=(--version_update true)
+
+        fi
+
+        if [[ "$CREATE_EMBEDDINGS" == "1" ]]; then
+          build_args+=(--create_embeddings)
+        fi
+        ./build.py "${build_args[@]}"
+    fi
+
+    # Clean volumes if not skipped
+    if [[ "$SKIP_CLEAN" != "1" ]]; then
+        ./clean_volumes.sh "$db_type"
+    else
         echo "Skipping clean"
-      else
-        ./clean_volumes.sh licensed
-      fi
-  fi
-
-echo "Finished setup of licensed DB"
-
-
-if [ "${SKIP_OPEN}" == "1" ]; then
-  exit 0
-fi
-echo "Starting setup of open DB"
-if [ "${SKIP_UPDATE}" == "1" ]; then
-  ./build.py restart-live --conf .open_config.toml
-else
-  ./build.py update --conf .open_config.toml
-  ./set_metadata.py --config .open_config.toml --version live
-fi
-if [ "${SKIP_CLEAN}" == "1" ]; then
-  echo "Skipping clean"
-else
-  ./clean_volumes.sh open
-fi
-echo "Finished setup of open DB"
+    fi
+
+    echo "Finished setup of $db_type DB"
+}
+
+# Setup licensed DB if not skipped
+[[ "$SKIP_LICENSED" != "1" ]] &&  setup_db licensed
+# Setup open DB if not skipped
+[[ "$SKIP_OPEN" != "1" ]] && setup_db open
\ No newline at end of file
diff --git a/config/.dockerignore b/config/.dockerignore
deleted file mode 100644
index 485dee6..0000000
--- a/config/.dockerignore
+++ /dev/null
@@ -1 +0,0 @@
-.idea
diff --git a/config/open_config.toml b/config/open_config.toml
index a01f332..ef10723 100755
--- a/config/open_config.toml
+++ b/config/open_config.toml
@@ -3,7 +3,7 @@ mode="open"
 status="live"
 port=7123
 host="127.0.0.1"
-base="/"
+base="/open"
 
 rate_limiting_enabled = false
 rate_limit = "1/second"
@@ -60,19 +60,28 @@ edge_collections = [
 
 [api.directories]
 static = "/data/nedrex_files/nedrex_api/static"
-static_outside = "/home/andim/projects/nedrex/nedrexdb_v2d/nedrex_files/nedrex_api/static"
+static_outside = "/localscratch/nedrex_files/nedrex_api/static"
 data = "/data/nedrex_files/nedrex_api/data"
-data_outside = "/home/andim/projects/nedrex/nedrexdb_v2d/nedrex_files/nedrex_api/data"
+data_outside = "/localscratch/nedrex_files/nedrex_api/data"
 scripts = "/app/nedrexapi/scripts"
 
 [tools]
 bicon_python = "/opt/conda/envs/bicon/bin/python"
 
+[embeddings]
+server_base="None"
+model="None"               
+path="embeddings"
+user="None"
+pass="none"
 
+[chat]
+server_base="None"  
+model="None"
 [db]
 version = "open"
-neo4j_image = "neo4j:3.5.34"
-mongo_image = "mongo:4.4.10"
+neo4j_image = "ghcr.io/repotrial/nedrexdb_v2d-neo4j:dev"
+mongo_image = "mongo:5.0.27"
 mongo_express_image = "mongo-express:0.54.0"
 mongo_db = "nedrex"
 root_directory = "/data/nedrex_files/nedrex_data"
@@ -108,23 +117,35 @@ express_container_name = "open_nedrex_live_express"
 
 [sources]
 directory = "downloads"
+default_version = "2.2.0"
 
 [sources.biogrid]
 [sources.biogrid.human_data]
 filename = "homo_sapiens.tab3"
 
 [sources.bioontology]
+version = "2022AB"
+
 [sources.bioontology.meddra_mappings]
 filename = "meddra.json"
 
+
+
 [sources.chembl]
+version_url = "https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/"
+version_pattern = '''href="chembl_\d+_sqlite\.tar\.gz"'''
+
 [sources.chembl.sqlite]
-url = "https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_34_sqlite.tar.gz"
+url = "https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_{}_sqlite.tar.gz"
+
 
 [sources.chembl.unichem]
-url = "https://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/src_id1/src1src2.txt.gz"
+url = "ftp://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/src_id1/src1src2.txt.gz"
 
 [sources.clinvar]
+version_url = "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/"
+version_pattern = '''href="clinvar_\d+\.vcf\.error\.txt"'''
+
 [sources.clinvar.human_data]
 url = "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz"
 
@@ -132,23 +153,41 @@ url = "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz"
 url = "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarVCVRelease_00-latest.xml.gz"
 
 [sources.ctd]
+version_url = "https://ctdbase.org/reports/"
+version_pattern = '''>CTD_chemicals_diseases\.tsv\.gz</a></td><td align="right">[\d-]+'''
+
 [sources.ctd.chemical_disease_relationships]
-url = "https://ctdbase.org/reports/CTD_chemicals_diseases.tsv.gz"
+url = "http://ctdbase.org/reports/CTD_chemicals_diseases.tsv.gz"
+
 
 [sources.disgenet]
+version = "24.1"
+
 [sources.disgenet.gene_disease_associations]
 url = "https://www.disgenet.org/static/disgenet_ap1/files/downloads/curated_gene_disease_associations.tsv.gz"
 
+
 [sources.drugbank]
+version = "5.1.10"
+
+[sources.drugbank.all]
+filename = "full database.xml"
+
 [sources.drugbank.open]
 filename = "all_drugbank_vocabulary.zip"
 
 [sources.drug_central]
+version = "2023-01-11"
+
 [sources.drug_central.postgres_dump]
 url = "https://unmtid-shinyapps.net/download/drugcentral.dump.11012023.sql.gz"
 filename = "drug_central.sql.gz"
 
+
 [sources.go]
+version_url = "https://current.geneontology.org/release_stats/go-stats-summary.json"
+version_pattern = '''"release_date": "[\d-]+'''
+
 [sources.go.go_core_owl]
 url = "http://purl.obolibrary.org/obo/go.owl"
 
@@ -156,37 +195,71 @@ url = "http://purl.obolibrary.org/obo/go.owl"
 url = "http://geneontology.org/gene-associations/goa_human.gaf.gz"
 
 [sources.hpa]
+version_url = "https://www.proteinatlas.org/about/download"
+version_pattern = '''data available in the Human Protein Atlas version \d+\.\d+'''
+version_mode = "serial"
+
 [sources.hpa.all]
 url = "https://www.proteinatlas.org/download/proteinatlas.xml.gz"
 
 [sources.hpo]
+version_url = "https://github.com/obophenotype/human-phenotype-ontology/releases/"
+version_pattern = '''href="/obophenotype/human-phenotype-ontology/releases/tag/v[\d-]+'''
+
 [sources.hpo.obo]
 url = "http://purl.obolibrary.org/obo/hp.obo"
 
 [sources.hpo.annotations]
 url = "http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa"
 
+
 [sources.iid]
+version_url = "http://iid.ophid.utoronto.ca/static/Search_By_Proteins.css"
+version_pattern = '''content: "version [\d-]+'''
+
 [sources.iid.human]
 url = "http://iid.ophid.utoronto.ca/static/download/human_annotated_PPIs.txt.gz"
 
+
 [sources.intact]
+version_url = "https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/"
+version_pattern = '''>intact\.zip</a></td><td align="right">[\d-]+'''
+
 [sources.intact.psimitab]
-url = "http://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip"
+url = "https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip"
+
 
 [sources.mondo]
+version_url = "https://github.com/monarch-initiative/mondo/tags"
+version_pattern = '''/monarch-initiative/mondo/releases/tag/v[\d-]+'''
+
 [sources.mondo.json]
 url = "http://purl.obolibrary.org/obo/mondo.json"
 
+
 [sources.ncbi]
+version_url = "https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/"
+version_pattern = '''>Homo_sapiens\.gene_info\.gz</a>      [\d-]+'''
+
 [sources.ncbi.gene_info]
 url = "https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz"
 
+
+[sources.omim]
+[sources.omim.genemap2]
+url = "https://data.omim.org/downloads/DIcI6kd8S96Xx9TDthBjCw/genemap2.txt"
+
+
 [sources.sider]
+version = "4.1"
+
 [sources.sider.frequency_data]
 url = "http://sideeffects.embl.de/media/download/meddra_freq.tsv.gz"
 
+
 [sources.repotrial]
+version = "1.0.0"
+
 [sources.repotrial.mappings]
 filename = "repotrial_mappings.tsv"
 
@@ -194,18 +267,32 @@ filename = "repotrial_mappings.tsv"
 filename = "matching_icd10_cmwho.json"
 
 [sources.unichem]
+version_url = "http://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/src_id2/"
+version_pattern = '''>src2src22\.txt\.gz</a></td><td align="right">[\d-]+'''
+skip_digits = 3
+
 [sources.unichem.pubchem_drugbank_map]
-url = "http://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/src_id2/src2src22.txt.gz"
+url = "ftp://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/src_id2/src2src22.txt.gz"
 
 [sources.uberon]
+version = "2022-04-05"
+
 [sources.uberon.ext]
 url = "https://github.com/obophenotype/uberon/releases/download/v2022-04-05/ext.json"
 
 [sources.reactome]
+version_url = "https://reactome.org/download/current/"
+version_pattern = '''>UniProt2Reactome_All_Levels\.txt</a></td><td align="right">[\d-]+'''
+skip_digits = 1
+
 [sources.reactome.uniprot_annotations]
 url = "https://reactome.org/download/current/UniProt2Reactome_PE_All_Levels.txt"
 
+
 [sources.uniprot]
+version_url = "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions"
+version_pattern = '''>uniprot_sprot_human\.dat\.gz</a></td><td align="right">[\d-]+'''
+
 [sources.uniprot.swissprot]
 url = "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_human.dat.gz"
 
diff --git a/cron/cron.prod b/cron/cron.prod
index 5aea624..dc8bcf7 100644
--- a/cron/cron.prod
+++ b/cron/cron.prod
@@ -1,3 +1,3 @@
 #HOME=/app/nedrexdb/
 #SHELL=/usr/bin/bash
-0 20 * * 7 cd /app/nedrexdb/ && bash update.sh >>/var/log/nedrexdb.log 2>&1
+0 20 * * 6 cd /app/nedrexdb/ && bash update.sh >>/var/log/nedrexdb.log 2>&1
diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
index e656982..480707a 100644
--- a/docker-compose.dev.yml
+++ b/docker-compose.dev.yml
@@ -2,13 +2,17 @@ version: '3.3'
 
 services:
   db:
+#    image: nedrexdb_v2d:dev
+    image: ghcr.io/repotrial/nedrexdb_v2d:dev
     container_name: nedrexdb_v2
     build: .
     environment:
-      - DOWNLOAD_ON_STARTUP=0
+      - DOWNLOAD_ON_STARTUP=1
       - SKIP_UPDATE=0
-      - SKIP_OPEN=1
+      - SKIP_OPEN=0
       - SKIP_CLEAN=0
+      - TEST_MINIMUM=0
+      - CREATE_EMBEDDINGS=0
     volumes:
       - /var/run/docker.sock:/var/run/docker.sock
       - /tmp/nedrexdb_v2:/tmp
diff --git a/docker-compose.yml b/docker-compose.yml
index 07b3d97..12569b6 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -6,6 +6,9 @@ services:
     container_name: nedrexdb_v2
     environment:
       - DOWNLOAD_ON_STARTUP=1
+      - SKIP_UPDATE=0
+      - SKIP_OPEN=0
+      - SKIP_CLEAN=0
     volumes:
       - /var/run/docker.sock:/var/run/docker.sock
       - /tmp/nedrexdb_v2:/tmp
diff --git a/nedrexdb/__init__.py b/nedrexdb/__init__.py
index d92133f..0c4e830 100644
--- a/nedrexdb/__init__.py
+++ b/nedrexdb/__init__.py
@@ -20,6 +20,122 @@ def __repr__(self):
     def from_file(self, infile):
         with open(infile, "r") as f:
             self.data = _toml.load(f)
+            # from here on, set defaults for minimal config
+            if "version_type" in self.data.keys():
+                print("USING MINIMAL CONFIG MODE")
+                vt = self.data["version_type"]
+                defaults_dict = {'api': {'mode': f'{vt}',
+                                         'status': 'live',
+                                         'base': f'/{vt}',
+                                         'rate_limiting_enabled': False,
+                                         'rate_limit': '1/second',
+                                         'require_api_keys': True if vt == "licensed" else False,
+                                         'pagination_max': 10000,
+                                         'redis_port_internal': 6379,
+                                         'redis_host': f'{vt}-nedrex-redis',
+                                         'redis_nedrex_db': 1,
+                                         'redis_rate_limit_db': 2,
+                                         'redis_queue_db': 3,
+                                         'mongo_port_internal': 27017,
+                                         'mongo_db': 'nedrexapi',
+                                         'node_collections': ['disorder',
+                                                              'drug',
+                                                              'gene',
+                                                              'genomic_variant',
+                                                              'go',
+                                                              'pathway',
+                                                              'protein',
+                                                              'phenotype',
+                                                              'tissue',
+                                                              'side_effect',
+                                                              'signature'],
+                                         'edge_collections': ['disorder_has_phenotype',
+                                                              'disorder_is_subtype_of_disorder',
+                                                              'drug_has_contraindication',
+                                                              'drug_has_indication',
+                                                              'drug_has_target',
+                                                              'drug_has_side_effect',
+                                                              'gene_associated_with_disorder',
+                                                              'go_is_subtype_of_go',
+                                                              'molecule_similarity_molecule',
+                                                              'protein_encoded_by_gene',
+                                                              'protein_has_go_annotation',
+                                                              'protein_has_signature',
+                                                              'protein_in_pathway',
+                                                              'protein_interacts_with_protein',
+                                                              'protein_expressed_in_tissue',
+                                                              'gene_expressed_in_tissue',
+                                                              'side_effect_same_as_phenotype',
+                                                              'variant_affects_gene',
+                                                              'variant_associated_with_disorder'],
+                                         'directories': {'static': '/data/nedrex_files/nedrex_api/static',
+                                                         'static_outside': self.data['static_outside'],
+                                                         'data': '/data/nedrex_files/nedrex_api/data',
+                                                         'data_outside': self.data['data_outside'],
+                                                         'scripts': '/app/nedrexapi/scripts'}},
+                                 'tools': {'bicon_python': '/opt/conda/envs/bicon/bin/python'},
+                                 'chat': {'server_base': "",
+                                          'model': 'gemma3:latest'},
+                                 'embeddings': {'server_base': "",
+                                                'model': "snowflake-arctic-embed2:latest",
+                                                'path': "embeddings",
+                                                'api_key': None},
+                                 'db': {'version': f'{vt}',
+                                        'neo4j_image': "ghcr.io/repotrial/nedrexdb_v2d-neo4j:prod",
+                                        'mongo_image': 'mongo:4.4.10',
+                                        'mongo_express_image': 'mongo-express:0.54.0',
+                                        'mongo_db': 'nedrex',
+                                        'root_directory': '/data/nedrex_files/nedrex_data',
+                                        'volume_root': f'{vt}_nedrex',
+                                        'dev': {'mongo_port': 27017 if vt == "licensed" else 26017,
+                                                'mongo_name': f'{vt}_nedrex_dev',
+                                                'mongo_express_port': 8081 if vt == "licensed" else 7081,
+                                                'neo4j_http_port': 7478 if vt == "licensed" else 6478,
+                                                'neo4j_bolt_port': 7688 if vt == "licensed" else 6688,
+                                                'neo4j_name': f'{vt}_nedrex_dev_neo4j',
+                                                'container_name': f'{vt}_nedrex_dev',
+                                                'express_container_name': f'{vt}_nedrex_dev_express'},
+                                        'live': {'mongo_port': 27018 if vt == "licensed" else 26018,
+                                                 'mongo_port_internal': 27017,
+                                                 'mongo_express_port': 8082 if vt == "licensed" else 7082,
+                                                 'mongo_name': f'{vt}_nedrex_live',
+                                                 'neo4j_http_port': 7479 if vt == "licensed" else 6479,
+                                                 'neo4j_bolt_port': 7689 if vt == "licensed" else 6689,
+                                                 'neo4j_bolt_port_internal': 7687,
+                                                 'neo4j_name': f'{vt}_nedrex_live_neo4j',
+                                                 'container_name': f'{vt}_nedrex_live',
+                                                 'express_container_name': f'{vt}_nedrex_live_express'}}}
+
+                # overwrite defaults with config
+                overwrite_set = {'neo4j_image', 'mongo_image', 'mongo_image'}
+                for image in overwrite_set:
+                    if image in self.data.keys():
+                        defaults_dict["db"][image] = self.data[image]
+                if vt == "open":
+                    defaults_dict["api"]["redis_port"] = 5379
+                    defaults_dict["db"]["dev"]["mongo_port_internal"] = 27017
+                    defaults_dict["db"]["dev"]["neo4j_http_port_internal"] = 7474
+                    defaults_dict["db"]["dev"]["neo4j_bolt_port_internal"] = 7687
+                    defaults_dict["db"]["live"]["neo4j_http_port_internal"] = 7474
+
+                if "config_deep_merge" in self.data.keys() and self.data["config_deep_merge"] == False:
+                    self.data = defaults_dict | self.data
+                else:
+                    self.data = self.deep_merge(defaults_dict, self.data)
+
+    def deep_merge(self, dict1, dict2):
+        for key, value in dict2.items():
+            if key in dict1:
+                if isinstance(dict1[key], dict) and isinstance(value, dict):
+                    # Recursively merge dictionaries
+                    self.deep_merge(dict1[key], value)
+                else:
+                    # Overwrite the value in dict1 with the value from dict2
+                    dict1[key] = value
+            else:
+                # Add the key-value pair from dict2 to dict1
+                dict1[key] = value
+        return dict1
 
