rezacsedu / bio2rdf

Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences.

CWL workflows for RDF Bio2RDF conversion

The Common Workflow Language is used to describe workflows to transform heterogeneous structured data (CSV, TSV, RDB, XML, JSON) to the Bio2RDF RDF vocabularies. The user defines SPARQL queries to transform the generic RDF generated depending on the input data structure (AutoR2RML, xml2rdf) to the target Bio2RDF vocabulary.

• Install Docker to run the modules.
• Install cwltool to get cwl-runner to run workflows of Docker modules.
• Those workflows use Data2Services modules, see the data2services-pipeline project.

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Clone the bio2rdf project

git clone https://github.com/MaastrichtU-IDS/bio2rdf

Go to the cloned project

cd bio2rdf

Define absolute path and dataset folder as environment variables

In terminal type:

export ABS_PATH=/path/to/your/bio2rdf/folder

export DATASET=dataset_name

The folders of the dataset in input, output, mapping, support folders should be the same as the dataset name variable.

Start services

Apache Drill and GraphDB services must be running before executing CWL workflows.

# Start Apache Drill sharing volume with this repository.
# Here shared locally at /data/bio2rdf
docker run -dit --rm -v ${ABS_PATH}:/data:ro -p 8047:8047 -p 31010:31010 --name drill umids/apache-drill

Run your choice of triple store

For GraphDB:

• GraphDB needs to be built locally, for this
• Download GraphDB as a stand-alone server free version (zip): https://ontotext.com/products/graphdb/.
• Put the downloaded .zip file in the GraphDB repository (cloned from GitHub).
• Run docker build -t graphdb --build-arg version=CHANGE_ME . in the GraphDB repository.

# GraphDB needs to be downloaded manually and built. 
# Here shared locally at /data/graphdb and /data/graphdb-import
docker build -t graphdb --build-arg version=8.11.0 .
docker run -d --rm --name graphdb -p 7200:7200 -v ${ABS_PATH}/graphdb:/opt/graphdb/home -v ${ABS_PATH}/graphdb-import:/root/graphdb-import graphdb

For Virtuoso:

docker run --rm --name virtuoso \
    -p 8890:8890 -p 1111:1111 \
    -e DBA_PASSWORD=dba \
    -e SPARQL_UPDATE=true \
    -e DEFAULT_GRAPH=http://bio2rdf.com/bio2rdf_vocabulary: \
    -v ${ABS_PATH}/virtuoso:/data \
    -v /tmp:/tmp \
    -d tenforce/virtuoso:1.3.2-virtuoso7.2.1

---

Prepare workflow

For GraphDB:

Create a GraphDB repository

After running the docker of GraphDB, go to: http://localhost:7200/

Create new repository in GraphDB that will store your data.

Modify the workflow config file

Navigate to the folder of the dataset you want to convert following this path: support/_dataset_name/graphdb-workflow/config-workflow.yml

edit the file config-workflow.yml to set the following parameter depending on your environment:

sparql_triplestore_url: url_of_running_graphdb

sparql_triplestore_repository: the_repository_name_you_created_in_previous_step

working_directory: the_path_of_bio2rdf_folder

For Virtuoso:

Edit config in the folder of the dataset you want to convert following this path: support/_dataset_name/virtuoso-workflow/config-workflow.yml

• change the working directory to the bio2rdf cloned project

working_directory: the_path_of_bio2rdf_folder

• change these parameters according to your environment if you are using different virtuoso endpoint:

sparql_triplestore_url: http://virtuoso:8890/sparql

triple_store_password: dba triple_store_username: dba

Run with CWL

• Go to the bio2rdf root folder (the root of the cloned repository)

  • e.g. /data/bio2rdf to run the CWL workflows.

• You will need to put the SPARQL mapping queries in /mapping/$dataset_name and provide 3 parameters:

  • --outdir: the output directory for files outputted by the workflow (except for the downloaded source files that goes automatically to /input).
    • e.g. ${ABS_PATH}/output/${DATASET}.
  • The .cwl workflow file
    • e.g. ${ABS_PATH}/support/${DATASET}/virtuoso-workflow/workflow.cwl
  • The .yml configuration file with all parameters required to run the workflow
    • e.g. ${ABS_PATH}/support/${DATASET}/virtuoso-workflow/config-workflow.yml

• 3 types of workflows can be run depending on the input data:

  • Convert XML to RDF
  • Convert CSV to RDF
  • Convert CSV to RDF and split a property

Convert CSV/TSV with AutoR2RML

cwl-runner --outdir ${ABS_PATH}/output/${DATASET} ${ABS_PATH}/support/${DATASET}/virtuoso-workflow/workflow.cwl ${ABS_PATH}/support/${DATASET}/virtuoso-workflow/config-workflow.yml

See config file:

working_directory: /media/apc/DATA1/Maastricht/bio2rdf-github

dataset: sider

# R2RML params
input_data_jdbc: "jdbc:drill:drillbit=drill:31010"
sparql_tmp_graph_uri: "https://w3id.org/data2services/graph/autor2rml/sider"
sparql_base_uri: "https://w3id.org/data2services/"
#autor2rml_column_header: "test1,test2,test3,test5"

# RdfUpload params
sparql_triplestore_url: http://graphdb:7200
sparql_triplestore_repository: sider


sparql_transform_queries_path: /data/mapping/sider/transform
sparql_insert_metadata_path: /data/mapping/sider/metadata

Convert CSV/TSV with AutoR2RML and split a property (Will be available shortly)

Run in the background

Will write all terminal output to nohup.out.

cwl-runner --outdir  ${ABS_PATH}/output/${DATASET}  ${ABS_PATH}/support/${DATASET}/virtuoso-workflow/workflow.cwl  ${ABS_PATH}/support/${DATASET}/virtuoso-workflow/config-workflow.yml