Transcript The Johns Hopkins University - American University of Beirut

Retrieving Information:
Using Entrez
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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.
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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.
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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
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Central Dogma: NCBI version
DNA
RNA
Write a paper
about it
protein
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Entrez: Pathway to Discovery
Term frequency
statistics
1993
Literature
citations in
sequence
databases
MEDLINE
abstracts
Nucleotide
sequences
Nucleotide
sequence
similarity
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Literature
citations in
sequence
databases
Protein
sequences
Coding region
features
Amino acid
sequence similarity
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Type in your last name and find a paper
form one of your teammates
Related Articles
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Hard link DNA to protein
L12345
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From Fig 1 of
Entrez search and retrieval system
Jim Ostell
Chapter 14, the NCBI Handbook.
2003
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Ctrl-F
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Getting started in Entrez
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“ouellette bf” [au] AND yeast
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MeSH: Medical Subject Heading
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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
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hieter p [au]
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Limit in Time: 1993-01-01 1993-12-31
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No abstract
With abstract
Full Text on-line
Full Text in PubMed Central
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boguski m [au]
99
boguski ms [au]
80
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#24 NOT #23
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Other types of links in Entrez
• Next slides to explore other kind of
things linked into Entrez records.
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“hieter p” [au] cdc16p
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“Books”
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(2)
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Link to Genome
View of Chromosome I
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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.
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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
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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
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RefSeq Accession Number Space
NC_123456
Genomic
Complete genomic molecules
including genomes, chromosomes,
organelles, plasmids.
NG_123456
Genomic
Incomplete genomic region; supplied
to support the NCBI Genome
Annotation pipeline.
NM_123456
mRNA
NR_123456
RNA
NP_123456
Protein
NP_12345678 Protein
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Non-coding transcripts including
structural RNAs, transcribed
pseudogenes, and others
Planned expansion of accession
series
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Automated Assemblies
NT_123456
Genomic
Intermediate genomic assemblies of BAC
sequence data
NW_123456
Genomic
Intermediate genomic assemblies of Whole
Genome Shotgun sequence data
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Model RefSeq records
XM_123456
mRNA
model mRNA provided by the Genome
Annotation process; sequence
corresponds to the genomic contig.
XR_123456
RNA
model non-coding transcripts provided
by the Genome Annotation process;
sequence corresponds to the genomic
contig.
XP_123456
Protein
model proteins provided by the Genome
Annotation process; sequence
corresponds to the genomic contig.
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WGS special case
NZ_ABCD123
45678
Genomic
A collection of whole genome shotgun
sequence data for a project. Accessions
are not tracked between releases. The
first four characters following the
underscore (e.g. 'ABCD') identifies a
genome project.
ZP_12345678
Protein
Proteins annotated on NZ_ accessions
(often via computational methods).
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Download all the data
Entrez and RefSeq
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Locus Link
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Things to watch out for:
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