     def __getitem__(self, path):
         if self.data is None:
@@ -44,9 +160,13 @@ def get(self, path):
 
 
 config = _Config()
-
+mconfig = _Config()
 
 def parse_config(infile):
     global config
     logger.info("Parsing config file: %s" % infile)
     config.from_file(infile)
+
+def parse_mconfig(infile):
+    global mconfig
+    mconfig.from_file(infile)
diff --git a/nedrexdb/common.py b/nedrexdb/common.py
index c9b1dce..c0581e4 100644
--- a/nedrexdb/common.py
+++ b/nedrexdb/common.py
@@ -28,11 +28,11 @@ class Downloader(_BaseModel):
     password: _Optional[str]
 
     @_validator("url")
-    def url_https_or_http(cls, v):
-        if any(v.startswith(i) for i in ("http://", "https://")):
+    def url_https_or_http_or_ftp(cls, v):
+        if any(v.startswith(i) for i in ("ftp://", "http://", "https://")):
             return v
         else:
-            raise ValueError(f"url {v!r} is not http(s)")
+            raise ValueError(f"url {v!r} is not http(s) or ftp")
 
     def download(self):
         for _ in range(3):
@@ -69,6 +69,7 @@ def _download(self):
                     "--no-verbose",
                     "--read-timeout",
                     "10",
+                    "-q",
                     "-O",
                     f"{self.target.resolve()}",
                     self.url,
diff --git a/nedrexdb/control/docker.py b/nedrexdb/control/docker.py
index ef21158..1b7bf0c 100644
--- a/nedrexdb/control/docker.py
+++ b/nedrexdb/control/docker.py
@@ -1,10 +1,14 @@
+import time
 import time as _time
 from abc import ABC as _ABC, abstractmethod as _abstractmethod
 
 import docker as _docker
+from docker.errors import NotFound, APIError
+from subprocess import run, CalledProcessError
 
 from nedrexdb import config as _config
 
+
 _client = _docker.from_env()
 
 
@@ -39,6 +43,16 @@ def get_mongo_volumes():
     volumes.sort(key=lambda i: i.name, reverse=True)
     return volumes
 
+def update_neo4j_image_version():
+    command = ["docker", "pull", _config["db.neo4j_image"]]
+    result = run(
+        command,
+        capture_output=True,
+        text=True
+    )
+    print(result.stdout)
+    print(result.stderr)
+
 
 def generate_neo4j_volume_name():
     timestamp = _time.time_ns() // 1_000_000  # time in ms
@@ -71,6 +85,8 @@ def remove(self):
 
 
 class _NeDRexBaseInstance(_NeDRexInstance):
+    GRACEFUL_SHUTDOWN_TIMEOUT = 1200
+
     @property
     def mongo_container_name(self):
         return _config[f"db.{self.version}.container_name"]
@@ -79,6 +95,10 @@ def mongo_container_name(self):
     def neo4j_container_name(self):
         return f'{_config[f"db.{self.version}.container_name"]}_neo4j'
 
+    @property
+    def db_mode(self):
+        return f'{_config["api.mode"]}'
+
     @property
     def neo4j_http_port(self):
         return _config[f"db.{self.version}.neo4j_http_port"]
@@ -151,24 +171,40 @@ def _set_up_neo4j(self, neo4j_mode, use_existing_volume):
             "image": get_neo4j_image(),
             "detach": True,
             "name": self.neo4j_container_name,
-            "volumes": {volume: {"mode": "rw", "bind": "/data"}, "/tmp/nedrexdb_v2": {"mode": "ro", "bind": "/import"}},
+            "volumes": {volume: {"bind": "/data", "mode": "rw"}},
             "ports": {7474: ("127.0.0.1", self.neo4j_http_port), 7687: ("127.0.0.1", self.neo4j_bolt_port)},
-            "environment": {"NEO4J_AUTH": "none"},
+            "environment": {
+                "NEO4J_AUTH": "none",
+                "NEO4J_PLUGINS": '["apoc"]',
+                "NEO4J_ACCEPT_LICENSE_AGREEMENT": "yes",
+                "NEO4J_server_config_strict__validation_enabled": "false",
+            },
             "network": self.network_name,
             "remove": False,
-            "restart_policy":{"Name":"always"}
+            "restart_policy": {"Name": "always"}
         }
 
+        if self.db_mode == "open":
+            kwargs["ports"][7474] = self.neo4j_http_port
+            kwargs["ports"][7687] = self.neo4j_bolt_port
+
         if neo4j_mode == "import":
+            kwargs["volumes"].update({"/tmp/nedrexdb_v2": {"bind": "/import", "mode": "ro"}})
+            kwargs["environment"]["NEO4J_dbms_memory_heap_max__size"] = "4G"
+            kwargs["environment"]["NEO4J_dbms_memory_pagecache_size"] = "2G"
             kwargs["stdin_open"] = True
             kwargs["tty"] = True
             kwargs["entrypoint"] = "/bin/bash"
 
         elif neo4j_mode == "db":
-            kwargs["environment"]["NEO4J_dbms_read__only"] = "true"
+            kwargs["environment"]["NEO4J_server_databases_read__only"] = "true"
+            kwargs["environment"]["NEO4J_server_databases_default__to__read__only"] = "true"
+        elif neo4j_mode == "db-write":
+            kwargs["environment"]["NEO4J_server_databases_read__only"] = "false"
+            kwargs["environment"]["NEO4J_server_databases_default__to__read__only"] = "false"
+
         else:
             raise Exception(f"neo4j_mode {neo4j_mode!r} is invalid")
-
         _client.containers.run(**kwargs)
 
     def _set_up_mongo(self, use_existing_volume):
@@ -191,7 +227,7 @@ def _set_up_mongo(self, use_existing_volume):
             ports={27017: ("127.0.0.1", self.mongo_port)},
             network=self.network_name,
             remove=False,
-            restart_policy={"Name":"always"}
+            restart_policy={"Name": "always"}
         )
 
     def _set_up_express(self):
@@ -206,10 +242,72 @@ def _set_up_express(self):
             network=self.network_name,
             environment={"ME_CONFIG_MONGODB_SERVER": self.mongo_container_name},
             remove=False,
-            restart_policy={"Name":"always"},
+            restart_policy={"Name": "always"}
         )
 
-    def _remove_neo4j(self, remove_db_volume=False):
+
+
+
+    def shutdown_neo4j_container(self) -> bool:
+        """
+        Gracefully shut down and remove the Neo4j container.
+
+        Returns:
+            bool: True if shutdown was successful, False otherwise
+        """
+        if not self._stop_neo4j_process():
+            print("Failed to gracefully stop Neo4j process")
+            # try:
+            #     self.neo4j_container.remove()
+            # except Exception:
+            #     pass
+
+        return self._remove_neo4_container()
+
+    def _stop_neo4j_process(self) -> bool:
+        """Attempt to gracefully stop the Neo4j process within the container."""
+        print("Attempting to gracefully stop Neo4j process")
+        update_command = ["docker", "update", "--restart=no", self.neo4j_container_name]
+        update = run(update_command)
+        update.check_returncode()
+        try:
+            result = run(
+                ["docker", "exec", self.neo4j_container_name, "neo4j", "stop"],
+                capture_output=True,
+                text=True,
+                timeout=self.GRACEFUL_SHUTDOWN_TIMEOUT
+            )
+            result = result.stdout == "Stopping Neo4j............" and result.returncode == 137
+            if result:
+                print("Neo4j process stopped")
+            time.sleep(5)
+            return result
+
+        except (CalledProcessError, TimeoutError) as e:
+            print(f"Failed to stop Neo4j process: {str(e)}")
+            return False
+
+    def _stop_neo4j_container(self) -> bool:
+        """Stop the Docker container."""
+        try:
+            self.neo4j_container.stop(timeout=self.GRACEFUL_SHUTDOWN_TIMEOUT)
+            return True
+
+        except (NotFound, APIError) as e:
+            print(f"Failed to stop container: {str(e)}")
+            return False
+
+    def _remove_neo4_container(self) -> bool:
+        """Remove the Docker container."""
+        try:
+            self.neo4j_container.remove(force=True)
+            return True
+
+        except (NotFound, APIError) as e:
+            print(f"Failed to remove container: {str(e)}")
+            return False
+
+    def _remove_neo4j(self, remove_db_volume=False, neo4j_mode="db"):
         if not self.neo4j_container:
             return
 
@@ -221,8 +319,10 @@ def _remove_neo4j(self, remove_db_volume=False):
         volumes_to_remove = [
             mount["Name"] for mount in mounts if mount["Type"] == "volume" and mount["Destination"] in volumes_to_remove
         ]
-
-        self.neo4j_container.remove(force=True)
+        if neo4j_mode=='import':
+            self.neo4j_container.remove(force=True)
+        else:
+            self.shutdown_neo4j_container()
 
         for vol_name in volumes_to_remove:
             _client.volumes.get(vol_name).remove(force=True)
@@ -261,20 +361,19 @@ def _remove_network(self):
             pass
 
     def set_up(self, use_existing_volume=True, neo4j_mode="db"):
-        print("Setting up Live NeDRex instance...")
-        # self._set_up_network()
-        self._set_up_mongo(use_existing_volume=use_existing_volume)
+        print(f"Setting up {self.db_mode} NeDRex instance...")
         self._set_up_neo4j(use_existing_volume=use_existing_volume, neo4j_mode=neo4j_mode)
-        self._set_up_express()
+        if neo4j_mode != "db-write":
+            self._set_up_mongo(use_existing_volume=use_existing_volume)
+            self._set_up_express()
 
-    def remove(self, remove_db_volume=False, remove_configdb_volume=True):
+    def remove(self, remove_db_volume=False, remove_configdb_volume=True, neo4j_mode="db"):
         self._remove_mongo(
             remove_db_volume=remove_db_volume,
             remove_configdb_volume=remove_configdb_volume,
         )
-        self._remove_neo4j(remove_db_volume=remove_db_volume)
         self._remove_express()
-        # self._remove_network()
+        self._remove_neo4j(remove_db_volume=remove_db_volume, neo4j_mode=neo4j_mode)
 
 
 class NeDRexLiveInstance(_NeDRexBaseInstance):
diff --git a/nedrexdb/db/collection_stats.py b/nedrexdb/db/collection_stats.py
index 4a3c01b..8e3b0c1 100644
--- a/nedrexdb/db/collection_stats.py
+++ b/nedrexdb/db/collection_stats.py
@@ -10,25 +10,51 @@ def profile_collections(db):
     edges = _config["api.edge_collections"]
 
     collections = nodes + edges
+    print("Starting collection profiling...")
     for coll in collections:
-        print(coll)
+        if coll not in db.list_collection_names():
+            print(f"WARNING: Collection '{coll}' does not exist in database, skipping...")
+            continue
+
+        print(f"Profiling collection: {coll}")
         doc_count = 0
         attr_counts = defaultdict(int)
 
-        for doc in tqdm(db[coll].find(), leave=False):
-            doc_count += 1
-            for attr in doc.keys():
-                attr_counts[attr] += 1
+        try:
+            total_docs = db[coll].count_documents({})
+            if total_docs == 0:
+                print(f"WARNING: Collection '{coll}' is empty")
+                continue
+
+            for doc in tqdm(db[coll].find(), total=total_docs, desc=f"Processing {coll}", leave=False):
+                doc_count += 1
+                for attr in doc.keys():
+                    attr_counts[attr] += 1
+
+            unique_attrs = list(attr_counts.keys())
 
-        unique_attrs = list(attr_counts.keys())
-        db["_collections"].update_one(
-            {"collection": coll},
-            {
-                "$set": {
+            db["_collections"].replace_one(
+                {"collection": coll},
+                {
+                    "collection": coll,
                     "document_count": doc_count,
                     "unique_attributes": unique_attrs,
                     "attribute_counts": dict(attr_counts),
                 },
-            },
-            upsert=True,
-        )
+                upsert=True
+            )
+            print(f"Successfully profiled {coll}: {doc_count} documents")
+        except Exception as e:
+            print(f"Error profiling {coll}: {str(e)}")
+            raise
+
+
+def verify_collections_after_profiling(db):
+    actual_collections = set(coll for coll in db.list_collection_names()
+                             if not coll.startswith("system.")
+                             and coll not in ["_collections", "metadata"])
+    metadata_collections = set(doc["collection"] for doc in db["_collections"].find())
+
+    missing = actual_collections - metadata_collections
+    if missing:
+        raise Exception(f"Collections missing from metadata after profiling: {missing}")
diff --git a/nedrexdb/db/mongo_to_neo.py b/nedrexdb/db/mongo_to_neo.py
index 838c3f2..8de8caf 100644
--- a/nedrexdb/db/mongo_to_neo.py
+++ b/nedrexdb/db/mongo_to_neo.py
@@ -115,6 +115,12 @@ def mongo_to_neo(nedrex_instance, db):
         cols.append(":TYPE")
         df.to_csv(f"{workdir}/{edge}.csv", columns=cols, index=False)
 
