南瓜-py 0.0.2

PumpkinPy - 在Python中实现的语义相似度

关于

PumpkinPy使用IC有序位图进行快速排名基因和疾病（表型按频率降序排序并使用one-hot编码）。这对于更大的本体，如Upheno，以及大型数据集，如给定一组输入HPO术语的所有小鼠基因的排名，非常有用。这种方法最初在OWLTools和OwlSim-v3中使用。

该项目目标是构建PhenoDigm算法的Python实现。还包括距离和相似度（欧几里得、余弦、Jin-Conrath、Resnik、Jaccard）的常用度量实现

免责声明：这是一个副项目，需要更多的文档和测试

入门指南

安装pyroaring需要Python 3.8+和python3-dev

从PyPI安装

pip install pumpkin_py

本地构建

要本地构建，首先安装poetry-

https://poetry.pythonlang.cn/docs/#installation

然后运行make

make

用法

获取实现的相似度度量列表

from pumpkin_py import get_methods
get_methods()
['jaccard', 'cosine', 'phenodigm', 'symmetric_phenodigm', 'resnik', 'symmetric_resnik', 'ic_cosine', 'sim_gic']

加载闭包和注释

import gzip
from pathlib import Path

from pumpkin_py import build_ic_graph_from_closures, flat_to_annotations, search

closures = Path('.') / 'data' / 'hpo' / 'hp-closures.tsv.gz'
annotations = Path('.') / 'data' / 'hpo' / 'phenotype-annotations.tsv.gz'

root = "HP:0000118"

with gzip.open(annotations, 'rt') as annot_file:
    annot_map = flat_to_annotations(annot_file)

with gzip.open(closures, 'rt') as closure_file:
    graph = build_ic_graph_from_closures(closure_file, root, annot_map)

根据表型配置文件搜索最佳匹配的疾病

import pprint
from pumpkin_py import search

profile_a = (
    "HP:0000403,HP:0000518,HP:0000565,HP:0000767,"
    "HP:0000872,HP:0001257,HP:0001263,HP:0001290,"
    "HP:0001629,HP:0002019,HP:0002072".split(',')
)

search_results = search(profile_a, annot_map, graph, 'phenodigm')

pprint.pprint(search_results.results[0:5])

[SimMatch(id='ORPHA:94125', rank=1, score=72.67599348696685),
 SimMatch(id='ORPHA:79137', rank=2, score=71.57368233248252),
 SimMatch(id='OMIM:619352', rank=3, score=70.98305459477629),
 SimMatch(id='OMIM:618624', rank=4, score=70.94596234638497),
 SimMatch(id='OMIM:617106', rank=5, score=70.83097366257857)]

获取Monarch注释和闭包的示例脚本

使用robot和sparql生成闭包和类标签

注释数据来自最新的Monarch版本

• 需要>Java 8

cd data/monarch/ && make

PhenoDigm参考： https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3649640/
Exomiser: https://github.com/exomiser/Exomiser
OWLTools: https://github.com/owlcollab/owltools
OWLSim-v3: https://github.com/monarch-initiative/owlsim-v3