1. Lecture 1: Introduction to Entrez October 16-19, 2007 NCBI PowerScripting

2. The Entrez Query System at NCBI

4. Entrez Help Document

5. Search one or all of 31 databases. Generate brief “document summaries” for a list of records. Link from one list of records to another. Perform boolean operations on lists of records. Format records for display and download. Entrez Functions

6. Genomes Taxonomy PubMed abstracts Nucleotide sequences Protein sequences 3-D Structure 3 -D Structures Word weight VAST BLAST Phylogeny Computational Links Between and Within Nodes

7. Each record in an Entrez database is assigned an integer called a UID, or “unique identifier”. Entrez transactions are performed on lists of UIDs. Transactions include boolean operations and the tracking of links within and between database records. Entrez Transactions

8. Entrez supports text searches with field restrictions, boolean operators (sometimes implicit), and term grouping Field restrictions vary among the databases Term-mapping happens Explicitly fielded searches are not term- mapped Quoted phrases are searched as a unit Entrez Database Queries

9. Untagged terms that are entered in the search box are matched (in this order) against: - a MeSH (Medical Subject Headings) translation table - a Journals translation table - the Full Author translation table - Author index - the Full Investigator (Collaborator) translation table - and an Investigator (Collaborator) index Term Mapping (PubMed)

10. PubMed : "chronic obstructive pulmonary disease"[Text Word] OR "pulmonary disease, chronic obstructive"[MeSH Terms] OR ("common cold"[TIAB] NOT Medline[SB]) OR "common cold"[MeSH Terms] OR "cold"[MeSH Terms] OR cold[Text Word] PMC : "pulmonary disease, chronic obstructive"[MeSH Terms] OR "common cold"[MeSH Terms] OR "cold"[MeSH Terms] OR cold[Text Word] Nucleotide : cold[All Fields] Taxonomy : cold[All Names] Term: cold

11. PubMed : ("mice"[TIAB] NOT Medline[SB]) OR "mice"[MeSH Terms] OR mouse[Text Word] PMC : "mice"[MeSH Terms] OR mouse[Text Word] Nucleotide : "Mus musculus"[Organism] OR mouse[All Fields] Taxonomy : mouse[All Names] Genome : "Mus musculus"[Organism] OR mouse[All Fields] Term: mouse

12. Entrez Help Document

14. Viewing Indexed Terms on the Web Preview-Index Tab

15. miller baker: miller[All Fields] AND baker[All Fields] miller j baker m: miller j[Author] AND baker m[Author] AF123456, P12243,555 : direct retrieval of record PubMed, PMC, Nucleotide, Protein, Structure and others All Databases Patterns are Recognized

16. Separate search history is maintained for each database. Previous searches can be recalled and combined using a query key and a cookie, called a “WebEnv”. Available on the Web under the 'History Tab' Search History

17. Brief summaries of database records are generated quickly on frontend servers. Full records are retrieved from backend machines. DocSums

18. Overview of Key Entrez Databases

20. The Entrez Bubblegram: via einfo.fcgi

21. Key Field Restrictions – [author] – [title] – [pdat] – publication date – [mesh] Medical Subject Headings – [journal] – [volume] Pubmed 17,454,100 Records biomedical literature citations and abstracts

22. CoreNucleotide 41,888,768 Records sequence database (GenBank) Key Field Restrictions – [organism] – [accession] – [author] – [title] – [sequence length] – [properties] – [gene]

23. Protein 18,192,257 Records Protein sequence records Key Field Restrictions – [organism] – [title] – [author] – [molecular weight] – [sequence length] – [gene] – [ecno] enzyme commission number

24. Gene 3,723,441 Records Gene database: locus-centered records Key Field Restrictions – [organism] – [gene] official symbol of gene locus – [chromosome] – [title] – [accession]

25. A set of eight server-side programs. Support a uniform URL syntax. Translate a standard set of URL-encoded input parameters for the array of programs comprising the Entrez system. Eutilities

26. Searches: esearch.fcgi DocSums: esummary.fcgi Links: elink.fcgi Uploads: epost.fcgi Downloads: efetch.fcgi Global Query: egquery.fcgi Spelling: espell.fcgi Information: einfo.fcgi Entrez Functions and EUtils

27. A Docsum via esummary.fcgi and via the Web

28. A Simple Eutilities Pipeline

31. An Esearch Followed by Multiple Rounds of Efetch http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?usehistory=y&db=gene&term=mammalia[orgn] Elapsed time: 0 seconds 0%, 0 records of 161815 retrieved. Tue Jan 25 20:46:32 EST 2005 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=datahog&db=gene&retmax=500&retstart=0&rettype=native&WebEnv=0ImHxGDH2z I93UMwxrTRTh-nretlso4ZBZO_FNE7AFZXOOxNd9Rz@Qfb2dYIOFhUAABd9ei4&query_key=1&retmode=xmlElapsed time: 40 seconds 0.3%, 500 records of 161815 retrieved. Tue Jan 25 20:47:09 EST 2005 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=datahog&db=gene&retmax=500&retstart=500&rettype=native&WebEnv=0ImHxGDH 2zI93UMwxrTRTh-nretlso4ZBZO_FNE7AFZXOOxNd9Rz@Qfb2dYIOFhUAABd9ei4&query_key=1&retmode=xmlElapsed time: 79 seconds 0.61%, 1000 records of 161815 retrieved. Tue Jan 25 20:47:48 EST 2005 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=datahog&db=gene&retmax=500&retstart=1000&rettype=native&WebEnv=0ImHxGD H2zI93UMwxrTRTh-nretlso4ZBZO_FNE7AFZXOOxNd9Rz@Qfb2dYIOFhUAABd9ei4&query_key=1&retmode=xmlElapsed time: 118 seconds 0.92%, 1500 records of 161815 retrieved. Tue Jan 25 20:48:27 EST 2005 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=datahog&db=gene&retmax=500&retstart=1500&rettype=native&WebEnv=0ImHxGD H2zI93UMwxrTRTh-nretlso4ZBZO_FNE7AFZXOOxNd9Rz@Qfb2dYIOFhUAABd9ei4&query_key=1&retmode=xmlElapsed time: 158 seconds 1.23%, 2000 records of 161815 retrieved. Tue Jan 25 20:49:07 EST 2005 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=datahog&db=gene&retmax=500&retstart=2000&rettype=native&WebEnv=0ImHxGD H2zI93UMwxrTRTh-nretlso4ZBZO_FNE7AFZXOOxNd9Rz@Qfb2dYIOFhUAABd9ei4&query_key=1&retmode=xmlElapsed time: 204 seconds 1.54%, 2500 records of 161815 retrieved. Tue Jan 25 20:49:53 EST 2005 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=datahog&db=gene&retmax=500&retstart=2500&rettype=native&WebEnv=0ImHxGD H2zI93UMwxrTRTh-nretlso4ZBZO_FNE7AFZXOOxNd9Rz@Qfb2dYIOFhUAABd9ei4&query_key=1&retmode=xml

32. A Download of 161825 Mammalian Entrez Gene Records Efetch calls SECONDSSECONDS