The Wheat Genomics Scientific Literature KG (WheatGenomicsSLKG) is a FAIR knowledge graph that exploits the Semantic Web technologies to integrate information about Named Entities (NE) extracted automatically from a corpus of PubMed scientific articles on wheat genetics and genomics.
This repository is the backend part of a web application that demonstrates the interest and leveraging rich knowledge references. It provides a set of Web APIs (services) used by the frontend application available in the visualization repository.
The services exposed by the server are defined in routes/index.js.
With the exception of service autoComplete, the services submit SPARQL SELECT queries to the D2kAB SPARQL endpoint (property SEMANTIC_INDEX_SPARQL_ENDPOINT in .env)
using the d3-sparql library.
The response of the services is the output of the d3-sparql library itself, that only returns the "results.bindings" part
of the SPARQL response in JSON format, following this format:
{
"result": [
{
"var1": "value1",
"var2": "value2",
...
},
...
]}Therefore, the SELECT clause of the SPARQL queries are the de facto documentation of the services since they give the names of the variables (var1 and var2 in the example above).
Pre-requisite: node.js 17, yarn.
Install the dependencies with yarn install.
Run the application: yarn start
By default, the node.js server listens on port 3000. This can be changed in file .env.
Make sure the server is properly started and test the services by pointing your browser to:
http://localhost:3000/getArticleMetadata/?uri=https://pubmed.ncbi.nlm.nih.gov/10099937
http://localhost:3000/getArticleAuthors/?uri=https://pubmed.ncbi.nlm.nih.gov/10099937
http://localhost:3000/getAbstractNamedEntities/?uri=https://pubmed.ncbi.nlm.nih.gov/10099937
http://localhost:3000/autoComplete/?input=aestivum
http://localhost:3000/searchDocuments/?uri=http://purl.obolibrary.org/obo/NCBITaxon_49317
http://localhost:3000/searchDocumentsSubConcept/?uri=http://opendata.inrae.fr/wto/0000506
http://localhost:3000/searchDocumentsSubConcept/?uri=http://purl.obolibrary.org/obo/NCBITaxon_49317
In the get* services, uri is an example article that may no longer exist in the database at some point.
The repository comes with a Dockerfile and a docker-compose file. After cloning, build the application with this command:
docker-compose build
Then start the services with:
docker-compose up -d
Log traces are printed out in file log/application.log.
This can be changed by customizing file config/log4js.json. Refer to the Log4JS documentation.