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

1. git clone https://github.com/chrismattmann/shangridocs
2. cd shangridocs
3. mvn install

Starting instructions

Then, to start Shangridocs, you need:

Apache Tika Server

1. cd shangridocs
2. mkdir -p tika/server
3. mkdir -p tika/ctakes
4. cd tika/server
5. git clone https://github.com/apache/tika.git
6. cd tika && mvn install
7. java -jar tika-server/target/tika-server-1.11-SNAPSHOT.jar > ../tika-server.log 2>&1&

Apache cTAKES Server

1. See guide for installing cTAKES and Tika here: https://wiki.apache.org/tika/cTAKESParser
2. Start the server on port 9999

Start Shangridocs web app in testing mode

1. cd shangridocs/shangridocs-webapp
2. 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