GOSemSim

GOSemSim：GO-terms Semantic Similarity Measures

 

Installation

Install GOSemSim is easy, follow the guide in the Bioconductor page:

## try http:// if https:// URLs are not supportedsource("https://bioconductor.org/biocLite.R")## biocLite("BiocUpgrade") ## you may need thisbiocLite("GOSemSim")

 

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GO ID

找到 Gene Ontology (GO)勾选下面几个选项 

 

然后获得所有酵母蛋白的Gene ontology数据

 提取Gene Ontology ID

1. # -*- coding: utf-8 -*-
2. """
3. Created on Fri Oct 28 19:04:38 2016
5. @author: sun
6. """
7. import pandas as pd
8. import re
10. yeast=pd.read_csv('yeast.csv')
11. #Gene ontology (biological process)
12. #Gene ontology (molecular function)
13. #Gene ontology (cellular component)
15. bp=yeast['Gene ontology (biological process)']
16. bp=bp.fillna(value='')
17. for i in range(len(bp)):
18. temp=re.findall(r"GO:\d{7}",bp[i])
19. bp[i]=';'.join(temp)
21. mf=yeast['Gene ontology (molecular function)']
22. mf=mf.fillna(value='')
23. for i in range(len(mf)):
24. temp=re.findall(r"GO:\d{7}",mf[i])
25. mf[i]=';'.join(temp)
27. cc=yeast['Gene ontology (cellular component)']
28. cc=cc.fillna(value='')
29. for i in range(len(cc)):
30. temp=re.findall(r"GO:\d{7}",cc[i])
31. cc[i]=';'.join(temp)
33. yeast['Gene ontology (biological process)']=bp
34. yeast['Gene ontology (molecular function)']=mf
35. yeast['Gene ontology (cellular component)']=cc
36. yeast.to_csv('go.csv',index=False,columns =['Entry',
37. 'Gene ontology (cellular component)',
38. 'Gene ontology (molecular function)',
39. 'Gene ontology (biological process)'])

 

获得Gene ontology

 

获取gold_yeast的Gene ontology

yeast_gold_protein_pair.csv

 

1. yeast=pd.read_csv('yeast_gold_protein_pair.csv')
2. go=pd.read_csv('go.csv',index_col=0)
4. protein_a=go.loc[yeast.idA,:]
5. protein_b=go.loc[yeast.idB,:]
7. protein_a.to_csv('GOProteinA.csv')
8. protein_b.to_csv('GOProteinB.csv')

GOProteinA.csv

GOProteinB.csv