+    _subprocess.call([
+        "docker", "exec", nedrex_instance.neo4j_container_name,
+        "chown", "-R", "neo4j:neo4j", "/data", "/import", "/logs", "/var/lib/neo4j/plugins", "/app"
+    ])
+
+
     command = [
         "docker",
         "exec",
@@ -122,19 +128,28 @@ def mongo_to_neo(nedrex_instance, db):
         "neo4j",
         nedrex_instance.neo4j_container_name,
         "neo4j-admin",
+        "database",
         "import",
+        "full",
+        "neo4j",
         f"--array-delimiter={delimiter}",
         "--multiline-fields=true",
+        "--overwrite-destination=true",
+        "--ignore-empty-strings=true",
+        "--skip-bad-relationships=true",
+        "--skip-duplicate-nodes=true",
     ]
     for node in nodes:
-        command += ["--nodes", f"/import/{node}.csv"]
+        command += ["--nodes=/import/" + node + ".csv"]
     for edge in edges:
-        command += ["--relationships", f"/import/{edge}.csv"]
-    print(command)
+        command += ["--relationships=/import/" + edge + ".csv"]
+    # command += ["--database=nedrex"]
+
+    print(" ".join(command))
     _subprocess.call(command)
 
     # clean up
     for node in nodes:
-        _os.remove(f"{workdir}/{node}.csv")
+       _os.remove(f"{workdir}/{node}.csv")
     for edge in edges:
-        _os.remove(f"{workdir}/{edge}.csv")
+       _os.remove(f"{workdir}/{edge}.csv")
diff --git a/nedrexdb/db/parsers/chembl.py b/nedrexdb/db/parsers/chembl.py
index 4d675f1..68b789e 100644
--- a/nedrexdb/db/parsers/chembl.py
+++ b/nedrexdb/db/parsers/chembl.py
@@ -5,6 +5,7 @@
 from nedrexdb.db import MongoInstance
 from nedrexdb.db.parsers import _get_file_location_factory
 from nedrexdb.db.models.nodes.drug import Drug
+from nedrexdb.downloaders import get_latest_chembl_version
 
 get_file_location = _get_file_location_factory("chembl")
 
@@ -22,12 +23,15 @@ def get_chembl_drugbank_map():
 
 
 def decompress_if_necessary():
-    path = get_file_location("sqlite")
-    target = path.parents[0] / path.name.rsplit(".", 2)[0]
+    version = get_latest_chembl_version()
+    url_path = get_file_location("sqlite")
+
+    target = url_path.parents[0] / url_path.name.rsplit(".", 2)[0].format(version)
     if target.exists():
         return target
 
     target.mkdir(parents=True)
+    path = url_path.parents[0] / url_path.name.format(version)
     _sp.call(
         ["tar", "-zxvf", f"{path}", "-C", f"{target.resolve()}", "--strip-components", "1"], cwd=f"{path.parents[0]}"
     )
diff --git a/nedrexdb/db/parsers/clinvar.py b/nedrexdb/db/parsers/clinvar.py
index 4788136..f6baf18 100644
--- a/nedrexdb/db/parsers/clinvar.py
+++ b/nedrexdb/db/parsers/clinvar.py
@@ -1,9 +1,9 @@
 import gzip as _gzip
-import xml.etree.cElementTree as _et
+from itertools import chain
+from lxml import etree as _let
 from collections import defaultdict as _defaultdict
 from csv import DictReader as _DictReader
 from functools import lru_cache as _lru_cache
-from itertools import chain as _chain
 
 from more_itertools import chunked as _chunked
 from tqdm import tqdm as _tqdm
@@ -19,6 +19,7 @@
 
 get_file_location = _get_file_location_factory("clinvar")
 
+already_reported_missing_handlers = set()
 
 def xml_disorder_mapper(id, db):
     if db == "MONDO":
@@ -31,7 +32,8 @@ def xml_disorder_mapper(id, db):
         return f"mesh.{id}"
     elif db in {"Human Phenotype Ontology", "EFO", "Gene", "MedGen"}:
         return None
-    else:
+    elif db in already_reported_missing_handlers:
+        already_reported_missing_handlers.add(db)
         logger.warning(f"database given without handler: {db!r}")
 
 
@@ -68,76 +70,74 @@ def iter_parse(self):
         variant_ids = get_variant_list()
         disorder_domain_id_map = disorder_domain_id_to_primary_id_map()
 
-        # throws an error if variant_ids is None
         assert None not in variant_ids
 
-        # opens gz file, takes its xml file. Fails, if it is empty
-        with _gzip.open(self.fname, "rt") as f:
-            for _, elem in _et.iterparse(f, events=("end",)):
-                if elem.tag == "ReferenceClinVarAssertion":
-                    pass
-
-                elif elem.tag == "ClinVarSet":
-                    ms = elem.find("ReferenceClinVarAssertion").find("MeasureSet")
-                    if ms:
-                        variant_pdid = f"clinvar.{ms.attrib['ID']}"
-                    else:
-                        variant_pdid = None
-
-                    if ms and variant_pdid in variant_ids:
-                        traits = elem.find("ReferenceClinVarAssertion").find("TraitSet").findall("Trait")
-                        traits = _chain(
-                            *[
-                                [xref.attrib for xref in trait.findall("XRef")]
-                                for trait in traits
-                                if trait.attrib["Type"] == "Disease"
-                            ]
-                        )
-                        traits = {xml_disorder_mapper(item["ID"], item["DB"]) for item in traits}
-                        traits = set(
-                            _chain(*[disorder_domain_id_map.get(domain_id, []) for domain_id in traits if domain_id])
-                        )
-                        traits.discard(None)
-
-                        effects = [
-                            effect.strip()
-                            for effect in elem.find("ReferenceClinVarAssertion")
-                            .find("ClinicalSignificance")
-                            .find("Description")
-                            .text.split(",")
-                        ]
-                        review_status = (
-                            elem.find("ReferenceClinVarAssertion")
-                            .find("ClinicalSignificance")
-                            .find("ReviewStatus")
-                            .text
-                        )
-                        acc = elem.find("ReferenceClinVarAssertion").find("ClinVarAccession").attrib["Acc"]
-
-                        for trait in traits:
-                            vawd = VariantAssociatedWithDisorder(
-                                sourceDomainId=variant_pdid,
-                                targetDomainId=trait,
-                                accession=acc,
-                                effects=effects,
-                                reviewStatus=review_status,
-                                dataSources=["clinvar"],
-                            )
-
-                            yield vawd
-
-                    elem.clear()
-
-                elif elem.tag == "MeasureSet":
-                    pass
-                elif elem.tag == "ClinVarAccession":
-                    pass
-                elif elem.tag in {"ClinicalSignificance", "Description", "ReviewStatus"}:
-                    pass
-                elif elem.tag in {"TraitSet", "Trait", "XRef"}:
-                    pass
+        with _gzip.open(self.fname, "rb") as f:
+            for _, elem in _let.iterparse(f, events=("end",), tag="VariationArchive"):
+                if elem.get('VariationID') is not None:
+                    variant_pdid = f"clinvar.{elem.get('VariationID')}"
                 else:
-                    elem.clear()
+                    variant_pdid = None
+                if variant_pdid in variant_ids:
+                    classified_record = elem.find("ClassifiedRecord")
+
+                    if classified_record is not None:
+
+                        clinical_assertion_list = classified_record.find("ClinicalAssertionList")
+
+                        if clinical_assertion_list is not None:
+                            clinical_assertions = clinical_assertion_list.findall("ClinicalAssertion")
+
+                            for clinical_assertion in clinical_assertions:
+
+                                trait_set = clinical_assertion.find("TraitSet")
+                                if trait_set is not None:
+                                    traits = trait_set.findall("Trait")
+                                    traits = chain(
+                                        *[
+                                            [xref.attrib for xref in trait.findall("XRef")]
+                                            for trait in traits
+                                            if trait.get("Type") == "Disease"
+                                        ]
+                                    )
+                                    traits = {xml_disorder_mapper(item["ID"], item["DB"]) for item in traits}
+                                    traits = set(
+                                        chain(
+                                            *[disorder_domain_id_map.get(domain_id, []) for domain_id in traits if
+                                              domain_id]
+                                        )
+                                    )
+                                    traits.discard(None)
+
+                                classification = clinical_assertion.find("Classification")
+                                if classification is not None:
+                                    effects_elem = classification.find(
+                                        "GermlineClassification")
+                                    review_status_elem = classification.find("ReviewStatus")
+
+                                    effects = [
+                                        effects_elem.text] if effects_elem is not None and effects_elem.text else []
+                                    review_status = review_status_elem.text if review_status_elem is not None else "Unknown"
+
+                                clinvar_accession = clinical_assertion.find("ClinVarAccession")
+                                if clinvar_accession is not None:
+                                    acc = clinvar_accession.get("Accession")
+                                else:
+                                    acc = None
+
+                                if traits and acc:
+                                    for trait in traits:
+                                        vawd = VariantAssociatedWithDisorder(
+                                            sourceDomainId=variant_pdid,
+                                            targetDomainId=trait,
+                                            accession=acc,
+                                            effects=effects,
+                                            reviewStatus=review_status,
+                                            dataSources=["clinvar"],
+                                        )
+                                        yield vawd
+
+                elem.clear()
 
 
 class ClinVarVCFParser:
@@ -230,7 +230,7 @@ def parse():
     parser = ClinVarVCFParser(fname)
 
     updates = (ClinVarRow(i).parse_variant().generate_update() for i in parser.iter_rows())
-    for chunk in _tqdm(_chunked(updates, 1_000), desc="Parsing ClinVar genomic variants", leave=False):
+    for chunk in _tqdm(_chunked(updates, 10_000), desc="Parsing ClinVar genomic variants", leave=False):
         MongoInstance.DB[GenomicVariant.collection_name].bulk_write(chunk)
 
     def iter_variant_gene_relationships():
@@ -241,14 +241,34 @@ def iter_variant_gene_relationships():
 
     updates = (vgr.generate_update() for vgr in iter_variant_gene_relationships() if vgr.targetDomainId in gene_ids)
     for chunk in _tqdm(
-        _chunked(updates, 1_000), desc="Parsing ClinVar genomic variant-gene relationships", leave=False
+        _chunked(updates, 10_000), desc="Parsing ClinVar genomic variant-gene relationships", leave=False
     ):
         MongoInstance.DB[VariantAffectsGene.collection_name].bulk_write(chunk)
 
+
     fname = get_file_location("human_data_xml")
+
     parser = ClinVarXMLParser(fname)
     updates = (i.generate_update() for i in parser.iter_parse())
     for chunk in _tqdm(
-        _chunked(updates, 1_000), desc="Parsing ClinVar genomic variant-disorder relationships", leave=False
+        _chunked(updates, 10_000), desc="Parsing ClinVar genomic variant-disorder relationships", leave=False
     ):
         MongoInstance.DB[VariantAssociatedWithDisorder.collection_name].bulk_write(chunk)
+        db = MongoInstance.DB
+        coll = VariantAssociatedWithDisorder.collection_name
+        doc_count = db[coll].count_documents({})
+        sample_doc = db[coll].find_one()
+
+        if sample_doc:
+            attr_counts = {attr: db[coll].count_documents({attr: {"$exists": True}})
+                           for attr in sample_doc.keys()}
+            db["_collections"].replace_one(
+                {"collection": coll},
+                {
+                    "collection": coll,
+                    "document_count": doc_count,
+                    "unique_attributes": list(attr_counts.keys()),
+                    "attribute_counts": attr_counts
+                },
+                upsert=True
+            )
diff --git a/nedrexdb/db/parsers/intogen.py b/nedrexdb/db/parsers/intogen.py
index d8fa067..68a74d3 100644
--- a/nedrexdb/db/parsers/intogen.py
+++ b/nedrexdb/db/parsers/intogen.py
@@ -96,6 +96,18 @@ def parse(self):
 
         symbol2entrez = {gene["approvedSymbol"]: gene["primaryDomainId"]
                          for gene in Gene.find(MongoInstance.DB)}
+        
+        # remove rows with symbols that cannot be mapped to entrez
+        f_dict_tmp = []
+        not_mapped = []
+        for row in f_dict:
+            if row["SYMBOL"] in symbol2entrez:
+                f_dict_tmp.append(row)
+            else:
+                not_mapped.append(row["SYMBOL"])
+        if not_mapped:
+            logger.warning(f"{len(f_dict) - len(f_dict_tmp)} intogen rows were left out, because symbol2entrez could not map: {set(not_mapped)}")
+        f_dict = f_dict_tmp
 
         updates = (IntOGenRow(row).parse(self.intogen2mondo, symbol2entrez)
                    for row in f_dict)
diff --git a/nedrexdb/db/parsers/opentargets.py b/nedrexdb/db/parsers/opentargets.py
index 14dfc9f..d489a9c 100644
--- a/nedrexdb/db/parsers/opentargets.py
+++ b/nedrexdb/db/parsers/opentargets.py
@@ -74,6 +74,7 @@ def parse(self):
         spark = (
             _SparkSession.builder
             .master('local[*]')
+            .config("spark.driver.memory", "12g")
             .getOrCreate()
         )
 
diff --git a/nedrexdb/db/parsers/unichem.py b/nedrexdb/db/parsers/unichem.py
index c26578f..8539d50 100644
--- a/nedrexdb/db/parsers/unichem.py
+++ b/nedrexdb/db/parsers/unichem.py
@@ -10,6 +10,16 @@
 get_file_location = _get_file_location_factory("unichem")
 
 
+def validate_file(file) -> bool:
+    try:
+        with gzip.open(file, "rt") as f:
+            reader = csv.reader(f, delimiter="\t")
+            next(reader)  # Skip the header row
+    except:
+        return False
+    return True
+
+
 def parse():
     fname = get_file_location("pubchem_drugbank_map")
     updates = []
diff --git a/nedrexdb/db/parsers/uniprot.py b/nedrexdb/db/parsers/uniprot.py
index 99983b8..4182960 100644
--- a/nedrexdb/db/parsers/uniprot.py
+++ b/nedrexdb/db/parsers/uniprot.py
@@ -22,6 +22,7 @@
 )
 from nedrexdb.logger import logger
 
+from nedrexdb.logger import logger
 get_file_location = _get_file_location_factory("uniprot")
 
 _field_size_limit(_sys.maxsize)
diff --git a/nedrexdb/db/parsers/uniprot_signatures.py b/nedrexdb/db/parsers/uniprot_signatures.py
index 1ae4b06..b08bb87 100644
--- a/nedrexdb/db/parsers/uniprot_signatures.py
+++ b/nedrexdb/db/parsers/uniprot_signatures.py
@@ -49,6 +49,8 @@ def iter_records(fname):
             if line.strip() == "//":
                 yield _StringIO(text)
                 text = ""
+        #for line in f:
+        #    yield _StringIO(line.strip())
 
 
 @dataclass
@@ -78,37 +80,46 @@ def to_update(self):
 
 @dataclass
 class SwissRecordParser:
-    data: _StringIO
 
     @property
     def id(self):
-        self.data.seek(0)
-        for line in self.data:
-            if not line.startswith("AC"):
-                continue
-            return f"uniprot.{line.strip().split()[1][:-1]}"
+        return self._id
 
     @property
     def signatures(self):
-        signatures = []
+        return self._signatures
 
-        self.data.seek(0)
-        for line in self.data:
-            if not line.startswith("DR"):
-                continue
 
-            db, acc, desc = [i[:-1] for i in line.strip().split()[1:4]]
+    @id.setter
+    def id(self, value):
+        self._id = value
 
-            if db not in _INTERPRO_DATABASES:
-                continue
+    @signatures.setter
+    def signatures(self, value):
+        self._signatures = value
+
+    id: str
+    signatures: list[str]
+
+    def __init__(self, data):
+        self.signatures = []
+        data.seek(0)
+        for line in data:
+            if line.startswith("AC"):
+                self.id = f"uniprot.{line.strip().split()[1][:-1]}"
+            elif line.startswith("DR"):
+                db, acc, desc = [i[:-1] for i in line.strip().split()[1:4]]
 
