BioC Experimental Molecular Interaction Detection

BioCreative V - BioC Track (I) - Task 6 Implementation

• The code is under source directory.
• Target experimental methods from PSI-MI ontology are in methods file.
• The main class is com.ferhtaydn.biocemid.Main. You may need to modify annotation and evaluation configurations in order to obtain your desired operation.
• All the resources related to word2vecs, raw and annotated articles are located under files directory.
• The published data set, consists of 30 articles, is located in published dataset directory.

The versions of the libraries which are used:

• Java Version: 1.8.0_91
• Scala Version: 2.11.8
• Sbt Version: 0.13.11
• Scala Xml Version: 1.0.5
• Typesafe Config Version: 1.3.0
• Stanford CoreNLP Version: 3.6.0
• BioC_Java Version: 1.0.1
• Word2vec Version: Revision 42

• Working environment:

  • MacBook Pro (Early 2015)
  • OS X El Capitan Version 10.11.4
  • 2.7 GHz Intel Core i5
  • 8 GB 1867 MHz DDR3
  • 128 GB Flash Storage

• Word2vec is run on a cluster machine which has:

  • Ubuntu 14.04.4 LTS
  • Kernel: 3.19.0-43-generic
  • GCC: version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1)
  • Ram: 64GB
  • CPU:
    • Intel(R) Xeon(R) CPU E5410 @ 2.33GHz
    • Architecture: x86_64
    • CPU op-mode(s): 32-bit, 64-bit
    • Byte Order: Little Endian
    • CPU(s): 8
    • On-line CPU(s) list: 0-7
    • Thread(s) per core: 1
    • Core(s) per socket: 4
    • Socket(s): 2
    • NUMA node(s): 1
    • Vendor ID: GenuineIntel
    • CPU family: 6
    • Model: 23
    • Stepping: 6
    • CPU MHz: 2327.326
    • BogoMIPS: 4655.07
    • Virtualization: VT-x
    • L1d cache: 32K
    • L1i cache: 32K
    • L2 cache: 6144K
    • NUMA node0 CPU(s): 0-7