a basic cirq setup

Update 20200116_efo_analysis.py

mdoel3

implement model2 in pymc3, and add initial model3 impl (model3 is still WIP)

new csript for efo analysis and refact tidy efo

add plots to titdy efo script

script to make EFO dataset tidy!

a new notebook to generate tidy datasets from EFO kickoff datasets

move efo notebooks to its own project

fix efo file naming and cleanups

preproessed dataset

fix file name

fix file names

rename efo datasets and add a date tag

finally! PubMed dataset v2 is ready!

added a function to cleanup columns for suffixed hits

update efo scripts and add a new cleanup script

import efo/pubmed script

fix how headers is made for imcomplete data file

comment

add efo ontology v1 in owl format

cleanup

add new pubmed csv generator (v2) that supports several queries

a query builder and a smart code to fetch only unfetched queries from pubmed

query all rdfs:labels for efo, and generate a csv with pubmed results

a new script to query concepts and tasks from EFO ontology and then count pubmed papers for the combinations

add git lfs to handle data files

script to fetch publications for tasks and concepts of cognitive atlas

improve pubmed codes and refactor it as a function

script to fetch virtually unlimited abstracts without NCBI limitations