romanegloo

"Is Hirschsprung disease a mendelian or a multifactorial disorder?" 
"List signaling molecules (ligands) that interact with the receptor EGFR?" 
"Is the protein Papilin secreted?" 
"Are long non coding RNAs spliced?" 
"Is RANKL secreted from the cells?" 
"Does metformin interfere thyroxine absorption?" 
"Which miRNAs could be used as potential biomarkers for epithelial ovarian cancer?" 
"Which acetylcholinesterase inhibitors are used for treatment of myasthenia gravis?" 
"Has Denosumab (Prolia) been approved by FDA?" 
"List the human genes encoding for the dishevelled proteins?" 

romanegloo

Lab 03

Schedule

• Project 1 is due by Feb 8
• Lab2 submission is due Tonight

Tips for Lab 03

How to print a float number with a fixed precision

ex) 41.4451 to 41.45

romanegloo

Lab04

Objectives

• read input temperatures by day
• write summarization in an output file

from tempin.txt

01/24/2019 5 22 27 31 26 19
01/25/2019 8 20 25 30 35 40 38 32 29

romanegloo

Lab 05

Lab 05 instruction

Easiest so far!!!

Checklist

• menu option is single char
• use do-while for the menu loop

romanegloo

Lab 07

Lab 07 instruction

Review

struct definition

struct type_name {
 int var1, var2;

romanegloo

Lab 08

instruction note (lab8)

Lab 9 is canceled (lab 8 is extended by a week)

Reviews

1. include contact.h from contactList.h. Use double quotation marks
2. #pragma once tells the compiler to include the source code only once

romanegloo

import csv
import sqlite3

eval_file = "data/eval/MayoSRS_mesh.csv"
db_file = "data/pubtator/pubtator-20190725-6496be10.db"

words = []
with open(eval_file) as f:
    csv_reader = csv.DictReader(f)
    for row in csv_reader:

romanegloo

#!/usr/bin/env python3
"""Preprocess PubTator corpus and ScopeNotes of MeSH descriptors for language
model training (LmBMET).

1) Given the original PubTator biocepts annotated documents, this interpolates
the concept codes into document texts. Before that, this will count word
frequencies and generate vocabulary which will include the entire set of
bioconcepts (MeSH in particular). In case that a pre-trained embeddings file
(.vec) is provided, we obtain a vocabulary from the embeddings.

romanegloo

#!/usr/bin/env python3
"""
Parse PubTator raw data file, and creates ElasticSearch index, and populate the
corpus (index: 'pubtator')

You can download PubTator dataset from the following link:
    ftp://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator/bioconcepts2pubtator_offsets.gz
Place the file in 'data/' and run this code. Don't need to decompress the file.

We assume that ElasticSearch is properly installed and accessible via its API

romanegloo

#!/usr/bin/env python3
# pylint: disable=invalid-name
"""Reads UMNSRS datasets where CUIs are used, add corresponding MeSHes to the
CUIs"""

from pathlib import Path
import csv
from tqdm import tqdm
from BMET.uts_api_client import UtsClient