PubChem

https://pubchem.ncbi.nlm.nih.gov/docs/
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### Install Python3 on Linux

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Install Python3 using the system package manager.

```bash
sudo apt install python3
```

```bash
sudo yum install -y python3 
```

--------------------------------

### Install Python Dependencies

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Install the required Google Cloud Python libraries.

```bash
pip install google-cloud-compute google-auth google-api-python-client google-cloud-resource-manager
```

--------------------------------

### Perform Asynchronous Search Examples

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest

Historical examples of structure and property searches using the PUG-REST API.

```text
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/substructure/cid/2244/cids/XML?StripHydrogen=true
```

```text
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/identity/cid/5793/cids/TXT?identity_type=same_connectivity
```

```text
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/similarity_2d/cid/2244/cids/XML?Threshold=99
```

```text
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/similarity_3d/cid/2244/cids/JSON
```

```text
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/formula/C6H12O/cids/XML
```

--------------------------------

### Test Database Instances

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Verify the installation by querying the Virtuoso or QLever instance via curl.

```bash
curl -X POST -H "Content-Type: application/x-www-form-urlencoded" --data-urlencode "query=SELECT DISTINCT ?g WHERE { GRAPH ?g {?s a ?o} }" "http://vm_ip_address:8890/sparql"
```

```bash
curl -s vm_ip_address:7023 -H "Accept: text/tab-separated-values" --data-urlencode query="SELECT * WHERE { ?s ?p ?o } LIMIT 3"
```

--------------------------------

### Resolve Synonym URI

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-synonym

Example URI for resolving a specific synonym hash.

```text
http://rdf.ncbi.nlm.nih.gov/pubchem/synonym/MD5_8ab309455b7969e69fa0b7602239b203
```

--------------------------------

### RDF Triple Examples

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-synonym

RDF triples representing synonym types, values, and relationships.

```turtle
synonym:MD5_66d24a6dc023afb058efbbb5fc5ed1bb rdf:type vocab:Synonym .
```

```turtle
synonym:MD5_66d24a6dc023afb058efbbb5fc5ed1bb rdf:type cheminf:CHEMINF_000446 .
```

```turtle
synonym:MD5_00360c1760f9a153e24bea7b698516cf rdf:type cheminf:CHEMINF_000407 .
```

```turtle
synonym:MD5_0005639ad33bf7f927e632c29847b28a rdf:type cheminf:CHEMINF_000412 .
```

```turtle
synonym:MD5_4aa179283f871f4abe930c25833cea9b rdf:type cheminf:CHEMINF_000339 .
```

```turtle
synonym:MD5_02ebee683fb36446167606809e8ebed1 rdf:type cheminf:CHEMINF_000561 .
```

```turtle
synonym:MD5_00048b0c69b97e6ba6e81668c0d95b88 rdf:type cheminf:CHEMINF_000406 .
```

```turtle
synonym:MD5_05d8051bae0f9d0d24d7e184785afbc0 rdf:type cheminf:CHEMINF_000447 .
```

```turtle
synonym:MD5_01ab0278c5fcc77a5bb905c789b37f20 rdf:type cheminf:CHEMINF_000562 .
```

```turtle
synonym:MD5_003fdb1001358dcc64d1e25e24bea795 rdf:type cheminf:CHEMINF_000382 .
```

```turtle
synonym:MD5_035ae92c47f0774b625c99d9a40b319d rdf:type cheminf:CHEMINF_000409 .
```

```turtle
synonym:MD5_000272365f5e92d21081e8a4403b712c rdf:type cheminf:CHEMINF_000564 .
```

```turtle
synonym:MD5_1375c60b0b432c8ccb1554c856c5eab6 rdf:type cheminf:CHEMINF_000565 .
```

```turtle
synonym:MD5_0edb0d5a8d7232e10b4f2ba5434116a9 rdf:type cheminf:CHEMINF_000566 .
```

```turtle
synonym:MD5_1d202459af5a110a9422103af41569ad rdf:type cheminf:CHEMINF_000109 .
```

```turtle
synonym:MD5_2e899413e5efff4e1e3166e273cff7b7 rdf:type cheminf:CHEMINF_000563 .
```

```turtle
synonym:MD5_0000235e6bfa934c6182fbf40f071747 rdf:type cheminf:CHEMINF_000467 .
```

```turtle
synonym:MD5_4aa179283f871f4abe930c25833cea9b sio:SIO_000300 "benzoic acid, 2-(acetyloxy)-" .
```

```turtle
synonym:MD5_4aa179283f871f4abe930c25833cea9b dcterms:subject mesh:M0001864 .
```

```turtle
synonym:MD5_47a63fc97978537204b7a7371de13662 dcterms:subject concept:ATC_L01XE01 .
```

```turtle
synonym:MD5_4aa179283f871f4abe930c25833cea9b sio:SIO_000011 compound:CID2244 .
```

