Shangridocs
Introduction
Shangridocs is a document exploration tool for the biomedical domain which takes inspiration from Utopiadocs but provides the following killer features
- A fully functional Java EE Web Application (.war) for deployment in application servers such as Apache Tomcat
- Shangridocs consults many more biomedical data sources from which knowledge augmentation occurs and users can benefit
Build Instructions
- git clone https://github.com/chrismattmann/shangridocs
- cd shangridocs
- mvn install
Starting instructions
Then, to start Shangridocs, you need:
Apache Tika Server
- cd shangridocs
- mkdir -p tika/server
- mkdir -p tika/ctakes
- cd tika/server
- git clone https://github.com/apache/tika.git
- cd tika && mvn install
- java -jar tika-server/target/tika-server-1.11-SNAPSHOT.jar > ../tika-server.log 2>&1&
Apache cTAKES Server
- See guide for installing cTAKES and Tika here: https://wiki.apache.org/tika/cTAKESParser
- Start the server on port 9999
Start Shangridocs web app in testing mode
- cd shangridocs/shangridocs-webapp
- mvn tomcat7:run
Now visit http://localhost:8181/shangridocs/ and you should see the web app!
Deploying and Installing the Web Application
Testing out the Services
Query PubMed for IDs matching the text, “organ”
curl -X PUT -d "organ" -H "Content-type: text/plain" http://localhost:8181/shangridocs/services/pubmed/text
Query PubMed for abstract info on those IDs
curl -X PUT -d "26368927,26368857,26368567,26368552,26368505,26368301,26368042,26368024,26367958,26367780,26367742,26367591,26367387,26367361,26367113,26367090,26367026,26366861,26366794,26366793" -H "Content-type: text/plain" http://localhost:8181/shangridocs/services/pubmed/ids
Query GeneCard for gene information
curl -X PUT -d "ALB" http://localhost:8181/shangridocs-services/services/genecard/query -H "Content-Type: text/plain" -H "Accept: application/json" -v
Query Omim for mouse information
curl -X PUT -d "mouse" http://localhost:8181/shangridocs-services/services/omim/search -H "Content-Type: text/plain" -H "Accept: application/json"
Query Uniprot for mouse information
curl -X PUT -d "mouse" http://localhost:8181/shangridocs-services/services/uniprot/search -H "Content-Type: text/plain" -H "Accept: application/json"
License
Shangridocs source code and project is licensed and released under the Apache License v2.0