医学公开数据库查询与登记

references/sra.md

Overview

Sequencing run metadata: experiments, samples, studies, and runs. Accessible via E-utilities with db=sra. Returns XML metadata describing sequencing experiments, platforms, library strategies, and sample attributes.

Base URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

Authentication

• API key (recommended): Append &api_key=YOUR_KEY.
• Without key: 3 req/sec. With key: 10 req/sec.
• Provide tool and email parameters.

Key Endpoints

1. ESearch -- Search SRA records

GET esearch.fcgi?db=sra&term=QUERY&retmax=N&retmode=json

Example -- search RNA-seq experiments in human:

GET esearch.fcgi?db=sra&term=RNA-seq[Strategy] AND Homo sapiens[Organism]&retmax=5&retmode=json

Response:

{
  "esearchresult": {
    "count": "584231",
    "retmax": "5",
    "idlist": ["28574913", "28574912", "28574911", ...]
  }
}

Example -- search by accession:

GET esearch.fcgi?db=sra&term=SRP123456[Accession] OR SRR123456[Accession]&retmode=json

2. EFetch -- Retrieve full SRA metadata (XML only)

GET efetch.fcgi?db=sra&id=IDS&rettype=full&retmode=xml

Example -- fetch metadata for an SRA record:

GET efetch.fcgi?db=sra&id=28574913&rettype=full&retmode=xml

Response (abbreviated XML):

<EXPERIMENT_PACKAGE_SET>
  <EXPERIMENT_PACKAGE>
    <EXPERIMENT accession="SRX12345" alias="...">
      <TITLE>RNA-seq of human liver tissue</TITLE>
      <STUDY_REF accession="SRP12345"/>
      <DESIGN>
        <LIBRARY_DESCRIPTOR>
          <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
          <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
          <LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION>
          <LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT>
        </LIBRARY_DESCRIPTOR>
      </DESIGN>
      <PLATFORM>
        <ILLUMINA><INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL></ILLUMINA>
      </PLATFORM>
    </EXPERIMENT>
    <SUBMISSION accession="SRA12345" center_name="GEO"/>
    <Organization><Name>Some Institute</Name></Organization>
    <STUDY accession="SRP12345">
      <DESCRIPTOR>
        <STUDY_TITLE>Transcriptomic analysis of human tissues</STUDY_TITLE>
        <STUDY_TYPE existing_study_type="Transcriptome Analysis"/>
      </DESCRIPTOR>
    </STUDY>
    <SAMPLE accession="SRS12345">
      <TITLE>Human liver RNA</TITLE>
      <SAMPLE_ATTRIBUTES>
        <SAMPLE_ATTRIBUTE><TAG>tissue</TAG><VALUE>liver</VALUE></SAMPLE_ATTRIBUTE>
        <SAMPLE_ATTRIBUTE><TAG>cell_type</TAG><VALUE>hepatocyte</VALUE></SAMPLE_ATTRIBUTE>
      </SAMPLE_ATTRIBUTES>
    </SAMPLE>
    <RUN_SET>
      <RUN accession="SRR12345" total_spots="45000000" total_bases="9000000000">
        <Statistics nreads="2">
          <Read average="150" count="45000000"/>
        </Statistics>
      </RUN>
    </RUN_SET>
  </EXPERIMENT_PACKAGE>
</EXPERIMENT_PACKAGE_SET>

3. ESummary -- Brief SRA summaries

GET esummary.fcgi?db=sra&id=IDS&retmode=json

Returns: experiment title, platform, total runs/spots/bases, create date, study/sample accessions as an XML string in the expxml and runs fields.

4. ELink -- Cross-link to other NCBI databases

GET elink.fcgi?dbfrom=sra&db=biosample&id=SRA_UID
GET elink.fcgi?dbfrom=sra&db=gds&id=SRA_UID

SRA Accession Types

Prefix	Entity
SRP / ERP / DRP	Study
SRX / ERX / DRX	Experiment
SRS / ERS / DRS	Sample
SRR / ERR / DRR	Run
SRA	Submission

Common Search Patterns

# By organism and strategy
term=Mus musculus[Organism] AND WGS[Strategy]

# By platform
term=Illumina[Platform] AND ATAC-seq[Strategy] AND human[Organism]

# By study accession
term=SRP123456[Accession]

# By BioProject
term=PRJNA123456[BioProject]

# By date range
term=("2024/01/01"[Publication Date] : "2024/12/31"[Publication Date])

# By library source
term=GENOMIC[Source] AND ChIP-Seq[Strategy] AND cancer[Text Word]

# By read count range
# Download run metadata, then filter the reported read_count field locally.
# Read length and number of reads are different quantities.

# Combined complex query
term=(RNA-Seq[Strategy] AND paired[Layout] AND Homo sapiens[Organism] AND Illumina[Platform])

Rate Limits

• Without API key: 3 requests/second
• With API key: 10 requests/second
• For bulk metadata: use usehistory=y with WebEnv/query_key, fetch in batches
• Actual sequence data (FASTQ) is NOT available via E-utilities; use SRA Toolkit (fastq-dump/fasterq-dump) or the SRA cloud URLs