-            if not desc or desc == "-":
-                desc = None
+                if db not in _INTERPRO_DATABASES:
+                    continue
+
+                if not desc or desc == "-":
+                    desc = None
+
+                sig = Signature(f"{db.lower()}.{acc}", db, desc, dataSources=["uniprot"])
+                self.signatures.append(sig)
 
-            sig = Signature(f"{db.lower()}.{acc}", db, desc, dataSources=["uniprot"])
-            signatures.append(sig)
 
-        return signatures
 
 
 def generate_protein_signature_update(protein_id, signature_id):
@@ -139,19 +150,24 @@ def parse():
 
     protein_ids = {doc["primaryDomainId"] for doc in Protein.find(MongoInstance.DB)}
 
+    parsed_records = 0
+    missing_protein_ids = set()
     for chunk in _tqdm(_chunked(records_iter, 1_000), desc="Parsing signatures from UniProt", leave=False):
         signatures = []
         relationships = []
 
         records = [SwissRecordParser(data) for data in chunk]
-
         for record in records:
+            parsed_records+=1
             if record.id not in protein_ids:
-                raise Exception("Expected ID to be parsed already")
-
+                missing_protein_ids.add(record.id)
+                continue
             signatures += [sig.to_update() for sig in record.signatures]
             relationships += [generate_protein_signature_update(record.id, sig.domain_id) for sig in record.signatures]
-        if signatures:
+        if len(signatures) > 0:
             signature_coll.bulk_write(signatures)
-        if relationships:
+        if len(relationships) > 0:
             protein_has_sig_coll.bulk_write(relationships)
+    logger.info(f"Parsed {parsed_records} proteins, {len(missing_protein_ids)} were not parsed yet.")
+    logger.debug(f"Missing protein IDs: {missing_protein_ids}")
+
diff --git a/nedrexdb/db/update_db_version.py b/nedrexdb/db/update_db_version.py
deleted file mode 100644
index e09aa5e..0000000
--- a/nedrexdb/db/update_db_version.py
+++ /dev/null
@@ -1,121 +0,0 @@
-import os
-from typing import Literal
-from pathlib import Path
-from datetime import datetime
-
-from nedrexdb import config as _config
-from nedrexdb.logger import logger
-from nedrexdb.exceptions import NeDRexError
-
-from pymongo import MongoClient  # type: ignore
-from pymongo.database import Database  # type: ignore
-from pymongo.errors import ServerSelectionTimeoutError  # type: ignore
-
-
-def get_nedrex_version(db: Database, default_version="2.0.0"):
-    metadata = list(db["metadata"].find())
-    if len(metadata) > 1:
-        raise NeDRexError("metadata collection has more than one document in it")
-
-    if not metadata:
-        return default_version
-    metadata_doc = metadata[0]
-    if not metadata_doc.get("version"):
-        raise NeDRexError("metadata document does not have a version")
-    return metadata_doc["version"]
-
-
-def check_mongo_instance_exists(client: MongoClient):
-    logger.debug(f"Checking {client} for connection")
-    try:
-        client.server_info()
-    except ServerSelectionTimeoutError:
-        logger.debug("Got a SeverSelectionTimeoutError")
-        return False
-    logger.debug("Successfully connected to client")
-    return True
-
-
-def update_version(version, part_to_update: Literal["major", "minor", "patch", None], pre_release=None, build=None):
-    version = version.split(".")
-
-    if part_to_update == "major":
-        version[0] = f"{int(version[0]) + 1}"
-    elif part_to_update == "minor":
-        version[1] = f"{int(version[1]) + 1}"
-    elif part_to_update == "patch":
-        version[2] = f"{int(version[2]) + 1}"
-
-    # join version as a string
-    version = ".".join(version)
-
-    if pre_release:
-        version = f"{version}-{pre_release}"
-    if build:
-        version = f"{version}+{build}"
-
-    return version
-
-
-def generate_update_document(version, data_directory):
-    sources = list(_config["sources"].keys())
-    sources.remove("directory")
-
-    metadata = {"version": version, "source_databases": {}}
-    for source in sources:
-        dir = data_directory / source
-        earliest_date = datetime.now()
-
-        for _, options in _config[f"sources.{source}"].items():
-            if "filename" in options:
-                filename = options["filename"]
-            else:
-                filename = options["url"].rsplit("/", 1)[1]
-
-            path = dir / filename
-            ts = datetime.fromtimestamp(os.path.getctime(path))
-            if ts < earliest_date:
-                earliest_date = ts
-
-            metadata["source_databases"][source] = {"version": None, "date": f"{earliest_date.date()}"}
-
-    return metadata
-
-
-def update_db_version(default_version="2.0.0"):
-    logger.info("Updating NeDRexDB version number")
-
-    mongo_dbname = _config["db.mongo_db"]
-    mongo_dev_name = _config["db.dev.mongo_name"]
-    mongo_live_port = _config["db.live.mongo_port_internal"]
-    mongo_host = _config["db.live.mongo_name"]
-
-    download_directory = Path(_config["db.root_directory"]) / _config["sources.directory"]
-
-    logger.debug("Creating client for live DB")
-    live_client = MongoClient(port=mongo_live_port, host=mongo_host)
-    logger.debug(f"Created client with port {mongo_live_port}")
-    live_db = live_client[mongo_dbname]
-    logger.debug(f"Created DB instance with DB name {mongo_dbname}")
-
-    if not check_mongo_instance_exists(live_client):
-        logger.debug(f"Live version of NeDRexDB not found, using default version number of {default_version!r}")
-        current_version = default_version
-    else:
-        logger.debug("Live version of NeDRexDB exists - getting version of the current live instance")
-        current_version = get_nedrex_version(live_db, default_version=default_version)
-        logger.debug(f"Current version found: {current_version!r}")
-
-    logger.debug("Closing client to live version of NeDRexDB")
-    live_client.close()
-
-    logger.debug("Incrementing version number for NeDRexDB")
-    next_version = update_version(current_version, "minor")
-    logger.debug(f"New version number is {next_version!r}")
-    logger.debug("Generating metadata")
-    metadata = generate_update_document(next_version, download_directory)
-
-    dev_client = MongoClient(host=mongo_dev_name, port=27017)
-    dev_db = dev_client[mongo_dbname]
-    dev_db["metadata"].replace_one({}, metadata, upsert=True)
-
diff --git a/nedrexdb/downloaders/__init__.py b/nedrexdb/downloaders/__init__.py
index 98e2af2..cc05826 100644
--- a/nedrexdb/downloaders/__init__.py
+++ b/nedrexdb/downloaders/__init__.py
@@ -1,17 +1,34 @@
 import datetime as _datetime
+import logging
+import os
 import shutil as _shutil
+import re as _re
+import ast
+import time
+from pymongo import MongoClient
+from pymongo.errors import PyMongoError
+import toml
+
+
+import requests
 from pathlib import Path as _Path
 
+import nedrexdb
 from nedrexdb import config as _config
+from nedrexdb import mconfig as _mconfig
 from nedrexdb.common import Downloader
 from nedrexdb.db import MongoInstance
-from nedrexdb.downloaders.biogrid import download_biogrid as _download_biogrid
-from nedrexdb.downloaders.chembl import download_chembl as _download_chembl
+from nedrexdb.db.parsers import unichem
+from nedrexdb.downloaders.biogrid import download_biogrid as _download_biogrid, get_latest_biogrid_version
+from nedrexdb.downloaders.chembl import download_chembl as _download_chembl, get_latest_chembl_version
 from nedrexdb.downloaders.ncg import download_ncg as _download_ncg
 from nedrexdb.downloaders.cosmic import download_cosmic as _download_cosmic
 from nedrexdb.downloaders.intogen import download_intogen as _download_intogen
 from nedrexdb.downloaders.orphanet import download_orphanet as _download_orphanet
 from nedrexdb.downloaders.opentargets import download_opentargets as _download_opentargets
+from nedrexdb.exceptions import (
+    ProcessError as _ProcessError,
+)
 
 
 class Version:
@@ -29,8 +46,29 @@ def increment(self, level):
     def __repr__(self):
         return f"{self.major}.{self.minor}.{self.patch}"
 
+def update_version(name, source_url, unique_pattern, mode="date", skip_digits=0):
+    try:
+        response = requests.get(source_url)
+        if response.status_code != 200:
+            raise _ProcessError(f"got non-zero status code while updating metadata.\n source:{name}\n URL: {source_url}")
+        result = _re.findall(unique_pattern, response.text)
+        text = str(result[0])
+        if mode == "date":
+            # create version number from date
+            version = "".join(_re.findall(r"\d+", text))
+            version = version[skip_digits:]
+            version = f"{version[0:4]}-{version[4:6]}-{version[6:]}"
+        else:
+            version = "".join(_re.findall(r"\d+", text))
+            version = version[skip_digits:]
+            version = f"{version[0:2]}.{version[2:]}"
+    except:
+        version = "N/A"
+    date = _datetime.datetime.now().date()
+    print(f"{name}: date: {date}, version: {version}")
+    return {"date": f"{date}", "version": version}
 
-def download_all(force=False):
+def download_all(force=False, ignored_sources=set(), prev_metadata={}, current_metadata={}):
     base = _Path(_config["db.root_directory"])
     download_dir = base / _config["sources.directory"]
 
@@ -40,73 +78,248 @@ def download_all(force=False):
 
     sources = _config["sources"]
     # Remove the source keys (in filter)
-    exclude_keys = {"directory", "username", "password"}
-
-    metadata = {"source_databases": {}}
+    exclude_keys = {"directory", "username", "password", "default_version", "version",
+                    "version_url", "version_pattern", "version_mode", "skip_digits"}
+    exclude_keys.update(ignored_sources)
 
-    _download_opentargets()
-    _download_ncg()
-    #_download_cosmic()
-    _download_intogen()
-    _download_orphanet()
+    print(f"ignore sources for download: {ignored_sources}")
 
-    chembl_date = _datetime.datetime.now().date()
-    chembl_version = _download_chembl()
-    metadata["source_databases"]["chembl"] = {"date": f"{chembl_date}", "version": chembl_version}
-
-    biogrid_date = _datetime.datetime.now().date()
-    biogrid_version = _download_biogrid()
-
-    metadata["source_databases"]["biogrid"] = {"date": f"{biogrid_date}", "version": biogrid_version}
+    # already up-to-date data
+    no_download = [key for key in prev_metadata if key in current_metadata and
+                   prev_metadata[key] == current_metadata[key]]
+    
+    if "opentargets" not in ignored_sources:
+        if "opentargets" not in no_download:
+            _download_opentargets()
+        else:
+            print("opentargets is already up-to-date")
+    if "ncg" not in ignored_sources:
+        if "ncg" not in no_download:
+            _download_ncg()
+        else:
+            print("ncg is already up-to-date")
+    if "intogen" not in ignored_sources:
+        if "intogen" not in no_download:
+            _download_intogen()
+        else:
+            print("intogen is already up-to-date")
+    if "orphanet" not in ignored_sources:
+        if "orphanet" not in no_download:
+            _download_orphanet()
+        else:
+            print("orphanet is already up-to-date")
+    if "chembl" not in ignored_sources:
+        if "chembl" not in no_download:
+            _download_chembl()
+        else:
+            print("chembl is already up-to-date")
+    if "biogrid" not in ignored_sources:
+        if "biogrid" not in no_download:
+            _download_biogrid()
+        else:
+            print("biogrid is already up-to-date")
 
     for source in filter(lambda i: i not in exclude_keys, sources):
-        metadata["source_databases"][source] = {"date": f"{_datetime.datetime.now().date()}", "version": None}
 
-        # Catch case to skip sources with bespoke downloaders.
+        # Catch case to skip sources with bespoke downloaders entirely.
         if source in {
             "biogrid",
-            "drugbank",
             "chembl",
             "ncg",
+            "opentargets",
             "cosmic",
             "intogen",
-            "orphanet",
-            "opentargets",
         }:
             continue
-        (download_dir / source).mkdir(exist_ok=True)
-
-        data = sources[source]
-        username = data.get("username")
-        password = data.get("password")
-
-        for _, download in filter(lambda i: i[0] not in exclude_keys, data.items()):
-            url = download.get("url")
-            filename = download.get("filename")
-            if url is None:
-                continue
-            if filename is None:
-                filename = url.rsplit("/", 1)[1]
-
-            d = Downloader(
-                url=url,
-                target=download_dir / source / filename,
-                username=username,
-                password=password,
-            )
-            d.download()
+
+        # Catch case to skip sources with bespoke downloaders after setting metadata.
+        if source in {
+            "drugbank",
+            "disgenet"
+        }:
+            continue
+
+        # only download if necessary (by checking previous metadata)
+        if source not in no_download:
+            (download_dir / source).mkdir(exist_ok=True)
+
+            data = sources[source]
+            username = data.get("username")
+            password = data.get("password")
+
+            for _, download in filter(lambda i: i[0] not in exclude_keys, data.items()):
+                url = download.get("url")
+                filename = download.get("filename")
+                if url is None:
+                    continue
+                if filename is None:
+                    filename = url.rsplit("/", 1)[1]
+
+                d = Downloader(
+                    url=url,
+                    target=download_dir / source / filename,
+                    username=username,
+                    password=password,
+                )
+                validated = False
+                retries = 3
+                timeout = 30
+                while not validated and retries > 0:
+                    d.download()
+                    validated = validate_download(download_dir / source / filename, source)
+                    if not validated:
+                        logging.error(f"failed to verify download of {filename} for {source}! Retrying in {timeout} seconds.")
+                        retries -= 1
+                        time.sleep(timeout)
+        else:
+            print(f"{source} is already up-to-date")
+
+def validate_download(file, source):
+    if source == "unichem":
+        return unichem.validate_file(file)
+    return True
+
+def update_versions(ignored_sources=set(), default_version=None):
+    sources = _config["sources"]
+    # Remove the source keys (in filter)
+    exclude_keys = {"directory", "username", "password", "default_version", "version",
+                    "version_url", "version_pattern", "version_mode", "skip_digits"}
+    exclude_keys.update(ignored_sources)
+
+    metadata = {"source_databases": {}}
+
+    print(f"ignore sources for versions: {ignored_sources}")
+
+    if "chembl" not in ignored_sources:
+        chembl_date = _datetime.datetime.now().date()
+        chembl_version = get_latest_chembl_version()
+        metadata["source_databases"]["chembl"] = {"date": f"{chembl_date}", "version": chembl_version}
+        # Catch case to skip sources with bespoke version grabbers entirely.
+        exclude_keys.add("chembl")
+
+    if "biogrid" not in ignored_sources:
+        biogrid_date = _datetime.datetime.now().date()
+        biogrid_version = get_latest_biogrid_version()
+        metadata["source_databases"]["biogrid"] = {"date": f"{biogrid_date}", "version": biogrid_version}
+        # Catch case to skip sources with bespoke version grabbers entirely.
+        exclude_keys.add("biogrid")
+
+    for source in filter(lambda i: i not in exclude_keys, sources):
+
+        print(f"checking version of {source}")
+
+        # update metadata
+        meta = sources[source]
+        if "version_url" in meta.keys():
+            version_url = meta["version_url"]
+            version_pattern = rf"{meta['version_pattern']}"
+            skip_digits = meta["skip_digits"] if "skip_digits" in meta.keys() else 0
+            version_mode = meta["version_mode"] if "version_mode" in meta.keys() else "date"
+            metadata["source_databases"][source] = update_version(name=source,
+                                                                  source_url=version_url,
+                                                                  unique_pattern=version_pattern,
+                                                                  mode=version_mode,
+                                                                  skip_digits=skip_digits)
+        else:
+            date = _datetime.datetime.now().date()
+            version = meta["version"] if "version" in meta.keys() else f"{date}"
+            metadata["source_databases"][source] = {"date": f"{date}", "version": version}
+
 
     docs = list(MongoInstance.DB["metadata"].find())
     if len(docs) == 1:
         version = docs[0]["version"]
     elif len(docs) == 0:
-        version = "0.0.0"
+        if default_version is None:
+            default_version = sources["default_version"]
+        version = default_version
     else:
         raise Exception("should only be one document in the metadata collection")
 