--------------------------------

### Resolve InChIKey URI

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-inchikey

Example URI structure for resolving a specific InChIKey.

```text
http://rdf.ncbi.nlm.nih.gov/pubchem/inchikey/BSYNRYMUTXBXSQ-UHFFFAOYSA-N
```

--------------------------------

### Initialize GCP Project

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Run the initialization script to prepare the GCP project environment.

```bash
python3 create_cloud_vm.py initialize_project
```

--------------------------------

### Download Local QLever Docker Files

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Download and prepare the Docker configuration files for a local QLever instance.

```bash
curl -s ftp://ftp.ncbi.nlm.nih.gov/pubchem/cloud/local_qlever_docker.tar -o local_qlever_docker.tar
tar -xvf local_qlever_docker.tar
cd docker-files
```

--------------------------------

### Build and Run Local QLever Container

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Build the QLever Docker image and start the container with appropriate port mappings.

```bash
sudo docker build -t cloud-graph-db .
sudo docker run --rm -d --name graph-db-container -p 7023:7023 cloud-graph-db
```

```bash
docker build -t cloud-graph-db .
docker run --rm -d --name graph-db-container -p 7023:7023 cloud-graph-db
```

--------------------------------

### GET /rest/pug_view/data/key/{key}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view

Retrieves annotation attachments.

```APIDOC
## GET /rest/pug_view/data/key/{key}

### Description
Retrieves attachments associated with records, such as spectral images.

### Method
GET

### Endpoint
/rest/pug_view/data/key/{key}

### Parameters
#### Path Parameters
- **key** (string) - Required - The attachment key value.
```

--------------------------------

### Create Cloud VM Instances

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Commands to create cloud virtual machines for different database configurations.

```bash
python3 create_cloud_vm.py virtuoso_db
```

```bash
python3 create_cloud_vm.py virtuoso_ttl
```

```bash
python3 create_cloud_vm.py qlever
```

--------------------------------

### GET /rest/pug_view/image/biologic/{id}/SVG

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view

Retrieves a biologic image for a compound.

```APIDOC
## GET /rest/pug_view/image/biologic/{id}/SVG

### Description
Displays biologic images associated with compounds using an internal identifier.

### Method
GET

### Endpoint
/rest/pug_view/image/biologic/{id}/SVG

### Parameters
#### Path Parameters
- **id** (integer) - Required - The internal biologic identifier.
```

--------------------------------

### GET /rest/pug_view/literature/compound/{cid}/{format}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view

Retrieves literature associated with a compound.

```APIDOC
## GET /rest/pug_view/literature/compound/{cid}/{format}

### Description
Provides URLs into PubMed for literature associated with a compound, organized by subheading.

### Method
GET

### Endpoint
/rest/pug_view/literature/compound/{cid}/{format}

### Parameters
#### Path Parameters
- **cid** (integer) - Required - The PubChem Compound ID.
- **format** (string) - Required - The response format (e.g., JSON).
```

--------------------------------

### Download Local Virtuoso Docker Files

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Download and prepare the Docker configuration files for a local Virtuoso instance.

```bash
    curl -s ftp://ftp.ncbi.nlm.nih.gov/pubchem/cloud/local_virtuoso_docker.tar -o local_virtuoso_docker.tar  
    tar -xvf local_virtuoso_docker.tar  
    cd docker-files  
```

--------------------------------

### GET /rest/rdf/query

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-reference

Queries the reference graph using a specific identifier.

```APIDOC
## GET /rest/rdf/query

### Description
Queries the reference RDF graph using a PMID, DOI, or PMCID.

### Method
GET

### Endpoint
https://pubchem.ncbi.nlm.nih.gov/rest/rdf/query

### Parameters
#### Query Parameters
- **graph** (string) - Required - The graph name, must be 'reference'.
- **pmid** (string) - Optional - Search reference by PMID.
- **doi** (string) - Optional - Search reference by DOI.
- **pmcid** (string) - Optional - Search reference by PMCID.

### Request Example
https://pubchem.ncbi.nlm.nih.gov/rest/rdf/query?graph=reference&pmid=460526
```

