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Introducing… Entrez Direct
The E-utilities on the UNIX
command line
esearch –db gene –query “foxp2[gene]
AND human[orgn]” |
elink –target protein –name
gene_protein_refseq |
efetch –format fasta
ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/](https://image.slidesharecdn.com/umcpcstalk11316v1-161221161036/75/Umcp-cs-talk_11_3_16_v1-62-2048.jpg)
Uploaded byBen Busby
Umcp cs talk_11_3_16_v1
This document summarizes genomic variation and individual genome sequencing. It discusses the rising number of subjects with genome sequences available, from 14,201 in 2007 to over 1 million in 2015. It also provides information about genomic analysis tools from NCBI including the SAM format, genome browsers, E-Utilities, Entrez Direct, and upcoming APIs. Finally, it advertises upcoming hackathons in January and March for developing tools and apps to work with NCBI genomic data and APIs.
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- 1. Ben Busby, Ph.D. GenomicsOutreach Coordinator NCBI ben.busby@nih.gov Genomic Variation in the Rising Era of Individual Genome Sequence
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- 6. http://1.usa.gov/1J1xmYs NCBI NGS OnlineWorkshop – Available on the NCBI YouTube Channel!
- 10. 14,201 53,216 139,311 374,464 485,727 566,181 660,665 876,849 1,002,935 2007 2008 20092010 2011 2012 2013 2014 2015 Subjects
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- 60. E-Utilities (Eutils) Video availableat: http://www.ncbi.nlm.nih.gov/education/webinars/
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- 62. 62 Introducing… Entrez Direct TheE-utilities on the UNIX command line esearch –db gene –query “foxp2[gene] AND human[orgn]” | elink –target protein –name gene_protein_refseq | efetch –format fasta ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/
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- 64. 64 Moving from FTP-scraping cronjobs to on-demand APIs
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- 67. 67 Generating apps thatwork with our APIs and Data Structures, and Improve Metadata: NCBI Hackathons!
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- 75. First 5 lectures nowavailable on
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- 83. 6 Functional SoftwareProducts 3 Days
- 90. January 2016 6functional software products 3 days
- 97. Combined score is theaverage of SVs, mappability, GC.. NCBI region list Encode blacklist
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- 99. Biomedical Informatics HackathonJanuary 9th – 11th NIH Campus, Bethesda! NCBI Genomics Hackathon March 20-22nd NIH Campus, Bethesda
Editor's Notes
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- #85 Partnering with the Society for Canadian Women in Science and Technology
- #98 All cancer cells arise from a normal somatic cell, therefore most primary cancers express adequate amounts of HLA identify the specific peptides that mark the tumor as 'dangerous’ T cells recognize peptides that are presented by human leukocyte antigen tumors harbor hundreds of putative neoepitopes without the benefit of information from T cell responses, it’s virtually impossible to develop a vaccine, but we can aim at narrowing down the candidate peptides
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