+    if os.environ.get("FORCE_VERSION_OVERRIDE", "0") == "1":
+        if "default_version" in sources.keys():
+            version = sources["default_version"]
+
+
     v = Version(version)
     v.increment("patch")
 
     metadata["version"] = f"{v}"
 
     MongoInstance.DB["metadata"].replace_one({}, metadata, upsert=True)
+
+
+    return metadata
+
+    # metadata debugging file. Use to check metadata if DB does not work as intended.
+    #with open("./metadata.txt", "w") as f:
+    #    f.write(f"Last Download: {_datetime.datetime.now().date()}\n\n")
+    #    f.write("Current metadata: \n")
+    #    f.write(f"version:\t{metadata['version']}\n")
+    #    f.write("source_databases:\n")
+    #    for key in metadata["source_databases"].keys():
+    #        f.write(f"V\t{key}:\t{metadata['source_databases'][key]}\n")
+    # can be parsed with this code:
+    #metadata = {"source_databases": {}}
+    #with open("./metadata.txt") as f:
+    #    for line in f:
+    #        if line.startswith("V"):
+    #            sd_split = line.rstrip().split("\t")
+    #            metadata["source_databases"][sd_split[1][:-1]] = ast.literal_eval(sd_split[2])
+    #        elif line.startswith("version"):
+    #            metadata["version"] = line.rstrip().split("\t")[1]
+
+
+def get_versions(no_download):
+    increment = False
+    # no_download is either "true" or path to metadata config -> mconfig
+
+    # so in this case no_download contains the path to the licensed_config
+    if not no_download == "true":
+        licensed_config = no_download
+        nedrexdb.parse_mconfig(licensed_config)
+        mconfig = _mconfig
+
+    else:
+        increment = True
+        mconfig = _config
+
+    version = "live"
+
+    mongo_port = 27017
+    mongo_host = mconfig["db"][version.lower()]["mongo_name"]
+    db_name = mconfig["db"]["mongo_db"]
+
+    try:
+        client = MongoClient(port=mongo_port, host=mongo_host)
+        db = client[db_name]
+
+        metadata = db["metadata"].find_one()
+    except:
+        metadata = None
+    metadata = metadata if metadata is not None else {"version": "0.0.0"}
+    if "source_databases" not in metadata:
+        metadata["source_databases"] = {}
+
+    if increment:
+        v = Version(metadata["version"])
+        v.increment("patch")
+        metadata["version"] = f"{v}"
+
+    for source in metadata["source_databases"].keys():
+        if source not in _config["sources"]:
+            del metadata["source_databases"][source]
+
+
+    max_retries = 5
+    retry_delay = 1  # seconds
+
+    for attempt in range(1, max_retries + 1):
+        try:
+            MongoInstance.DB["metadata"].replace_one({}, metadata, upsert=True)
+            break  # Success, exit the loop
+        except PyMongoError as e:
+            print(f"Attempt {attempt} failed: {e}")
+            if attempt == max_retries:
+                raise  # Re-raise the exception after final attempt
+            time.sleep(retry_delay)
\ No newline at end of file
diff --git a/nedrexdb/downloaders/biogrid.py b/nedrexdb/downloaders/biogrid.py
index 396754a..568568d 100644
--- a/nedrexdb/downloaders/biogrid.py
+++ b/nedrexdb/downloaders/biogrid.py
@@ -18,6 +18,7 @@
 
 
 def get_latest_biogrid_version() -> str:
+    logger.info("Identifying latest BioGRID version")
     url = "https://wiki.thebiogrid.org/doku.php/statistics"
     response = requests.get(url)
     if response.status_code != 200:
@@ -33,12 +34,9 @@ def get_latest_biogrid_version() -> str:
 def download_biogrid():
     version = get_latest_biogrid_version()
 
-    url = (
-        "https://downloads.thebiogrid.org/"
-        "Download/BioGRID/Release-Archive/"
-        f"BIOGRID-{version}/"
-        f"BIOGRID-ORGANISM-{version}.tab3.zip"
-    )
+    url = f"https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-{version}/BIOGRID-ORGANISM-{version}.tab3.zip"
+
+    logger.info(f"Downloading BioGRID v{version} from {url}")
 
     zip_fname = url.rsplit("/", 1)[1]
     target_fname = _config.get("sources.biogrid.human_data.filename")
@@ -52,7 +50,6 @@ def download_biogrid():
         if _os.path.isfile(target_fname):
             _os.remove(target_fname)
 
-        logger.debug("Downloading BioGRID v%s" % version)
         _urlretrieve(url, zip_fname)
         _subprocess.call(
             ["unzip", zip_fname],
diff --git a/nedrexdb/downloaders/chembl.py b/nedrexdb/downloaders/chembl.py
index 447972d..e9591da 100644
--- a/nedrexdb/downloaders/chembl.py
+++ b/nedrexdb/downloaders/chembl.py
@@ -11,27 +11,32 @@
 )
 from nedrexdb.logger import logger
 
+version_cache = None
 
 def get_latest_chembl_version() -> str:
-    # correct source urls to match latest version names
-    url = "https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/"
-    response = requests.get(url)
-    if response.status_code != 200:
-        raise _ProcessError("got non-zero status code while scraping ChEMBL to get latest version")
-    pattern = r'href="chembl_\d+_sqlite\.tar\.gz"'
-    result = _re.findall(pattern, response.text)
-    text = str(result[0])
-    version = text.split("_")[1]
+
+    global version_cache
+    if not version_cache:
+        # correct source urls to match latest version names
+        url = _config["sources.chembl.version_url"]
+        response = requests.get(url)
+        if response.status_code != 200:
+            raise _ProcessError("got non-zero status code while scraping ChEMBL to get latest version")
+        pattern = _config["sources.chembl.version_pattern"]
+        result = _re.findall(pattern, response.text)
+        text = str(result[0])
+        version = text.split("_")[1]
+        version_cache = version
+    else:
+        version = version_cache
     return version
 
 
 def download_chembl():
     version = get_latest_chembl_version()
 
-    url = (
-        "https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/"
-        f"chembl_{version}_sqlite.tar.gz"
-    )
+    url = _config["sources.chembl.sqlite.url"].format(version)
+    logger.info(f"Downloading ChEMBL v{version} from {url}")
 
     zip_fname = url.rsplit("/", 1)[1]
     chembl_dir = _Path(_config.get("db.root_directory")) / _config.get("sources.directory") / "chembl"
@@ -41,7 +46,6 @@ def download_chembl():
     chembl_dir.mkdir(exist_ok=True, parents=True)
 
     with _cd(chembl_dir):
-        logger.debug("Downloading ChEMBL v%s" % version)
         _urlretrieve(url, zip_fname)
         _urlretrieve(unichem_url, unichem_name)
     return version
\ No newline at end of file
diff --git a/nedrexdb/downloaders/ncg.py b/nedrexdb/downloaders/ncg.py
index 4f7257b..1366829 100644
--- a/nedrexdb/downloaders/ncg.py
+++ b/nedrexdb/downloaders/ncg.py
@@ -24,7 +24,7 @@ def download_ncg():
         if _os.path.isfile(target_fname):
             _os.remove(target_fname)
 
