pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms

Table 1 Disease enrichment analysis of the genes assigned to the MHs before and after addition of MH-gene pairs from SCR and non-MeSH groups

OMIM diseases¹		MH-gene pairs (MH group / all)²	Enriched UMLS diseases with DOSE			P value (MH group / all)⁴
MH ID	MH description	MH-gene pairs (MH group / all)²	UMLS ID	UMLS description	MH ID³	P value (MH group / all)⁴
D057130	Leber Congenital Amaurosis	17/22	C0339527	Leber Congenital Amaurosis	D057130	3.43E-33 / 1.45E-42
D020754	Spinocerebellar Ataxias	23/28	C0087012	Ataxia, Spinocerebellar	D020754	1.93E-30 / 2.84E-38
D052177	Kidney Diseases, Cystic	19/25	C1691228	Cystic Kidney Diseases	D052177	8.05E-19 / 2.37E-20
D010009	Osteochondrodysplasias	14/64	C0029422	Osteochondrodysplasias	D010009	8.87E-19 / 6.57E-35
D002925	Ciliary Motility Disorders	26/31	C0008780	Ciliary Motility Disorders	D002925	1.60E-23 / 3.90E-33
D015419	Spastic Paraplegia, Hereditary	28/36	C0037773	Spastic Paraplegia, Hereditary	D015419	1.22E-37 / 2.71E-45
D007938	Leukemia	18/51	C0085669	Acute leukemia	D007938	3.26E-10 / 6.63E-26

¹ The OMIM diseases were collected from the database disease-connect (34) with at least five MH-gene pairs outside the MH group.
² (Number of MH-gene pairs in MH group) / (number of MH-gene pairs in all the three groups including MH, SCR and non-MeSH group).
³ The MH ID was mapped from the UMLS ID by pyMeSHSim.
⁴ (The enrichment P value of genes in MH group) / (The enrichment P value of genes in all the three groups).

ISSN: 1471-2105