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README.md

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