Entrez Programming Utilities简介¶

NCBI的数据接口，包含了38个数据库，涵盖各种生物医学数据，包括核苷酸和蛋白质序列、基因记录、三维分子结构和生物医学文献。

base URL¶

所有接口都以 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/为base URL

支持数据库¶

Entrez Database	UID common name	E-utility Database Name
BioProject	BioProject ID	bioproject
BioSample	BioSample ID	biosample
Books	Book ID	books
Conserved Domains	PSSM-ID	cdd
dbGaP	dbGaP ID	gap
dbVar	dbVar ID	dbvar
Gene	Gene ID	gene
Genome	Genome ID	genome
GEO Datasets	GDS ID	gds
GEO Profiles	GEO ID	geoprofiles
HomoloGene	HomoloGene ID	homologene
MeSH	MeSH ID	mesh
NCBI C++ Toolkit	Toolkit ID	toolkit
NLM Catalog	NLM Catalog ID	nlmcatalog
Nucleotide	GI number	nuccore
PopSet	PopSet ID	popset
Probe	Probe ID	probe
Protein	GI number	protein
Protein Clusters	Protein Cluster ID	proteinclusters
PubChem BioAssay	AID	pcassay
PubChem Compound	CID	pccompound
PubChem Substance	SID	pcsubstance
PubMed	PMID	pubmed
PubMed Central	PMCID	pmc
SNP	rs number	snp
SRA	SRA ID	sra
Structure	MMDB-ID	structure
Taxonomy	TaxID	taxonomy

支持的方法¶

EInfo (database statistics) eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
ESearch (text searches) eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
EPost (UID uploads) eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi
ESummary (document summary downloads) eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi
EFetch (data record downloads) eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
ELink (Entrez links) eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi
EGQuery (global query) eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi
ESpell (spelling suggestions) eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi
ECitMatch (batch citation searching in PubMed) eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi

使用案例¶

#1、利用esearch检索query_term,返回Web environment (WebEnv) 和 query key (query_key) 
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={query_term}&usehistory=y&retmode=json&api_key={api_key}

#2、利用efetch下载检索结果(全面，但是慢)
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&rettype=exp&WebEnv={WebEnv}&query_key={querykey}&retmode=xml&api_key={API_KEY}

也可以用esummary接口
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=sra&WebEnv={WebEnv}&query_key={querykey}&retmode=xml&api_key={API_KEY}

Note

也可以使用非官方接口，可能效率更高，但是稳定性较差！

参考资料¶

https://www.ncbi.nlm.nih.gov/books/NBK25499

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Authors: Wind