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Retrieving Information: Using Entrez

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: Using Entrez

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  1. Retrieving Information: Using Entrez

  2. 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.

  3. 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.

  4. 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

  5. Central Dogma: NCBI version DNA RNA Write a paper about it protein

  6. 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

  7. Related Articles Type in your last name and find a paper form one of your teammates

  8. Hard link DNA to protein L12345

  9. From Fig 1 ofEntrez search and retrieval system Jim Ostell Chapter 14, the NCBI Handbook. 2003

  10. Ctrl-F

  11. Getting started in Entrez

  12. “ouellette bf” [au] AND yeast

  13. MeSH: Medical Subject Heading

  14. 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

  15. hieter p [au]

  16. Limit in Time: 1993-01-01 1993-12-31

  17. No abstract With abstract Full Text on-line Full Text in PubMed Central

  18. boguski m [au] 99 boguski ms [au] 80

  19. #24 NOT #23 19

  20. Other types of links in Entrez • Next slides to explore other kind of things linked into Entrez records.

  21. “hieter p” [au] cdc16p

  22. “Books”

  23. (2)

  24. Link to Genome View of Chromosome I

  25. 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.

  26. 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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