MeSH Tree Data

import json
from collections import Counter

MeSH Tree

This MeSH tree data is available at National Library of Medicine (NLM) website. MeSH descriptors are organized in 16 categories: category A for anatomic terms, category B for organisms, C for diseases, D for drugs and chemicals, etc. Each category is further divided into subcategories. Within each subcategory, descriptors are arrayed hierarchically from most general to most specific in up to thirteen hierarchical levels. Because of the branching structure of the hierarchies, these lists are sometimes referred to as "trees". Each MeSH descriptor appears in at least one place in the trees, and may appear in as many additional places as may be appropriate. Those who use MeSH should find the most specific MeSH descriptor that is available to represent each concept of interest.Source

• View CVD MeSH Tree Online

meshtree_file = "./input/mtrees2020.bin" 

Tree = []
id2name = {}
name2id = {}
with open(meshtree_file, "r") as ftree:
    for line in ftree:
        term_tree = line.strip().split(";")
        cur_term = term_tree[0]
        cur_tree = term_tree[1]

        id2name.update({cur_tree:cur_term})                        
        name2id.update({cur_term:cur_tree})
        Tree.append({'id':cur_tree ,'name':cur_term})

CVDTree = []
for name,ID in name2id.items():
    if ID[0:3] == 'C14':
            CVDTree.append({"name": name, "ID":ID})

len(list(CVDTree))

204

CVD = pd.DataFrame(CVDTree)
CVD = CVD.set_index('name')
CVD = CVD.sort_values("ID",ascending =True)

CVD.head(50)

CVD.to_csv("cvd.csv")

View CVD MeSH Tree Online