twktheainur / llodumls

a LLOD (Lemon-Ontolex) converter for UMLS

llodumls

a LLOD (Lemon-Ontolex) converter for UMLS

Table of Contents

• llodumls
  • I. Requirements
    • I.1. Installing Redis
  • II. Development
    • II.1. Building
    • II.2. Creating runnable jar
  • III. Resources

I. Requirements

• An internet connection to retrive dependencies through maven
• Java 1.8
• Apache maven 3+
• Redis (caching)

I.1. Installing Redis

The evaluation programme uses a Redis cache server to minimise redundent network activity and to allow resuming the annotation in case of network failure. You need to install redis on you machine:

• On macOS, you can use home-brew to install redis.

  1. First install home-brew if you don't already have it. Open a terminal and run:

     $ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

  2. Install redis:

     $ brew install redis

  3. Run redis by opening a terminal and typing:

     $ redis-server

  Redis will run in the foreground, please leave the window open, unless you want to close redis. You can interrupt the execution with Ctrl + C. Redis will create a database file named dump.rdb, you may delete the file after you have finished with the reprodction. Please use Redis's default port: 6379.

• On Linux:

  • Debian or Ubuntu:

    https://www.digitalocean.com/community/tutorials/how-to-install-and-use-redis

  • Fedora/CentOs:

    http://blog.andolasoft.com/2013/07/how-to-install-and-configure-redis-server-on-centosfedora-server.html

  • ArchLinux:

    https://wiki.archlinux.org/index.php/Redis

  • On other distributions, the instructions are similar to the Debian or Fedora instructions, except for the installation of the dependencies: make sure you have build tools installed (gcc toolchain with automake/autoheader) as well as tcl.

• On Windows:

  • You can use a native Windows fork of redis like so: https://github.com/ServiceStack/redis-windows#running-microsofts-native-port-of-redis
  • Or start the native unix redis using vagrant like so: https://github.com/ServiceStack/redis-windows#running-the-latest-version-of-redis-with-vagrant

II. Development

This is maven project. I recommend that we all use IntelliJ IDEA as an IDE, there is a free community edition (https://www.jetbrains.com/idea/download).

II.1. Building

$ mvn install 

II.2. Creating runnable jar

$ mvn assembly:assembly

III. Resources

• Ontolex specification:
  • Core: https://www.w3.org/community/ontolex/wiki/Final_Model_Specification#Core
  • Vartrans: https://www.w3.org/community/ontolex/wiki/Final_Model_Specification#Variation_.26_Translation_.28vartrans.29
• NIF Specification: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core/nif-core.html
• NIF Paper with examples [Page 8]: http://svn.aksw.org/papers/2013/ISWC_NIF/public.pdf
• UMLS Format Documentation: https://www.ncbi.nlm.nih.gov/books/NBK9685/
• Quaero Corpus for Evaluation: https://quaerofrenchmed.limsi.fr
• Very comprehensive slides about UMLS: https://www.nlm.nih.gov/research/umls/pdf/UMLS_Basics.pdf
• Mapping between a relational database and RDF: http://d2rq.org/d2rq-language The R2RQ Language.