-        logger.debug("Downloading NCG")
+        logger.info("Downloading NCG")
         try:
             # Send the request and save response directly to a file
             response = requests.post(url, data=data)
diff --git a/nedrexdb/downloaders/opentargets.py b/nedrexdb/downloaders/opentargets.py
index 3074844..b402694 100644
--- a/nedrexdb/downloaders/opentargets.py
+++ b/nedrexdb/downloaders/opentargets.py
@@ -22,7 +22,7 @@ def getData(target_dir, url):
             "--no-parent",
             "--no-host-directories",
             "--cut-dirs",
-            "8",
+            "6",
             "-P",
             f"{target_dir.resolve()}/",
             url,
diff --git a/nedrexdb/downloaders/orphanet.py b/nedrexdb/downloaders/orphanet.py
index 5df7eec..801249d 100644
--- a/nedrexdb/downloaders/orphanet.py
+++ b/nedrexdb/downloaders/orphanet.py
@@ -34,15 +34,14 @@ def download_orphanet():
         username=None,
         password=None,
     )
-    print("Downloader step passed", zip_fname)
+
     try:
         d.download()
     except _HTTPError as E:
         logger.warning(f"Unable to download Orphanet mapping: {E}")
         return
     files = list(target_dir.iterdir())
-    print(files)
-    print("download step passed")
+
     # Unzip the zip
     with change_directory(target_dir):
         _sp.call(["unzip", f"{zip_fname.resolve()}"])
diff --git a/nedrexdb/llm.py b/nedrexdb/llm.py
new file mode 100644
index 0000000..558b5c4
--- /dev/null
+++ b/nedrexdb/llm.py
@@ -0,0 +1,7 @@
+from nedrexdb import config as _config
+
+_LLM_BASE=_config["embeddings.server_base"]
+_LLM_model=_config[f"embeddings.model"]
+_LLM_path=_config[f"embeddings.path"]
+
+_LLM_API_KEY=_config[f"embeddings"].get("api_key", "no-key")
diff --git a/nedrexdb/post_integration/neo4j_db_adjustments.py b/nedrexdb/post_integration/neo4j_db_adjustments.py
new file mode 100644
index 0000000..e63b68a
--- /dev/null
+++ b/nedrexdb/post_integration/neo4j_db_adjustments.py
@@ -0,0 +1,480 @@
+from langchain_neo4j import Neo4jGraph
+from nedrexdb import config as _config
+import time
+
+NODE_EMBEDDING_CONFIG = {
+    "Disorder": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "synonyms": {"prefix": "Synonyms: ", "suffix": "", "type": "list"},
+        "description": {"prefix": "Description: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+    },
+    "Gene": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "approvedSymbol": {"prefix": "Approved Symbol: ", "suffix": "", "type": "string"},
+        "description": {"prefix": "Description: ", "suffix": "", "type": "string"},
+        "geneType": {"prefix": "GeneType: ", "suffix": "", "type": "string"},
+        "synonyms": {"prefix": "Synonyms: ", "suffix": "", "type": "list"},
+        "symbols": {"prefix": "Alternative Symbols: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+    },
+    "Drug": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+        "casNumber": {"prefix": "This exact CAS number: ", "suffix": "", "type": "string"},
+    },
+    "Protein": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "geneName": {"prefix": "Gene name: ", "suffix": "", "type": "string"},
+        "synonyms": {"prefix": "Synonyms: ", "suffix": "", "type": "list"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+        "reviewed": {"prefix": "Review status: ", "suffix": "", "type": "boolean"},
+        "comments": {"prefix": "the following comments: ", "suffix": "", "type": "string"},
+    },
+    "GO": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "synonyms": {"prefix": "Synonyms: ", "suffix": "", "type": "list"},
+        "description": {"prefix": "Description: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+    },
+    # "GenomicVariant": {
+    #     "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+    #     "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+    #     "referenceSequence": {"prefix": "Reference Sequence: ", "suffix": "", "type": "string"},
+    #     "alternativeSequence": {"prefix": "Alternative Sequence: ", "suffix": "", "type": "string"},
+    #     "chromosome": {"prefix": "Chromosome: ", "suffix": "", "type": "string"},
+    #     "position": {"prefix": "Position: ", "suffix": "", "type": "string"},
+    #     "variantType": {"prefix": "Variant Type: ", "suffix": "", "type": "string"},
+    # },
+    "Pathway": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+        # "species": {"prefix": "Species: ", "suffix": "", "type": "string"},
+        # "taxid": {"prefix": "taxid: ", "suffix": "", "type": "string"},
+    },
+    "Phenotype": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "synonyms": {"prefix": "Synonyms: ", "suffix": "", "type": "list"},
+        "description": {"prefix": "Description: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+    },
+    "SideEffect": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+    },
+    "Signature": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+        # "database": {"prefix": "Database: ", "suffix": "", "type": "string"},
+    },
+    "Tissue": {
+        "displayName": {"prefix": "DisplayName: ", "suffix": "", "type": "string"},
+        "domainIds": {"prefix": "Other used IDs: ", "suffix": "", "type": "list"},
+        # "dataSources": {"prefix": "Data Sources: ", "suffix": "", "type": "list"},
+    }
+}
+
+EDGE_EMBEDDING_CONFIG = {
+    "GeneAssociatedWithDisorder": {
+        "source": "Gene",
+        "link_term": "is associated with",
+        "target": "Disorder",
+        "attributes": {
+            "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        }
+    },
+    "DrugHasIndication": {
+        "source": "Drug",
+        "link_term": "has an indication for",
+        "target": "Disorder",
+        "attributes": {
+            "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        }
+    },
+    "DrugHasTarget": {
+        "source": "Drug",
+        "link_term": "has the known target",
+        "target": "Protein",
+        "attributes": {
+            "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        }
+    },
+    "DisorderHasPhenotype": {
+        "source": "Disorder",
+        "link_term": "exhibits the known phenotype",
+        "target": "Phenotype",
+        # "attributes": {
+        #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        # }
+    },
+    "DisorderIsSubtypeOfDisorder": {
+        "source": "Disorder",
+        "link_term": "is subtype of",
+        "target": "Disorder",
+        # "attributes": {
+        #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        # }
+    },
+    "DrugHasContraindication": {
+        "source": "Drug",
+        "link_term": "is contraindicated in",
+        "target": "Disorder",
+        # "attributes": {
+        #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        # }
+    },
+    "DrugHasSideEffect": {
+        "source": "Drug",
+        "link_term": "has the known side effect",
+        "target": "SideEffect",
+        # "attributes": {
+        #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"},
+        #     "maximum_frequency": {"prefix": "Maximum Frequency: ", "suffix": "", "type": "string"},
+        #     "minimum_frequency": {"prefix": "Minimum Frequency: ", "suffix": "", "type": "string"}
+        # }
+    },
+    # "GOIsSubtypeOfGO": {
+    #     "source": "GO",
+    #     "link_term": "is subtype of",
+    #     "target": "GO",
+    #     "attributes": {
+    #         "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+    #     }
+    # },
+    "GeneExpressedInTissue": {
+        "source": "Gene",
+        "link_term": "is expressed in",
+        "target": "Tissue",
+        # "attributes": {
+        #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"},
+        # "TPM": {"prefix": "TPM: ", "suffix": "", "type": "string"},
+        # "nTPM": {"prefix": "nTPM: ", "suffix": "", "type": "string"},
+        # "pTPM": {"prefix": "pTPM: ", "suffix": "", "type": "string"},
+        # }
+    },
+    "ProteinEncodedByGene": {
+        "source": "Protein",
+        "link_term": "is encoded by",
+        "target": "Gene",
+        "attributes": {
+            "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        }
+    },
+    # "ProteinExpressedInTissue": {
+    #     "source": "Protein",
+    #     "link_term": "is expressed by",
+    #     "target": "Tissue",
+    # "attributes": {
+    #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"},
+    # "level": {"prefix": "Expression level: ", "suffix": "", "type": "string"},
+    # }
+    # },
+    "ProteinHasGoAnnotation": {
+        "source": "Protein",
+        "link_term": "has GO annotation",
+        "target": "GO",
+        # "attributes": {
+        #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"},
+        #     "qualifiers": {"prefix": "Qualifiers: ", "suffix": "", "type": "list"},
+        # }
+    },
+    # "ProteinHasSignature": {
+    #     "source": "Protein",
+    #     "link_term": "has signature",
+    #     "target": "Signature",
+    #     "attributes": {
+    #         "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+    #     }
+    # },
+    # "ProteinInPathway": {
+    #     "source": "Protein",
+    #     "link_term": "is in the pathway",
+    #     "target": "Pathway",
+    # "attributes": {
+    #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+    # }
+    # },
+    # "ProteinInteractsWithProtein": {
+    #     "source": "Protein",
+    #     "link_term": "interacts with",
+    #     "target": "Protein",
+    # "attributes": {
+    #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"},
+    #     "evidenceTypes": {"prefix": "Evidence Type: ", "suffix": "", "type": "list"},
+    #     "methods": {"prefix": "Method/Approach: ", "suffix": "", "type": "list"},
+    #     "subcellularLocations": {"prefix": "Subcellular Locations: ", "suffix": "", "type": "list"},
+    #     "tissues": {"prefix": "Tissues: ", "suffix": "", "type": "list"},
+    # }
+    # },
+    "SideEffectSameAsPhenotype": {
+        "source": "SideEffect",
+        "link_term": "is the same as",
+        "target": "Phenotype",
+        # "attributes": {
+        #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+        # }
+    },
+    # "VariantAffectsGene": {
+    #     "source": "GenomicVariant",
+    #     "link_term": "effects",
+    #     "target": "Gene",
+    # "attributes": {
+    #     "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"}
+    # }
+    # },
+    "VariantAssociatedWithDisorder": {
+        "source": "GenomicVariant",
+        "link_term": "is associated with",
+        "target": "Disorder",
+        # "attributes": {
+        #     # "dataSources": {"prefix": "Data Source: ", "suffix": "", "type": "list"},
+        #     "effects": {"prefix": "Effects: ", "suffix": "", "type": "list"},
+        #     # "accession": {"prefix": "Accession: ", "suffix": "", "type": "string"},
+        #     "reviewStatus": {"prefix": "Review Status: ", "suffix": "", "type": "string"}
+        # }
+    },
+}
+
+# only building embeddings for dev nodes and edges, except they are None.
+# dev_nodes = ["Disorder", "Gene"]
+# dev_edges = []
+dev_nodes = None
+dev_edges = None
+
+
+def get_kg_connection() -> Neo4jGraph:
+    NEO4J_URI = f'bolt://{_config["db.dev.neo4j_name"]}:7687'
+
+    retry = 10
+    # kg = None
+    while retry > 0:
+        try:
+            kg = Neo4jGraph(
+                url=NEO4J_URI, username="", password="", database='neo4j'
+            )
+            return kg
+        except Exception:
+            retry -= 1
+            if retry == 0:
+                print("Could not connect to Neo4j database at " + NEO4J_URI)
+                return None
+            time.sleep(10)
+
+
+def create_unique_node_constraint(con, node_type, attribute):
+    query = f"CREATE CONSTRAINT {node_type.lower()}_{attribute.lower()}_unique FOR (n:{node_type}) REQUIRE n.{attribute} IS UNIQUE"
+    con.query(query)
+
+def create_constraints():
+    kg = get_kg_connection()
+    node_list = NODE_EMBEDDING_CONFIG.keys() if not dev_nodes else dev_nodes
+    for node in node_list:
+        create_unique_node_constraint(kg, node, "primaryDomainId")
+
+
+def create_vector_indices():
+    print("Starting indexing")
+
+    kg = get_kg_connection()
+
+    index_names = []
+
+    node_list = NODE_EMBEDDING_CONFIG.keys() if not dev_nodes else dev_nodes
+
+    # Only building embeddings for specified nodes
+    retry_list = []
+    num_retries = 5
+    while num_retries > 0:
+        for node in node_list:
+            if not fill_vector_index(kg, "NODE", node):
+                retry_list.append(node)
+            else:
+                index_names.append(f"{node.lower()}Embeddings")
+        node_list = [node for node in retry_list]
+        retry_list = []
+        num_retries -= 1
+
+    if len(node_list) > 0:
+        print(f"Could not create embeddings successfully for the following nodes: {node_list}")
+
+    edge_list = EDGE_EMBEDDING_CONFIG.keys() if not dev_edges else dev_edges
+    retry_list = []
+    num_retries = 5
+    while num_retries > 0:
+        for edge in edge_list:
+            if not fill_vector_index(kg, "RELATIONSHIP", edge):
+                retry_list.append(edge)
+            else:
+                index_names.append(f"{edge.lower()}Embeddings")
+        edge_list = [edge for edge in retry_list]
+        retry_list = []
+        num_retries -= 1
+
+    if len(edge_list) > 0:
+        print(f"Could not create embeddings successfully for the following edges: {edge_list}")
+
+    if wait_for_database_ready(kg, index_names):
+        print("Ready to switch to read-only mode")
+    else:
+        print("Something went wrong with the index build")
+
+
+def get_node_info_string(node_name):
+    info_string = """coalesce(x.type, '') +  ' with ID ' + x.primaryDomainId +':'"""
+    for attribute, format in NODE_EMBEDDING_CONFIG[node_name].items():
+        prefix = f" {format.get('prefix', ' ')} "
+        suffix = f" {format.get('suffix', ' ')} "
+        attribute_type = format.get('type', 'string')
+
+        info_string += f"+ '{prefix}'"
+        if attribute_type == "list":
+            info_string += f"+ coalesce( apoc.text.join(x.{attribute},', '), '')"
+        else:
+            info_string += f"+ coalesce(x.{attribute}, '')"
+        info_string += f"+ '{suffix};'"
+    return info_string
+
+
+def get_edge_info_string(edge_name):
+    link_term = EDGE_EMBEDDING_CONFIG[edge_name]["link_term"]
+    info_string = f"coalesce(entry.s.type, '') +' '+ coalesce(entry.s.displayName, '') +' with ID ' + entry.s.primaryDomainId + ' {link_term} ' + coalesce(entry.t.type, '') +' '+coalesce(entry.t.displayName, '')+'  with ID '+ entry.t.primaryDomainId +' and has properties:'"
+    if "attributes" in EDGE_EMBEDDING_CONFIG[edge_name].keys():
+        for attribute, format in EDGE_EMBEDDING_CONFIG[edge_name]["attributes"].items():
+            prefix = format.get('prefix', ' ')
+            suffix = format.get('suffix', ' ')
+            attribute_type = format.get('type', 'string')
+
+            info_string += f"+'{prefix}'"
+            if attribute_type == "list":
+                info_string += f"+ coalesce( apoc.text.join(entry.r.{attribute},', '), '')"
+            else:
+                info_string += f"+ coalesce(d.{attribute}, '')"
+            info_string += f"+ '{suffix};'"
+    return info_string
+
+
+def fill_vector_index(con, entityType, name) -> bool:
+    try:
+        start = time.time()
+        create_vector_index(con, entityType, name)
+        from nedrexdb.llm import (_LLM_API_KEY, _LLM_BASE, _LLM_path, _LLM_model)
+        params = {"api_key": _LLM_API_KEY, "llm_base": _LLM_BASE, "llm_path": _LLM_path, "llm_model": _LLM_model}
+        if entityType == "NODE":
+            info_string = get_node_info_string(name)
+            query = create_node_vector_query(info_string, name)
+            con.query(query, params=params)
+        else:
+            info_string = get_edge_info_string(name)
+            source_name = EDGE_EMBEDDING_CONFIG[name]["source"]
+            target_name = EDGE_EMBEDDING_CONFIG[name]["target"]
+            query = create_edge_vector_query(info_string, source_name, name, target_name)
+            con.query(query, params=params)
+        duration = time.time() - start
+        print(f"Building {name} embedding indexes finished after {duration} seconds")
+        return True
+    except Exception as e:
+        print(e)
+        print("Could not create vector index for " + name)
+        return False
+
+
+def create_node_vector_query(node_info_string, name):
+    query = """
+      MATCH (n: """ + name + """)
+WITH collect(n) as allNodes
+UNWIND range(0, size(allNodes)-1, 500) as i
+WITH i, allNodes[i..i+500] as batchNodes
+WHERE size(batchNodes) > 0
+CALL apoc.ml.openai.embedding(
+    [x in batchNodes | """ + node_info_string + """], 
+    $api_key, 
+    {
+        endpoint: $llm_base,
+        path: $llm_path,
+        model: $llm_model,
+        enableBackOffRetries: true,
+        backOffRetries: 20,
+        exponentialBackoff: true
+    }
+) YIELD index, embedding
+WITH batchNodes[index] as n, embedding CALL db.create.setNodeVectorProperty(n, "embedding", embedding);"""
+    return query
+
+
+def create_edge_vector_query(edge_info_string, source_name, name, target_name):
+    query = """MATCH (s: """ + source_name + """)-[r: """ + name + """]-(t: """ + target_name + """)
+    WITH collect({s:s,r:r,t:t}) as allEntries
+    UNWIND range(0, size(allEntries)-1, 500) as i
+    WITH i, allEntries[i..i+500] as batchEntries
+    WHERE size(batchEntries) > 0
+    CALL apoc.ml.openai.embedding(
+        [entry in batchEntries | """ + edge_info_string + """
+        ], 
+        "$api_key", 
+        {
+            endpoint: $llm_base,
+            path: $llm_path,
+            model: $llm_model,
+            enableBackOffRetries: true,
+            backOffRetries: 20,
+            exponentialBackoff: true
+        }
+    ) YIELD index, embedding
+    WITH batchEntries[index] as entry, embedding CALL db.create.setRelationshipVectorProperty(entry.r, "embedding", embedding);"""
+    return query
+
+
+def create_vector_index(con, entityType, name):
+    props = {"index_name": f"{name.lower()}Embeddings"}
+    if entityType == "NODE":
+        con.query("""CREATE VECTOR INDEX $index_name IF NOT EXISTS
+        FOR (d: """ + name + """) ON (d.embedding) 
+        OPTIONS { indexConfig: {
+          `vector.dimensions`: 1024,
+          `vector.similarity_function`: 'cosine'
+        }}""", params=props)
+    else:
+        con.query("""CREATE VECTOR INDEX $index_name IF NOT EXISTS
+               FOR ()-[r:""" + name + """]-() ON (r.embedding) 
+               OPTIONS { indexConfig: {
+                 `vector.dimensions`: 1024,
+                 `vector.similarity_function`: 'cosine'
+               }}""", params=props)
+
+
+def wait_for_database_ready(con, index_names=['bad_default']):
+    for index_name in index_names:
+        try:
+            result = list(con.query("""
+                SHOW INDEXES
+                YIELD name, state, type, labelsOrTypes, properties
+                WHERE name = $name
+                RETURN *
+            """, {"name": index_name}))
+
+            if result:
+                index = result[0]
+                print(f"\nIndex details:")
+                print(f"- Name: {index['name']}")
+                print(f"- State: {index['state']}")
+                print(f"- Type: {index['type']}")
+                print(f"- Labels: {index['labelsOrTypes']}")
+                print(f"- Properties: {index['properties']}")
+
+                return index['state'] == 'ONLINE'
+            else:
+                print(f"\nNo index found with name {index_name}")
+                return False
+
+        except Exception as e:
+            print(f"\nError checking index: {str(e)}")
+            return False
diff --git a/neo4j/Dockerfile b/neo4j/Dockerfile
new file mode 100644
index 0000000..a4d72be
--- /dev/null
+++ b/neo4j/Dockerfile
@@ -0,0 +1,65 @@
+FROM neo4j:2025.06.2
+
+# Return to the original working directory
+RUN mkdir /app
+WORKDIR /app
+
+ENV APOC_VERSION=2025.06.0
+ENV NEO4J_USERNAME=neo4j
+ENV NEO4J_PASSWORD=password
+ENV NEO4J_AUTH=$NEO4J_USERNAME/$NEO4J_PASSWORD
+ENV NEO4J_ACCEPT_LICENSE_AGREEMENT=yes
+
+RUN apt-get update && apt-get install -y --fix-missing \
+    build-essential \
+    libffi-dev \
+    libgdbm-dev \
+    libc6-dev \
+    libssl-dev \
+    zlib1g-dev \
+    libbz2-dev \
+    libreadline-dev \
+    libsqlite3-dev \
+    wget \
+    curl \
+    llvm \
+    libncurses5-dev \
+    libncursesw5-dev \
+    xz-utils \
+    tk-dev \
+    libxml2-dev \
+    libxmlsec1-dev \
+    liblzma-dev \
+    unzip
+
+# Installiere APOC Plugin
+RUN wget -O /var/lib/neo4j/plugins/apoc-${APOC_VERSION}-core.jar https://github.com/neo4j/apoc/releases/download/${APOC_VERSION}/apoc-${APOC_VERSION}-core.jar
+RUN wget -O /var/lib/neo4j/plugins/apoc-${APOC_VERSION}-extended.jar https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/${APOC_VERSION}/apoc-${APOC_VERSION}-extended.jar
+
+ENV NEO4JLABS_PLUGINS='["apoc"]'
+ENV NEO4J_dbms_security_procedures_unrestricted=apoc.* \
+    NEO4J_dbms_security_procedures_allowlist=apoc.*
+
+
+# Copy any scripts if necessary
+COPY modify_neo4j_conf.sh /app/scripts/
+# Make scripts executable
+RUN chmod +x /app/scripts/*
+
+# Instanciate the Neo4j database
+RUN neo4j-admin dbms set-initial-password $NEO4J_PASSWORD
+
+# Run the modify_neo4j_conf script
+RUN /app/scripts/modify_neo4j_conf.sh
+RUN echo "configuration of neo4j ready"
+
+WORKDIR /var/lib/neo4j
+RUN mv products/neo4j-genai-* plugins/
+
+# # Expose the ports Neo4j and Jupyter Lab uses
+EXPOSE 7687
+EXPOSE 7474
+
+#ENTRYPOINT ["/startup/docker-entrypoint.sh"]
+
+#CMD ["neo4j-admin"]
\ No newline at end of file
diff --git a/neo4j/modify_neo4j_conf.sh b/neo4j/modify_neo4j_conf.sh
new file mode 100644
index 0000000..994d1fd
--- /dev/null
+++ b/neo4j/modify_neo4j_conf.sh
@@ -0,0 +1,102 @@
+#!/bin/bash
+
+# The path to your neo4j.conf file
+NEO4J_CONF="/var/lib/neo4j/conf/neo4j.conf"
+
+# The desired number of allowed failed authentication attempts
+MAX_FAILED_ATTEMPTS=100
+
+if grep -q "^#*dbms.security.auth_enabled=" "$NEO4J_CONF"; then
+    sed -i "s/^#*dbms.security.auth_enabled=.*/dbms.security.auth_enabled=false/g" "$NEO4J_CONF"
+else
+    echo "dbms.security.auth_enabled=false" >> "$NEO4J_CONF"
+fi
+
+# Uncomment the dbms.security.auth_max_failed_attempts line and set its value
+if grep -q "^#*dbms.security.auth_max_failed_attempts=" "$NEO4J_CONF"; then
+    sed -i "s/^#*dbms.security.auth_max_failed_attempts=.*/dbms.security.auth_max_failed_attempts=$MAX_FAILED_ATTEMPTS/g" "$NEO4J_CONF"
+else
+    echo "dbms.security.auth_max_failed_attempts=$MAX_FAILED_ATTEMPTS" >> "$NEO4J_CONF"
+fi
+
+# Enable Bolt connector
+if grep -q "^#*dbms.connector.bolt.enabled=" "$NEO4J_CONF"; then
+    sed -i "s/^#*dbms.connector.bolt.enabled=.*/dbms.connector.bolt.enabled=true/g" "$NEO4J_CONF"
+else
+    echo "dbms.connector.bolt.enabled=true" >> "$NEO4J_CONF"
+fi
+echo "Bolt connector enabled in neo4j.conf."
+
+# Enable HTTP connector
+if grep -q "^#*dbms.connector.http.enabled=" "$NEO4J_CONF"; then
+    sed -i "s/^#*dbms.connector.http.enabled=.*/dbms.connector.http.enabled=true/g" "$NEO4J_CONF"
+else
+    echo "dbms.connector.http.enabled=true" >> "$NEO4J_CONF"
+fi
+echo "HTTP connector enabled in neo4j.conf."
+
+# Unrestrict APOC procedures
+if grep -q "dbms.security.procedures.unrestricted=apoc.*,genai.*,vectorize.*" "$NEO4J_CONF"; then
+    echo "APOC procedures already unrestricted in neo4j.conf."
+else
+    echo 'dbms.security.procedures.unrestricted=apoc.*,genai.*,vectorize.*' >> "$NEO4J_CONF"
+    echo "Updated neo4j.conf to allow unrestricted APOC procedures."
+fi
+
+# Set Bolt connector listen address
+if grep -q "^#*dbms.connector.bolt.listen_address=" "$NEO4J_CONF"; then
+    sed -i 's/^#*dbms.connector.bolt.listen_address=.*/dbms.connector.bolt.listen_address=0.0.0.0:7687/g' "$NEO4J_CONF"
+else
+    echo "dbms.connector.bolt.listen_address=0.0.0.0:7687" >> "$NEO4J_CONF"
+fi
+echo "Bolt connector listen address set to 0.0.0.0:7687."
+
+# Set HTTP connector listen address
+if grep -q "^#*dbms.connector.http.listen_address=" "$NEO4J_CONF"; then
+    sed -i 's/^#*dbms.connector.http.listen_address=.*/dbms.connector.http.listen_address=0.0.0.0:7474/g' "$NEO4J_CONF"
+else
+    echo "dbms.connector.http.listen_address=0.0.0.0:7474" >> "$NEO4J_CONF"
+fi
+echo "HTTP connector listen address set to 0.0.0.0:7474."
+
+# Set Bolt connector TLS level to DISABLED
+if grep -q "^#*dbms.connector.bolt.tls_level=" "$NEO4J_CONF"; then
+    sed -i "s/^#*dbms.connector.bolt.tls_level=.*/dbms.connector.bolt.tls_level=DISABLED/g" "$NEO4J_CONF"
+else
+    echo "dbms.connector.bolt.tls_level=DISABLED" >> "$NEO4J_CONF"
+fi
+echo "Bolt connector TLS level set to DISABLED."
+
+
+# Enable Bolt over WebSocket
+#if grep -q "^#*dbms.connector.bolt.ws.enabled=" "$NEO4J_CONF"; then
+#    sed -i "s/^#*dbms.connector.bolt.ws.enabled=.*/dbms.connector.bolt.ws.enabled=true/g" "$NEO4J_CONF"
+#else
+#    echo "dbms.connector.bolt.ws.enabled=true" >> "$NEO4J_CONF"
+#fi
+#echo "Bolt over WebSocket enabled."
+
+# Set Bolt over WebSocket listen address
+#if grep -q "^#*dbms.connector.bolt.ws.listen_address=" "$NEO4J_CONF"; then
+#    sed -i "s/^#*dbms.connector.bolt.ws.listen_address=.*/dbms.connector.bolt.ws.listen_address=0.0.0.0:7687/g" "$NEO4J_CONF"
+#else
+#    echo "dbms.connector.bolt.ws.listen_address=0.0.0.0:7687" >> "$NEO4J_CONF"
+#fi
+#echo "Bolt over WebSocket listen address set to 0.0.0.0:7687."
+
+
+# Remove deprecated settings
+#sed -i 's/^#*dbms.default_listen_address=.*/# Deprecated setting removed/g'  "$NEO4J_CONF"
+
+# Add new settings for default listen address
+if ! grep -q "^server.default_listen_address="  "$NEO4J_CONF"; then
+    echo "server.default_listen_address=0.0.0.0" >> "$NEO4J_CONF"
+    echo "Added new default listen address configuration."
+fi
+
+# Add new settings for Bolt listen address
+if ! grep -q "^server.bolt.listen_address="  "$NEO4J_CONF"; then
+    echo "server.bolt.listen_address=0.0.0.0:7687" >> "$NEO4J_CONF"
+    echo "Added new Bolt listen address configuration."
+fi
+
diff --git a/poetry.lock b/poetry.lock
index 05b25c4..25da01e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,183 @@
 # This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
+[[package]]
+name = "aiohappyeyeballs"
+version = "2.6.1"
+description = "Happy Eyeballs for asyncio"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "aiohappyeyeballs-2.6.1-py3-none-any.whl", hash = "sha256:f349ba8f4b75cb25c99c5c2d84e997e485204d2902a9597802b0371f09331fb8"},
+    {file = "aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c3f9d0113123803ccadfdf3f0faa505bc78e6a72d1cc4806cbd719826e943558"},
+]
+
+[[package]]
+name = "aiohttp"
+version = "3.12.14"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.9"
+files = [
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+[package.dependencies]
+pycparser = "*"
+
 [[package]]
 name = "cfgv"
 version = "3.4.0"
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 ]
 
