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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:

  • 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