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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

RNA

protein

DNA

Write a paper about it

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Entrez: Pathway to Discovery

Amino acid sequence similarityCoding region

features

Nucleotide sequence similarity

Term frequency statistics

Literature citations in sequence databases

Literature citations in sequence databases

MEDLINE abstracts

Nucleotide sequences

Protein sequences

1993

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Related Articles

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

teammates

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Hard link DNA to proteinL12345

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From Fig 1 ofEntrez search and retrieval systemJim OstellChapter 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 19

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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 Non-coding transcripts including structural RNAs, transcribed pseudogenes, and others

NP_123456 Protein

NP_12345678 Protein 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_ABCD12345678

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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