 [[package]]
 name = "click"
-version = "8.1.7"
+version = "8.1.8"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
-    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+    {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
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 ]
 
 [package.dependencies]
@@ -281,53 +546,103 @@ files = [
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 ]
 
+[[package]]
+name = "dataclasses-json"
+version = "0.6.7"
+description = "Easily serialize dataclasses to and from JSON."
+optional = false
+python-versions = "<4.0,>=3.7"
+files = [
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+]
+
+[package.dependencies]
+marshmallow = ">=3.18.0,<4.0.0"
+typing-inspect = ">=0.4.0,<1"
+
 [[package]]
 name = "distlib"
-version = "0.3.8"
+version = "0.3.9"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
 files = [
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+    {file = "distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87"},
+    {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"},
 ]
 
+[[package]]
+name = "dnspython"
+version = "2.7.0"
+description = "DNS toolkit"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "dnspython-2.7.0-py3-none-any.whl", hash = "sha256:b4c34b7d10b51bcc3a5071e7b8dee77939f1e878477eeecc965e9835f63c6c86"},
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+]
+
+[package.extras]
+dev = ["black (>=23.1.0)", "coverage (>=7.0)", "flake8 (>=7)", "hypercorn (>=0.16.0)", "mypy (>=1.8)", "pylint (>=3)", "pytest (>=7.4)", "pytest-cov (>=4.1.0)", "quart-trio (>=0.11.0)", "sphinx (>=7.2.0)", "sphinx-rtd-theme (>=2.0.0)", "twine (>=4.0.0)", "wheel (>=0.42.0)"]
+dnssec = ["cryptography (>=43)"]
+doh = ["h2 (>=4.1.0)", "httpcore (>=1.0.0)", "httpx (>=0.26.0)"]
+doq = ["aioquic (>=1.0.0)"]
+idna = ["idna (>=3.7)"]
+trio = ["trio (>=0.23)"]
+wmi = ["wmi (>=1.5.1)"]
+
 [[package]]
 name = "docker"
-version = "6.1.3"
+version = "7.1.0"
 description = "A Python library for the Docker Engine API."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "docker-6.1.3.tar.gz", hash = "sha256:aa6d17830045ba5ef0168d5eaa34d37beeb113948c413affe1d5991fc11f9a20"},
+    {file = "docker-7.1.0-py3-none-any.whl", hash = "sha256:c96b93b7f0a746f9e77d325bcfb87422a3d8bd4f03136ae8a85b37f1898d5fc0"},
+    {file = "docker-7.1.0.tar.gz", hash = "sha256:ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c"},
 ]
 
 [package.dependencies]
-packaging = ">=14.0"
 pywin32 = {version = ">=304", markers = "sys_platform == \"win32\""}
 requests = ">=2.26.0"
 urllib3 = ">=1.26.0"
-websocket-client = ">=0.32.0"
 
 [package.extras]
+dev = ["coverage (==7.2.7)", "pytest (==7.4.2)", "pytest-cov (==4.1.0)", "pytest-timeout (==2.1.0)", "ruff (==0.1.8)"]
+docs = ["myst-parser (==0.18.0)", "sphinx (==5.1.1)"]
 ssh = ["paramiko (>=2.4.3)"]
+websockets = ["websocket-client (>=1.3.0)"]
+
+[[package]]
+name = "exceptiongroup"
+version = "1.2.2"
+description = "Backport of PEP 654 (exception groups)"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.extras]
+test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.13.4"
+version = "3.18.0"
 description = "A platform independent file lock."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "filelock-3.18.0-py3-none-any.whl", hash = "sha256:c401f4f8377c4464e6db25fff06205fd89bdd83b65eb0488ed1b160f780e21de"},
+    {file = "filelock-3.18.0.tar.gz", hash = "sha256:adbc88eabb99d2fec8c9c1b229b171f18afa655400173ddc653d5d01501fb9f2"},
 ]
 
 [package.extras]
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-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
-typing = ["typing-extensions (>=4.8)"]
+docs = ["furo (>=2024.8.6)", "sphinx (>=8.1.3)", "sphinx-autodoc-typehints (>=3)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.6.10)", "diff-cover (>=9.2.1)", "pytest (>=8.3.4)", "pytest-asyncio (>=0.25.2)", "pytest-cov (>=6)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.28.1)"]
+typing = ["typing-extensions (>=4.12.2)"]
 
 [[package]]
 name = "flake8"
@@ -345,86 +660,263 @@ mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.8.0,<2.9.0"
 pyflakes = ">=2.4.0,<2.5.0"
 
+[[package]]
+name = "frozenlist"
+version = "1.6.0"
+description = "A list-like structure which implements collections.abc.MutableSequence"
+optional = false
+python-versions = ">=3.9"
+files = [
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 test = ["objgraph", "psutil"]
 
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+
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+
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+optional = false
+python-versions = ">=3.8"
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-python-versions = ">=3.8"
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@@ -432,15 +924,18 @@ license = ["ukkonen"]
 
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 name = "idna"
-version = "3.7"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
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+
 [[package]]
 name = "isodate"
 version = "0.6.1"
@@ -455,15 +950,212 @@ files = [
 [package.dependencies]
 six = "*"
 
+[[package]]
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+version = "1.33"
+description = "Apply JSON-Patches (RFC 6902)"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
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+
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+optional = false
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+[package.extras]
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+fireworks = ["langchain-fireworks"]
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+xai = ["langchain-xai"]
+
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 python-versions = ">=3.5"
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 ]
 
 [package.dependencies]
@@ -471,7 +1163,7 @@ colorama = {version = ">=0.3.4", markers = "sys_platform == \"win32\""}
 win32-setctime = {version = ">=1.0.0", markers = "sys_platform == \"win32\""}
 
 [package.extras]
-dev = ["Sphinx (>=2.2.1)", "black (>=19.10b0)", "codecov (>=2.0.15)", "colorama (>=0.3.4)", "flake8 (>=3.7.7)", "isort (>=5.1.1)", "pytest (>=4.6.2)", "pytest-cov (>=2.7.1)", "sphinx-autobuild (>=0.7.1)", "sphinx-rtd-theme (>=0.4.3)", "tox (>=3.9.0)", "tox-travis (>=0.12)"]
+dev = ["Sphinx (>=4.1.1)", "black (>=19.10b0)", "colorama (>=0.3.4)", "docutils (==0.16)", "flake8 (>=3.7.7)", "isort (>=5.1.1)", "pytest (>=4.6.2)", "pytest-cov (>=2.7.1)", "sphinx-autobuild (>=0.7.1)", "sphinx-rtd-theme (>=0.4.3)", "tox (>=3.9.0)"]
 
 [[package]]
 name = "lxml"
@@ -581,6 +1273,25 @@ html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
 source = ["Cython (==0.29.37)"]
 
+[[package]]
+name = "marshmallow"
+version = "3.26.1"
+description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "marshmallow-3.26.1-py3-none-any.whl", hash = "sha256:3350409f20a70a7e4e11a27661187b77cdcaeb20abca41c1454fe33636bea09c"},
+    {file = "marshmallow-3.26.1.tar.gz", hash = "sha256:e6d8affb6cb61d39d26402096dc0aee12d5a26d490a121f118d2e81dc0719dc6"},
+]
+
+[package.dependencies]
+packaging = ">=17.0"
+
+[package.extras]
+dev = ["marshmallow[tests]", "pre-commit (>=3.5,<5.0)", "tox"]
+docs = ["autodocsumm (==0.2.14)", "furo (==2024.8.6)", "sphinx (==8.1.3)", "sphinx-copybutton (==0.5.2)", "sphinx-issues (==5.0.0)", "sphinxext-opengraph (==0.9.1)"]
+tests = ["pytest", "simplejson"]
+
 [[package]]
 name = "mccabe"
 version = "0.6.1"
@@ -594,17 +1305,17 @@ files = [
 
 [[package]]
 name = "mongoengine"
-version = "0.23.1"
+version = "0.28.2"
 description = "MongoEngine is a Python Object-Document Mapper for working with MongoDB."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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+    {file = "mongoengine-0.28.2-py3-none-any.whl", hash = "sha256:8e0f84a5ad3d335e5da98261454d4ab546c866241ed064adc6433fe2077d43c9"},
+    {file = "mongoengine-0.28.2.tar.gz", hash = "sha256:67c35a2ebe0ee7fd8eda3766dc251b9e0aada4489bb935f7a55b4c570d148ca7"},
 ]
 
 [package.dependencies]
-pymongo = ">=3.4,<4.0"
+pymongo = ">=3.4,<5.0"
 
 [[package]]
 name = "more-itertools"
@@ -617,6 +1328,122 @@ files = [
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 ]
 
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+
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+typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.11\""}
+
 [[package]]
 name = "mypy"
 version = "0.910"
@@ -668,6 +1495,25 @@ files = [
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 ]
 
+[[package]]
+name = "neo4j"
+version = "5.28.1"
+description = "Neo4j Bolt driver for Python"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.dependencies]
+pytz = "*"
+
+[package.extras]
+numpy = ["numpy (>=1.7.0,<3.0.0)"]
+pandas = ["numpy (>=1.7.0,<3.0.0)", "pandas (>=1.1.0,<3.0.0)"]
+pyarrow = ["pyarrow (>=1.0.0)"]
+
 [[package]]
 name = "networkx"
 version = "3.2.1"
@@ -688,18 +1534,15 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "nodeenv"
-version = "1.8.0"
+version = "1.9.1"
 description = "Node.js virtual environment builder"
 optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
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 ]
 
-[package.dependencies]
-setuptools = "*"
-
 [[package]]
 name = "numpy"
 version = "1.26.4"
@@ -747,13 +1590,13 @@ files = [
 
 [[package]]
 name = "obonet"
-version = "0.3.1"
+version = "1.1.1"
 description = "Parse OBO formatted ontologies into networkx"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -762,15 +1605,92 @@ networkx = "*"
 [package.extras]
 dev = ["pre-commit", "pytest"]
 
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+version = "3.10.16"
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+python-versions = ">=3.9"
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 [[package]]
 name = "pluggy"
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 pyyaml = ">=5.1"
 virtualenv = ">=20.10.0"
 
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 [[package]]
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 [package.dependencies]
@@ -1467,18 +2590,18 @@ Pillow = "*"
 
 [[package]]
 name = "requests"
-version = "2.31.0"
+version = "2.32.4"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<4"
+charset_normalizer = ">=2,<4"
 idna = ">=2.5,<4"
 urllib3 = ">=1.21.1,<3"
 
