1. Install the following projects

cogutil atomspace ure miner pln agi-bio

from the OpenCog github organization

https://github.com/opencog

To do that, for projects cogutil, atomspace, ure, miner, pln and agi-bio use the master branches of the opencog repositories. That is type the following:

git clone https://github.com/opencog/<PROJECT>.git
cd <PROJECT>
mkdir build
cd build
cmake ..
make -j4
sudo make install
sudo ldconfig /usr/local/lib/opencog

Download and unpack the datasets. From the root folder of that project, type the following

cd kbs
wget https://mozi.ai/datasets/gene-level-dataset.tar.gz
tar xvzf gene-level-dataset.tar.gz
cd ..

guile --no-auto-compile -l mine-bio-as.scm

should output a scheme file

results/miner-bio-as-results-<PARAMETERS>.scm

containing mined patterns.

guile --no-auto-compile -l pattern-to-relationship.scm

loads a file containing mined pattern (see previous step), and produces a file

results/subset-links.scm

containing inheritance relationships gotten by applying PLN to surprising patterns.

guile --no-auto-compile -l preprocess-kbs.scm

which should create

results/preprocess-kbs-<PARAMETERS>.scm

guile --no-auto-compile -l intensional-reasoning-test.scm

which should create

results/intentional-reasoning-test-<PARAMETERS>.scm

guile --no-auto-compile -l simple-pln-inference.scm

which should create

results/simple-pln-inference-<PARAMETERS>.scm

Warning: not working yet

guile --no-auto-compile -l 2015-pln-inference.scm

https://docs.google.com/document/d/16zfY7OZtHO66mfujLdZ0-3VALXUTvxeeo4dW2ASBiNs/edit

https://gitlab.com/opencog-bio/pln_mozi