--------------------------------

### GET /rest/pug/annotations/headings/{format}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view

Retrieves a list of all available annotation headings.

```APIDOC
## GET /rest/pug/annotations/headings/{format}

### Description
Returns a complete list of all annotation headings and their types for which PubChem has data.

### Method
GET

### Endpoint
/rest/pug/annotations/headings/{format}

### Parameters
#### Path Parameters
- **format** (string) - Required - The response format (e.g., JSON).
```

--------------------------------

### Build and Run Local Virtuoso Container

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Build the Virtuoso Docker image and start the container with appropriate port mappings.

```bash
sudo docker build -t cloud-graph-db .  
sudo docker run --rm -d --name graph-db-container -p 1111:1111 -p 8890:8890 cloud-graph-db  
```

```bash
docker build -t cloud-graph-db .
docker run --rm -d --name graph-db-container -p 1111:1111 -p 8890:8890 cloud-graph-db
```

--------------------------------

### GET /rest/rdf/query

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cooccurrence

Queries cooccurrence relationships or references between specified entities.

```APIDOC
## GET /rest/rdf/query

### Description
Queries the cooccurrence graph for relationships between entities or specific references.

### Method
GET

### Endpoint
https://pubchem.ncbi.nlm.nih.gov/rest/rdf/query

### Parameters
#### Query Parameters
- **graph** (string) - Required - Must be set to "cooccurrence"
- **entity1** (string) - Required - Identifier for the first entity (e.g., CID3672, DZID8173, ptgs2)
- **type** (string) - Required - The cooccurrence type (e.g., chemical_to_chemical, chemical_to_disease, chemical_to_gene, disease_to_disease, disease_to_chemical, disease_to_gene, gene_to_gene, gene_to_chemical, gene_to_disease)
- **entity2** (string) - Optional - Identifier for the second entity
- **ref** (boolean) - Optional - Set to true to query references; requires entity2 to be provided

### Request Example
https://pubchem.ncbi.nlm.nih.gov/rest/rdf/query?graph=cooccurrence&entity1=CID3672&type=chemical_to_gene&entity2=ptgs2&ref=true
```

--------------------------------

### Make download script executable

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-load

Set execution permissions for the download script.

```bash
chmod u+x download_script.sh
```

--------------------------------

### Handle Query Response

Source: https://pubchem.ncbi.nlm.nih.gov/docs/power-user-gateway

Example of the XML response received after a successful search, containing the Entrez query key and webenv.

```xml
<PCT-Data>  
  <PCT-Data_output>  
    <PCT-OutputData>  
      <PCT-OutputData_status>  
        <PCT-Status-Message>  
          <PCT-Status-Message_status>  
            <PCT-Status value="success"/>  
          </PCT-Status-Message_status>  
          <PCT-Status-Message_message>Your search has completed successfully!  
          </PCT-Status-Message_message>  
        </PCT-Status-Message>  
      </PCT-OutputData_status>  
      <PCT-OutputData_output>  
        <PCT-OutputData_output_entrez>  
          <PCT-Entrez>  
            <PCT-Entrez_db>pccompound</PCT-Entrez_db>  
            <PCT-Entrez_query-key>3</PCT-Entrez_query-key>  
            <PCT-Entrez_webenv>  
            0hJ--NzxiSKFxJzc4SnMb5PvxBP8HKJvZ-2s-XE19WBZSHG0xIO_k_xPrU@1FBE6DE17A397ED0_0011SID  
            </PCT-Entrez_webenv>  
          </PCT-Entrez>  
        </PCT-OutputData_output_entrez>  
      </PCT-OutputData_output>  
    </PCT-OutputData>  
  </PCT-Data_output>  
</PCT-Data>
```

--------------------------------

### Download

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-soap

Prepares a file containing records from a list key for download.

```APIDOC
## Download

### Description
Given a list key, prepare for download a file containing those records in the selected format. This is an asynchronous operation that returns a download key.
```

