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Archive for the ‘NCBI’ Category

NCBI HIV-1 Website Updated

The HIV-1, human interaction database has been updated and is now on an improved page. The improved interface includes help documentation and supports structured queries against Gene, as well as browsing, filtering and downloading the protein and replication interaction data sets. The most recent data release (June 2014) includes 12,785 HIV-1, human protein-protein interactions for 3,142 human genes and 1,316 replication interactions for 1,250 human genes. The HIV-1, human interactions project, collates published reports of two types of interactions – HIV-1, human protein interactions, and human gene knock-downs that affect virus replication which are reported as “replication interactions.”

Apply Now to Participate in the “A Librarian’s Guide to NCBI” 2015 Bioinformatics Course!

Health science librarians in the United States are invited to participate in the next offering of the bioinformatics training course, A Librarian’s Guide to NCBI, sponsored by the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the National Network of Libraries of Medicine, NLM Training Center (NTC). The course provides knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Prior knowledge of molecular biology and genetics is not required. Participating in the Librarian’s Guide course will improve your ability to initiate or extend bioinformatics services at your institution. Instructors will be NCBI staff and Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo. There is no charge for the classes. Travel and lodging costs for the in-person class are at the expense of the participant.

There are two parts to A Librarian’s Guide to NCBI, listed below. Applicants must complete both parts. Participants must complete the pre-course with full CE credit (Part 1) in order to advance to attend the 5-day in-person course (Part 2). Part 1: Fundamentals in Bioinformatics and Searching is an online (asynchronous) course, January 12-February 13, 2015, and Part 2 is a 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, MD, March 9-13, 2015. Students successfully completing the Fundamentals course (Part 1) will earn 18 MLA CE credits. Those successfully completing the 5-day in-person class (Part 2) will earn 36 additional MLA CE credits.

Applications are open to health science librarians in the United States. Applicants will be accepted both from libraries currently providing bioinformatics services as well as from those desiring to implement services. Enrollment is limited to 25 participants. The application deadline is November 17, 2014, and acceptance notification will be on or about December 15, 2014. Visit the A Librarian’s Guide to NCBI course page for additional information.

PubChem Turns Ten!

PubChem logoSeptember 16, 2004 is a special day in the history of PubChem. It marks the beginning of PubChem as an on-line resource! Now fast forward ten years. PubChem provides information daily to many tens of thousands of users. Despite the passage of time, PubChem’s primary mission remains the same: providing comprehensive information on the biological activities of chemical substances.

Providing chemical information to researchers in the biomedical science community is a key part of PubChem’s purpose. Over the years, PubChem introduced and incrementally developed several interfaces, each with its own distinct purpose and set of use cases. Primary to these is the Entrez search interface, where PubChem is organized as three distinct databases: Substance, Compound, and BioAssay. Substance provides substance descriptions (accession number: SID), Compound provides the unique small-molecule chemical content of Substance (accession number: CID), and BioAssay provides biological experiment results for substances (accession number: AID). Each of these databases has an advanced search interface and contain numerous indexes and filters, which can be combined to construct elaborate queries. Additional interfaces exist to search and analyze information in PubChem, including the ability to analyze bioactivity information, download chemical and assay data, search by chemical structure or protein sequence, navigate using integrated classifications, visualize chemical 3-D information, and more.

PubChem continues to evolve the way it provides on-line content. External search engines (like Google, Bing, and others) are now a key way in which researchers locate data. In addition, programmatic interfaces now account for a significant portion of PubChem’s overall usage (+50%). Key programmatic interfaces to PubChem include Entrez Utilities and PUG/REST.

NCBI RefSeq Release 67 Available on FTP

The full RefSeq release 67 is now available on the NCBI FTP site with over 61 million records describing 45,166,402 proteins; 8,163,775 RNAs; and sequences from 41,913 different NCBI TaxIDs. More details about the RefSeq release 67 are included in the release statistics and release notes. In addition, reports indicating the accessions included in the release and the files installed are available.

To subscribe to the ncbi-announce mailing list, visit http://www.ncbi.nlm.nih.gov/mailman/listinfo/ncbi-announce.

Upcoming NCBI Discovery Workshops at UC Davis and UC Berkeley!