@@ -1487,96 +2610,103 @@ socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
-name = "setuptools"
-version = "69.5.1"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
+name = "requests-toolbelt"
+version = "1.0.0"
+description = "A utility belt for advanced users of python-requests"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
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 ]
 
-[package.extras]
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+[package.dependencies]
+requests = ">=2.0.1,<3.0.0"
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
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+
+[[package]]
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+optional = false
+python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "soupsieve"
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 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
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 name = "sqlalchemy"
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 [package.dependencies]
@@ -1587,22 +2717,37 @@ aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
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-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)", "mariadb (>=1.0.1,!=1.1.2)"]
 mssql = ["pyodbc"]
-mssql-pymssql = ["pymssql"]
-mssql-pyodbc = ["pyodbc"]
+mssql-pymssql = ["pymssql", "pymssql"]
+mssql-pyodbc = ["pyodbc", "pyodbc"]
 mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
 mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
-mysql-connector = ["mysql-connector-python"]
+mysql-connector = ["mysql-connector-python", "mysql-connector-python"]
 oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"]
 postgresql = ["psycopg2 (>=2.7)"]
-postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
-postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
+postgresql-asyncpg = ["asyncpg", "asyncpg", "greenlet (!=0.4.17)", "greenlet (!=0.4.17)"]
+postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)", "pg8000 (>=1.16.6,!=1.29.0)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
 pymysql = ["pymysql", "pymysql (<1)"]
 sqlcipher = ["sqlcipher3_binary"]
 
+[[package]]
+name = "tenacity"
+version = "9.1.2"
+description = "Retry code until it succeeds"
+optional = false
+python-versions = ">=3.9"
+files = [
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+]
+
+[package.extras]
+doc = ["reno", "sphinx"]
+test = ["pytest", "tornado (>=4.5)", "typeguard"]
+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -1616,55 +2761,115 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
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+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744"},
+    {file = "tomli-2.2.1-cp313-cp313-win32.whl", hash = "sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec"},
+    {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
+    {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
 
 [[package]]
 name = "tqdm"
-version = "4.66.2"
+version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.2-py3-none-any.whl", hash = "sha256:1ee4f8a893eb9bef51c6e35730cebf234d5d0b6bd112b0271e10ed7c24a02bd9"},
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+    {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"},
+    {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"},
 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.11.0"
+version = "4.13.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
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+    {file = "typing_extensions-4.13.2-py3-none-any.whl", hash = "sha256:a439e7c04b49fec3e5d3e2beaa21755cadbbdc391694e28ccdd36ca4a1408f8c"},
+    {file = "typing_extensions-4.13.2.tar.gz", hash = "sha256:e6c81219bd689f51865d9e372991c540bda33a0379d5573cddb9a3a23f7caaef"},
+]
+
+[[package]]
+name = "typing-inspect"
+version = "0.9.0"
+description = "Runtime inspection utilities for typing module."
+optional = false
+python-versions = "*"
+files = [
+    {file = "typing_inspect-0.9.0-py3-none-any.whl", hash = "sha256:9ee6fc59062311ef8547596ab6b955e1b8aa46242d854bfc78f4f6b0eff35f9f"},
+    {file = "typing_inspect-0.9.0.tar.gz", hash = "sha256:b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78"},
+]
+
+[package.dependencies]
+mypy-extensions = ">=0.3.0"
+typing-extensions = ">=3.7.4"
+
+[[package]]
+name = "typing-inspection"
+version = "0.4.0"
+description = "Runtime typing introspection tools"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "typing_inspection-0.4.0-py3-none-any.whl", hash = "sha256:50e72559fcd2a6367a19f7a7e610e6afcb9fac940c650290eed893d61386832f"},
+    {file = "typing_inspection-0.4.0.tar.gz", hash = "sha256:9765c87de36671694a67904bf2c96e395be9c6439bb6c87b5142569dcdd65122"},
 ]
 
+[package.dependencies]
+typing-extensions = ">=4.12.0"
+
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.5.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+    {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
+    {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
 ]
 
 [package.extras]
@@ -1675,13 +2880,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.25.1"
+version = "20.30.0"
 description = "Virtual Python Environment builder"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"},
-    {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"},
+    {file = "virtualenv-20.30.0-py3-none-any.whl", hash = "sha256:e34302959180fca3af42d1800df014b35019490b119eba981af27f2fa486e5d6"},
+    {file = "virtualenv-20.30.0.tar.gz", hash = "sha256:800863162bcaa5450a6e4d721049730e7f2dae07720e0902b0e4040bd6f9ada8"},
 ]
 
 [package.dependencies]
@@ -1690,7 +2895,7 @@ filelock = ">=3.12.2,<4"
 platformdirs = ">=3.9.1,<5"
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
 test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
@@ -1704,31 +2909,15 @@ files = [
     {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
 ]
 
-[[package]]
-name = "websocket-client"
-version = "1.7.0"
-description = "WebSocket client for Python with low level API options"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"},
-    {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"},
-]
-
-[package.extras]
-docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"]
-optional = ["python-socks", "wsaccel"]
-test = ["websockets"]
-
 [[package]]
 name = "win32-setctime"
-version = "1.1.0"
+version = "1.2.0"
 description = "A small Python utility to set file creation time on Windows"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "win32_setctime-1.1.0-py3-none-any.whl", hash = "sha256:231db239e959c2fe7eb1d7dc129f11172354f98361c4fa2d6d2d7e278baa8aad"},
-    {file = "win32_setctime-1.1.0.tar.gz", hash = "sha256:15cf5750465118d6929ae4de4eb46e8edae9a5634350c01ba582df868e932cb2"},
+    {file = "win32_setctime-1.2.0-py3-none-any.whl", hash = "sha256:95d644c4e708aba81dc3704a116d8cbc974d70b3bdb8be1d150e36be6e9d1390"},
+    {file = "win32_setctime-1.2.0.tar.gz", hash = "sha256:ae1fdf948f5640aae05c511ade119313fb6a30d7eabe25fef9764dca5873c4c0"},
 ]
 
 [package.extras]
@@ -1745,7 +2934,237 @@ files = [
     {file = "xmljson-0.2.1.tar.gz", hash = "sha256:b4158e66aa1e62ee39f7f80eb2fe4f767670ba3c0d5de9804420dc53427fdec8"},
 ]
 
+[[package]]
+name = "yarl"
+version = "1.20.0"
+description = "Yet another URL library"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "yarl-1.20.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f1f6670b9ae3daedb325fa55fbe31c22c8228f6e0b513772c2e1c623caa6ab22"},
+    {file = "yarl-1.20.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:85a231fa250dfa3308f3c7896cc007a47bc76e9e8e8595c20b7426cac4884c62"},
+    {file = "yarl-1.20.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1a06701b647c9939d7019acdfa7ebbfbb78ba6aa05985bb195ad716ea759a569"},
+    {file = "yarl-1.20.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:7595498d085becc8fb9203aa314b136ab0516c7abd97e7d74f7bb4eb95042abe"},
+    {file = "yarl-1.20.0-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:af5607159085dcdb055d5678fc2d34949bd75ae6ea6b4381e784bbab1c3aa195"},
+    {file = "yarl-1.20.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:95b50910e496567434cb77a577493c26bce0f31c8a305135f3bda6a2483b8e10"},
+    {file = "yarl-1.20.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b594113a301ad537766b4e16a5a6750fcbb1497dcc1bc8a4daae889e6402a634"},
+    {file = "yarl-1.20.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:083ce0393ea173cd37834eb84df15b6853b555d20c52703e21fbababa8c129d2"},
+    {file = "yarl-1.20.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4f1a350a652bbbe12f666109fbddfdf049b3ff43696d18c9ab1531fbba1c977a"},
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+    {file = "yarl-1.20.0-cp310-cp310-musllinux_1_2_s390x.whl", hash = "sha256:06d06c9d5b5bc3eb56542ceeba6658d31f54cf401e8468512447834856fb0e61"},
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+    {file = "zstandard-0.23.0-cp39-cp39-win32.whl", hash = "sha256:43da0f0092281bf501f9c5f6f3b4c975a8a0ea82de49ba3f7100e64d422a1274"},
+    {file = "zstandard-0.23.0-cp39-cp39-win_amd64.whl", hash = "sha256:f8346bfa098532bc1fb6c7ef06783e969d87a99dd1d2a5a18a892c1d7a643c58"},
+    {file = "zstandard-0.23.0.tar.gz", hash = "sha256:b2d8c62d08e7255f68f7a740bae85b3c9b8e5466baa9cbf7f57f1cde0ac6bc09"},
+]
+
+[package.dependencies]
+cffi = {version = ">=1.11", markers = "platform_python_implementation == \"PyPy\""}
+
+[package.extras]
+cffi = ["cffi (>=1.11)"]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "caa5aa3fe2bb3dcd3fc6f428c27a4623cee3897b00fcf6568493f3a0d7561c7c"
+content-hash = "15ed4399f8cac5ff1b6765705995ca587405f7d5de6e92d3113ab6f26d8a3b2f"
diff --git a/pyproject.toml b/pyproject.toml
index 38c454b..4f1ae88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "nedrexdb"
-version = "0.2.0"
+version = "0.2.1"
 description = ""
 authors = ["james-skelton <james.skelton@newcastle.ac.uk>","andreas-maier <andreas.maier-1@uni-hamburg.de>"]
 
@@ -10,8 +10,8 @@ pymongo = "^4.8.0"
 mongoengine = "^0.28.2"
 docker = "^7.1.0"
 more-itertools = "^8.8.0"
-loguru = "^0.5.3"
-requests = "^2.32.3"
+loguru = "^0.6.0"
+requests = "^2.32.4"
 beautifulsoup4 = "^4.9.3"
 biopython = "^1.81"
 xmljson = "^0.2.1"
@@ -20,7 +20,7 @@ psycopg2-binary = "^2.9.1"
 pydantic = "2.7.4"
 tqdm = "^4.66.1"
 pandas = "^1.3.4"
-obonet = "^0.3.0"
+obonet = "^1.1.1"
 lxml = "^4.6.3"
 rdflib = "^6.0.2"
 black = "^24.3.0"
@@ -33,6 +33,10 @@ numpy = "1.26.4"
 langchain-community = "^0.3.14"
 langchain = "^0.3.14"
 langchain-neo4j = "^0.2.0"
+h11 = "^0.16.0"
+pillow = "^11.3.0"
+urllib3 = "^2.5.0"
+aiohttp = "^3.12.14"
 openpyxl = "^3.1.2"
 pyspark = "^3.5"
 
diff --git a/set_metadata.py b/set_metadata.py
deleted file mode 100755
index 0212882..0000000
--- a/set_metadata.py
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/usr/bin/env python3
-
-import datetime
-import os
-
-import click
-import toml  # type: ignore
-from pymongo import MongoClient
-
-
-@click.command()
-@click.option("--config", required=True, type=click.Path(exists=True))
-@click.option("--version", required=True, type=click.Choice(["live", "dev"], case_sensitive=False))
-def update(config, version):
-    """Updates the metadata collection based on the given config"""
-    with open(config) as f:
-        config = toml.load(f)
-
-    mongo_port = 27017
-    mongo_host = config["db"][version.lower()]["mongo_name"]
-    db_name = config["db"]["mongo_db"]
-    data_directory_root = config["db"]["root_directory"]
-    download_directory = f"{data_directory_root}/{config['sources']['directory']}"
-
-    sources = list(config["sources"].keys())
-    sources.remove("directory")
-    try:
-        client = MongoClient(port=mongo_port, host=mongo_host)
-        db = client[db_name]
-
-        metadata = db["metadata"].find_one()
-    except:
-        metadata = None
-    metadata = metadata if metadata is not None else {"version": "0.0.0"}
-    if "source_databases" not in metadata:
-        metadata["source_databases"] = {}
-
-    for source in sources:
-        dir = f"{download_directory}/{source}"
-        earliest_date = datetime.datetime.now()
-        for _, options in config["sources"][source].items():
-            if "filename" in options:
-                filename = options["filename"]
-            else:
-                filename = options["url"].rsplit("/", 1)[1]
-
-            path = f"{dir}/{filename}"
-            ts = datetime.datetime.fromtimestamp(os.path.getctime(path))
-            if ts < earliest_date:
-                ts = earliest_date
-
-        metadata["source_databases"][source] = {"version": None, "date": f"{earliest_date.date()}"}
-
-
-    db["metadata"].replace_one({}, metadata, upsert=True)
-
-
-if __name__ == "__main__":
-    update()
diff --git a/setup_data.sh b/setup_data.sh
index eb91bda..a50879f 100755
--- a/setup_data.sh
+++ b/setup_data.sh
@@ -4,12 +4,21 @@ DOWNLOADS=$NEDREX_FILES/nedrex_data/downloads
 
 mkdir -p $DOWNLOADS
 cd $DOWNLOADS
-wget -nv https://zenodo.org/records/12806709/files/cosmic.zip?download=1 -O cosmic.zip
-wget -nv https://zenodo.org/records/12806709/files/intogen.zip?download=1 -O intogen.zip
-wget -nv https://zenodo.org/records/12806709/files/ncg.zip?download=1 -O ncg.zip
-wget -nv https://cloud.uni-hamburg.de/s/RiAtjZC3bb7bg7n/download/bioontology.zip -O bioontology.zip
-wget -nv https://cloud.uni-hamburg.de/s/5meqDbTbgydo6Tj/download/drugbank.zip -O drugbank.zip
-wget -nv https://cloud.uni-hamburg.de/s/PxWXAMY5bfS3ZcA/download/repotrial.zip -O repotrial.zip
+echo "Starting dump downloads"
+wget https://cloud.uni-hamburg.de/s/RiAtjZC3bb7bg7n/download/bioontology.zip -q -O bioontology.zip
+echo "Downloaded bioontology.zip"
+wget https://cloud.uni-hamburg.de/s/5meqDbTbgydo6Tj/download/drugbank.zip -q -O drugbank.zip
+echo "Downloaded drugbank.zip"
+wget https://cloud.uni-hamburg.de/public.php/dav/files/9wNb5HWL7RBH6ng/?accept=zip -q -O disgenet.zip
+echo "Downloaded disgenet.zip"
+wget https://cloud.uni-hamburg.de/s/PxWXAMY5bfS3ZcA/download/repotrial.zip -q -O repotrial.zip
+echo "Downloaded repotrial.zip"
+wget -nv https://zenodo.org/records/12806709/files/cosmic.zip?download=1 -q -O cosmic.zip
+echo "Downloaded cosmic.zip"
+wget -nv https://zenodo.org/records/12806709/files/intogen.zip?download=1 -q -O intogen.zip
+echo "Downloaded intogen.zip"
+wget -nv https://zenodo.org/records/12806709/files/ncg.zip?download=1 -q -O ncg.zip
+echo "Downloaded ncg.zip"
 
 for file in *.zip; do
     echo "Unzipping $file..."
@@ -19,7 +28,8 @@ done
 cd ../../
 mkdir -p nedrex_api/static
 cd nedrex_api/static
-wget -nv https://cloud.uni-hamburg.de/s/PdXPnX77QpWzX7z/download -O static.zip
+wget https://cloud.uni-hamburg.de/s/PdXPnX77QpWzX7z/download -q -O static.zip
+echo "Downloaded static.zip"
 unzip -o static.zip
 mv static/* .
 rm -rf static
diff --git a/update.sh b/update.sh
index b87fd28..4669c48 100644
--- a/update.sh
+++ b/update.sh
@@ -2,4 +2,7 @@
 
 export PATH="/opt/conda/bin:${PATH}"
 echo $PATH
+if [[ "$AUTOUPDATE" != "0" ]]; then
+  export SKIP_UPDATE=0
+fi
 ./build.sh