Beginning Monday, March 5, 2018, the National Library of Medicine (NLM) will present EDirect for PubMed, part of the Insider’s Guide to Accessing NLM Data.
This newly expanded series of interactive workshops will introduce new users to the basics of using EDirect to access exactly the PubMed data you need, in the format you need. Over the course of five 90-minute sessions (plus an optional “office hours”), students will learn how to use EDirect commands to access PubMed, design custom output formats, create basic data pipelines to get data quickly and efficiently, and develop simple strategies for solving real-world PubMed data-gathering challenges. EDirect requires access to a Unix environment but we will send easy installation instructions for Windows and Mac computers before the class starts. No prior Unix knowledge is required; novice users are welcome! Continue reading →
The next NCBI Minute highlights some of the highly used classic textbooks available (for free!) on the NCBI Bookshelf, points out some new ones that have been recently added, introduces why several publishers and authors find this a valuable resource to boost their readership, and how to join in by adding new and updating existing textbooks on the NCBI Bookshelf.
Date and time: Wed, March 7, 2018 12:00 PM – 12:30 PM EST
Since 1999, NCBI has worked with publishers and authors to provide an additional way for readers to access their products. Housed at the U.S. National Library of Medicine, users of the NCBI Bookshelf can freely access Books, Reports, and Documents. Classic textbooks are some of the most popular and heavily used entries, with hundreds of thousands of people using their favorite book every month!
The NCBI Eukaryotic Genome Annotation Pipeline now includes the prediction of more non-coding RNAs. Starting with software release 8.0, rRNAs, snRNAs and snoRNAs are predicted by searching eukaryotic genomes with HMM models from RFAM. Below is an example of a rRNA cassette predicted in maize Annotation Release 102. These new small RNA types come in addition to the miRNAs and tRNAs that have long been annotated by the pipeline.
Fig.1: rRNA cassette on maize scaffold NW_017972167.1 of assembly B73 RefGen_v4. The top track displays the annotated 18S, 5.8S and 28S rRNA subunits in Annotation Release 102. These three genes were missing from the previous annotation, and replaced incorrect non-coding gene predictions (see Annotation Release 101, middle track). The bottom track shows the repeats identified by RepeatMasker. The boundaries of the rRNA repeats match precisely the predicted 18S and 28S rRNA genes.
See what we are annotating now on the Eukaryotic RefSeq Genome Annotation Status page.
For ease in accessing the orthology data subset, a new gene_orthologs FTP file has been created on the Gene FTP site. The file uses the same format as the gene_group file. As of January 31, 2018, the gene_group FTP file no longer includes orthologs.
In October of last year, we announced the replacement of NCBI’s Map viewer with the Genome Data Viewer (GDV). Here are some additional details on how to access to the older Map Viewer FTP content going forward and some information to help you with the transition to GDV.
As we announced last fall, we are no longer updating the data content of Map Viewer FTP directories. To help avoid any confusion over the meaning of the directory names, we will alter the CURRENT and PREVIOUS directories under the species directories in the Map Viewer FTP area so that they no longer point to data. However, the existing data will still be available on the FTP site.
NCBI is now producing a new set of taxonomy files that include the taxonomic lineage of taxa, information on type strains and material, and host information. These files are particularly helpful for people maintaining local installations of NCBI data.
You can download the new archive (new_taxdump.tar.gz) from the taxonomy directory on the FTP site (ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/). The new files are typematerial.dmp, typeoftype.dmp, rankedlineage.dmp, fullnamelineage.dmp, taxidlineage.dmp, and host.dmp. Please see the readme file for details of the file contents.
The original taxonomy file archive without the new content will remain available under its original name, taxdump.tar.gz. The section below shows the entries for the monkey species Cercopithecus lomamiensis from the new ranked lineage and type material files. Continue reading →
On Wednesday, February 14, 2018, NCBI will present a webinar that will show you how to quickly retrieve sequences in any format from NCBI.
Date & time: Wed, Feb 14, 2018 12:00 PM – 12:30 PM EST
Ever need to quickly grab a protein or nucleotide sequence in FASTA or another format from NCBI? This NCBI Minute will show you how to accomplish this using the nucleotide and protein web pages, an NCBI URL, and – the most flexible way – through the commandline EDirect client that accesses the E-Utilities API.
The UNC Curriculum in Bioinformatics and Computational Biology and NCBI will host a data science hackathon from March 12-14, 2018 on the campus of the University of North Carolina at Chapel Hill. Projects addressed during the hackathon will involve general bioinformatics and genomic analyses in addition to text, image, and sequence processing.
This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for analyses from high-throughput experiments. Some projects may involve other non-scientific developers, mathematicians, or librarians.
To be considered for the event, you must apply and be able to travel to the UNC campus in Chapel Hill (see details below). Applications are due Monday, February 12th, 2017 by 11:59 pm ET.
Want to extract just the PubMed data you need, in the format you want?
Dreaming of creating your own PubMed tool or interface, but don’t know where to start?
Join us on Tuesday, February 13 at 1pm EST for a one-hour introductory webinar designed to teach you more powerful and flexible ways of accessing NLM data, starting with the Application Programming Interfaces (APIs) for PubMed and other NCBI databases. This presentation is part of the Insider’s Guide, a series aimed at librarians and other information specialists who have experience using PubMed via the traditional Web interface, but now want to dig deeper. Continue reading →
NCBI organizes 2-3-day hackathons at sites throughout the United States. In these events, participants work in small collaborative groups on workflows, scripts or applications to create bioinformatic solutions to problems in fields such as text mining, next-gen sequence analysis, medical informatics, and many others. Code from Hackathon projects is available on the public NCBI Hackathon GitHub site.