--------------------------------

### GET /rest/pug_view/linkout/compound/{cid}/{format}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view

Retrieves NCBI LinkOut records for a compound.

```APIDOC
## GET /rest/pug_view/linkout/compound/{cid}/{format}

### Description
Lists all NCBI LinkOut records present for a substance, compound, or assay.

### Method
GET

### Endpoint
/rest/pug_view/linkout/compound/{cid}/{format}

### Parameters
#### Path Parameters
- **cid** (integer) - Required - The PubChem Compound ID.
- **format** (string) - Required - The response format (e.g., JSON).
```

--------------------------------

### GET /rest/pug_view/categories/compound/{cid}/{format}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view

Lists all depositors and their SIDs for a given compound.

```APIDOC
## GET /rest/pug_view/categories/compound/{cid}/{format}

### Description
Lists all PubChem depositors and their SIDs for a given compound, including source categorization.

### Method
GET

### Endpoint
/rest/pug_view/categories/compound/{cid}/{format}

### Parameters
#### Path Parameters
- **cid** (integer) - Required - The PubChem Compound ID.
- **format** (string) - Required - The response format (e.g., JSON).
```

--------------------------------

### Enable GCP API Services

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-cloud-install

Enable the necessary compute, IAM, and resource manager APIs for the GCP project.

```bash
gcloud services enable compute.googleapis.com  
gcloud services enable iam.googleapis.com  
gcloud services enable cloudresourcemanager.googleapis.com  
```

--------------------------------

### GET /rest/pug/assay/aid/{aid}/CSV

Source: https://pubchem.ncbi.nlm.nih.gov/docs/bioassays

Retrieves the full data table for an assay.

```APIDOC
## GET /rest/pug/assay/aid/{aid}/CSV

### Description
Retrieves the full bioactivity data table for a specific assay in CSV format.

### Method
GET

### Endpoint
/rest/pug/assay/aid/{aid}/CSV

### Parameters
#### Path Parameters
- **aid** (integer) - Required - The Assay ID.

#### Query Parameters
- **sid** (string) - Optional - Filter by Substance IDs.
- **cid** (string) - Optional - Filter by Compound IDs.
```

--------------------------------

### GET /rest/pug/assay/aid/{aid}/summary/{format}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/bioassays

Retrieves the summary of a specific assay.

```APIDOC
## GET /rest/pug/assay/aid/{aid}/summary/{format}

### Description
Retrieves the summary information for a given assay ID.

### Method
GET

### Endpoint
/rest/pug/assay/aid/{aid}/summary/{format}

### Parameters
#### Path Parameters
- **aid** (integer) - Required - The Assay ID.
- **format** (string) - Required - The output format (e.g., XML).
```

--------------------------------

### POST http://pubchem.ncbi.nlm.nih.gov/Download

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-soap-reference

Prepares a file for download containing records from a list key. Returns a download key or a data blob if synchronous single record mode is enabled.

```APIDOC
## POST http://pubchem.ncbi.nlm.nih.gov/Download

### Description
Prepares a file for download containing records from a list key. Returns a download key or a data blob if synchronous single record mode is enabled.

### Parameters
- **tns:ListKey** (string) - Required
- **tns:eFormat** (FormatType) - Required
- **tns:eCompress** (CompressType) - Optional
- **tns:Use3D** (boolean) - Optional
- **tns:N3DConformers** (int) - Optional
- **tns:SynchronousSingleRecord** (boolean) - Optional

### Response
- **tns:DownloadKey** (string) - Optional
- **tns:DataBlob** (DataBlobType) - Optional
```

--------------------------------

### AssayDownload

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-soap

Prepares an assay data table for download given an assay key.

```APIDOC
## AssayDownload

### Description
Given an assay key, prepare for download a file containing an assay data table in the selected format. This is an asynchronous operation that returns a download key.

### Parameters
- **assay key** (string) - Required - The key representing the assay.
- **format** (string) - Required - The selected file format.
- **compression** (boolean) - Optional - Compression status (defaults to gzip).
```

--------------------------------

### GET /rest/pug/assay/aid/{aid}/description/{format}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/bioassays

Retrieves the description of a specific assay.

```APIDOC
## GET /rest/pug/assay/aid/{aid}/description/{format}

### Description
Retrieves the description of a specific assay by its AID.

### Method
GET

### Endpoint
/rest/pug/assay/aid/{aid}/description/{format}

### Parameters
#### Path Parameters
- **aid** (integer) - Required - The Assay ID.
- **format** (string) - Required - The output format (e.g., XML).
```

