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Retrieving Information: Using Entrez. Retrieving information: how it works:. Servers have the records you want You need to understand the data they have, and how it is organized There are often many ways to get to an answer.

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retrieving information how it works
Retrieving information: how it works:
  • Servers have the records you want
  • You need to understand the data they have, and how it is organized
  • There are often many ways to get to an answer.
  • Route to get there is not always obvious, but you need to think of alternatives and traps.
  • Use some query language – each system has its own.
  • Retrieve data in a specified format.
  • Save it in a way that will be useful to you.
what you may be looking for
What you may be looking for:
  • Did a BLAST search – and you need more info about some of the proteins they found similarities to.
  • Heard on about a disease gene that was recently discovered, and you want to know more about it.
  • Want to build a dataset for local blast searches.
  • A colleague wants you to do an alignment of all sequences from a given protein family.
what you are looking for
What you are looking for:
  • PubMed paper from author X
  • Sequence from gene X in organism Y
  • All information about organelle W in model organism Y
  • All information about disease X in human
  • Orthologs of that disease genes in other model organisms
central dogma ncbi version
Central Dogma: NCBI version

DNA

RNA

Write a paper

about it

protein

entrez pathway to discovery
Entrez: Pathway to Discovery

Term frequency statistics

1993

MEDLINE abstracts

Literature citations in sequence databases

Literature citations in sequence databases

Protein sequences

Nucleotide sequences

Nucleotide sequence similarity

Amino acid sequence similarity

Coding region features

slide7

Related Articles

Type in your last name and find a paper form one of your teammates

slide9

From Fig 1 ofEntrez search and retrieval system

Jim Ostell

Chapter 14, the NCBI Handbook.

2003

a query
A query
  • Word <free text> : too many hits
    • More words (the Boolean ‘AND’ is the default)
    • Limit query to specified field
    • Limit query in time
    • Do Boolean on queries
      • #1 AND #2
      • #3 NOT #5
      • #7 OR #8
slide25

No abstract

With abstract

Full Text on-line

Full Text in PubMed Central

slide26

boguski m [au] 99

boguski ms [au] 80

other types of links in entrez
Other types of links in Entrez
  • Next slides to explore other kind of things linked into Entrez records.
refseq
RefSeq
  • RefSeq represents the NCBI curated “reference sequences” for all ‘worked’ genome.
  • Historically, these used to be referred to as “GenBank-Gold”.
  • RefSeq are either genomic, mRNA or protein sequences.
  • Not all sequences are in RefSeq
  • All RefSeq sequences are assembled/taken from things in GenBank.
some of the features of the refseq
Some of the features of the RefSeq:
  •  non-redundancy  
  • explicitly linked nucleotide and protein sequences  
  • updates to reflect current knowledge of sequence data and biology  
  • data validation and format consistency  
  • distinct accession series  
  • ongoing curation by NCBI staff and collaborators, with review status indicated on each record
accession number space
Accession number space
  • GenBank:
    • 1+5 (L12345, U00001)
    • 2+6 (AF000001, AC000003)
    • 4+2+6 (WGS)
      • All have accession.version
  • Protein:
    • 1+5 (SwissProt/UniProt)
    • 3+5 (GenPept)
      • All have accession.version
  • RefSeq:
    • N*_12345
slide56

Download all the data

Entrez and RefSeq