NCBI Discovery Workshops, consisting of four 2.5-hour hands-on training sessions emphasizing NCBI resources such as BLAST and Nucleotide, will be presented by NCBI staff at the University of California, Davis, on September 15-16, and at the University of California, Berkeley, on September 17-18:

  • Session 1: Navigating NCBI Molecular Data Through the Integrated Entrez System. 9 am – 11:30 am, 9/15 (UC Davis) & 9/17 (UC Berkeley)
  • Session 2: NCBI Genomes, Assemblies and Annotation Products: Microbes to Human. 1 pm – 3:30 pm, 9/15 (UC Davis) & 9/17 (UC Berkeley)
  • Session 3: Advanced NCBI BLAST. 9 am – 11:30 am, 9/16 (UC Davis) & 9/18 (UC Berkeley)
  • Session 4: Gene Expression Resources at NCBI. 1 pm – 3:30 pm, 9/16 (UC Davis) & 9/18 (UC Berkeley)

​For more information or to register:

For Questions:

NLM’s National Center for Biotechnology Information Receives HHSinnovates Award!

A collaborative project between the National Library of Medicine’s National Center for Biotechnology Information (NCBI) and several other federal and state partners, to reduce the time and improve the accuracy of detecting foodborne pathogens by using whole genome sequencing (WGS) techniques, received the HHSinnovates award on July 21, 2014. The HHSinnovates program was initiated in 2010 to recognize new ideas and solutions developed by HHS employees and their collaborators. Six finalist teams were recognized at the awards ceremony. The WGS Food Safety Project, which also involved the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), the US Department of Agriculture (USDA), and state public health laboratories, was one of three projects to be honored as “Secretary’s Picks” by HHS Secretary Sylvia Mathews Burwell. The award went to the specific individuals leading the project in the various agencies; in the case of NCBI, Senior Scientist William Klimke, PhD, was honored for his work in heading NCBI’s part of the project.

WGS provides greater specificity than other techniques, such as the commonly used pulsed-field gel electrophoresis (PFGE), in identifying the DNA fingerprint of bacteria. It also can more rapidly determine whether isolates are related to a foodborne disease outbreak. The demonstration project involves real-time sequencing of Listeria monocytogenes isolates from human DNA as well as the food supply chain. In the project, the whole genomes of isolates are sequenced and the sequencing data are sent to NCBI, which performs assembly, annotation and analysis, and then sends results back to CDC, FDA, USDA and the labs. Collaborative projects using WGS for other pathogens related to food safety are also underway.

Save the Dates: 2015 “A Librarian’s Guide to NCBI” Course

Attention health science librarians in the United States who wish to initiate and/or extend bioinformatics services at your institution! The National Center for Biotechnology Information (NCBI) and the NLM Training Center (NTC) will be offering “A Librarian’s Guide to NCBI” course in 2015. Participants who complete the class will be eligible for Medical Library Association (MLA) Continuing Education credits. The course is free, but travel costs are at the expense of the participant.

There are two parts to the course, and applicants must take both parts:

  • Part 1: “Fundamentals in Bioinformatics and Searching” is a six-week, online (asynchronous) pre-course.
  • Part 2: A five-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland.

Important Dates:

  • Monday, September 29, 2014 – Watch for a detailed announcement about the course and application process in the NLM Technical Bulletin.
  • Monday, November 17, 2014 – Application deadline.
  • Monday, December 15, 2014 – Acceptance notifications e-mailed.
  • Monday, January 12, 2015 – “Fundamentals in Bioinformatics and Searching” pre-course begins.
  • Monday, March 9, 2015 – “A Librarian’s Guide to NCBI” five-day in-person class begins at NLM.

Mark your calendars for this training opportunity!

New NCBI Bookshelf Item: The Art and Politics of Science, a Memoir

Dr. Harold Varmus’ memoir, The Art and Politics of Science, chronicles his path from a graduate student in English literature at Harvard to co-recipient of the Nobel Prize for cellular origin of retroviral oncogenes, to director of the National Institutes of Health, to President and CEO of Memorial Sloan-Kettering Cancer Center. The memoir is now freely available on the NCBI Bookshelf:

The Art and Politics of Science, by Dr. Harold Varmus. There are sections on PubMed: Virtues and Limitations and journal publishing from Chapter 15, Science Publishing and Science Libraries in the Internet Age.

Newly Released Entrez Direct from NCBI!

NCBI has just released Entrez Direct, a new software suite that allows you to use the UNIX command line to directly access NCBI’s data servers, as well as parse and format data to create customized data files. The latest NCBI News story discusses Entrez Direct and gives several examples of how the programs may be used, as well as links to the suite on FTP and documentation. Entrez Direct is available as a simple FTP download and has extensive documentation on the NCBI web site.