--------------------------------

### Execute bulk load

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-load

Run the rdf_loader_run function in parallel to load the registered files.

```bash
isql 1111 dba dba exec="rdf_loader_run();" &  
isql 1111 dba dba exec="rdf_loader_run();" &  
isql 1111 dba dba exec="rdf_loader_run();" &  
isql 1111 dba dba exec="rdf_loader_run();" &  
isql 1111 dba dba exec="rdf_loader_run();" &  
isql 1111 dba dba exec="rdf_loader_run();" &  
isql 1111 dba dba exec="rdf_loader_run();" &  
wait  
isql 111 dba dba exec="checkpoint;"
```

--------------------------------

### GET /rest/pug/classification/hnid/{integer}/{id_type}/{format}

Source: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest

Retrieves lists of identifiers from classification nodes.

```APIDOC
## GET /rest/pug/classification/hnid/{integer}/{id_type}/{format}

### Description
Retrieves lists of identifiers from specific classification nodes.

### Method
GET

### Endpoint
/rest/pug/classification/hnid/{integer}/{id_type}/{format}

### Parameters
#### Path Parameters
- **integer** (integer) - Required - The HNID identifier for a specific classification node.
- **id_type** (string) - Required - The output identifier type (e.g., cid, sid, aid, patent, pmid, doi, gene, protein, taxonomy, pathway, disease, cell).
- **format** (string) - Required - The output format: TXT, XML, JSON, JSONP, or ASNT/B.

#### Query Parameters
- **list_return** (string) - Optional - Set to 'cachekey' to retrieve the list as a cache key.
```

--------------------------------

### Register files for bulk loading

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-load

Register RDF files in a directory to specific graphs using the ld_dir or ld_dir_all functions in isql.

```sql
ld_dir('<Path>/anatomy', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/anatomy');
ld_dir('<Path>/author', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/author');
ld_dir('<Path>/bioassay', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/bioassay');
ld_dir('<Path>/book', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/book');
ld_dir('<Path>/cell', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/cell');
ld_dir('<Path>/compound/general', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/compound');
ld_dir('<Path>/concept', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/concept');
ld_dir('<Path>/conserveddomain', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/conserveddomain');
ld_dir('<Path>/cooccurrence', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/cooccurrence');
ld_dir_all('<Path>/descriptor', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/descriptor');
ld_dir('<Path>/disease', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/disease');
ld_dir('<Path>/endpoint', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/endpoint');
ld_dir('<Path>/gene', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/gene');
ld_dir('<Path>/grant', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/grant');
ld_dir('<Path>/inchikey', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/inchikey');
ld_dir('<Path>/journal', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/journal');
ld_dir('<Path>/measuregroup', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/measuregroup');
ld_dir('<Path>/organization', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/organization');
ld_dir('<Path>/patent/cpc', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/patentcpc');
ld_dir('<Path>/patent/ipc', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/patentipc');
ld_dir('<Path>/patent', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/patent');
ld_dir('<Path>/pathway', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/pathway');
ld_dir('<Path>/protein', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/protein');
ld_dir('<Path>/reference', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/reference');
ld_dir('<Path>/ruleset', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/ruleset');
ld_dir('<Path>/source', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/source');
ld_dir('<Path>/substance', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/substance');
ld_dir('<Path>/synonym', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/synonym');
ld_dir('<Path>/taxonomy', '*.ttl.gz', 'http://rdf.ncbi.nlm.nih.gov/pubchem/taxonomy');
checkpoint;
```

--------------------------------

### GET /rest/rdf/query?graph=cooccurrence

Source: https://pubchem.ncbi.nlm.nih.gov/docs/rdf-rest

Queries cooccurrence relationships between entities such as compounds, diseases, and genes.

```APIDOC
## GET /rest/rdf/query?graph=cooccurrence

### Description
Queries cooccurrence data between entities. Supports querying relationships and associated references.

### Method
GET

### Endpoint
/rest/rdf/query

### Parameters
#### Query Parameters
- **graph** (string) - Required - Must be set to 'cooccurrence'.
- **entity1** (string) - Required - Compound, disease, or gene identifier.
- **type** (string) - Required - The type of cooccurrence (e.g., chemical_to_chemical, chemical_to_disease).
- **entity2** (string) - Optional - Secondary entity identifier.
- **ref** (boolean) - Optional - Set to 'true' to query references for the cooccurrence.
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