Tag: API

NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel!

Introducing GaPTools for dbGaP Submitters

This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools uses the same preliminary validation checks as the dbGaP submission portal.

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Automate your workflow with the ClinVar Submission API

ClinVar and our scientific and patient-care community rely on your submissions. With our new Application Programming Interface (API) for submissions, we’ve made it even easier for you to provide us with your most up-to-date classification of variants. The new RESTful API allows you to automate your submission workflow so that you can submit new records and update existing records faster. Setting up your account to use the API requires three one-time activities:

ClinVar Submission API Setup

 

 

 

 

 

 

Click on each of the steps in order to set up your account to use the API!

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Programmatic access to Gene data using Datasets command-line and API

In March, we announced NCBI Datasets, a new resource that lets you easily retrieve and download data from across NCBI databases. Did you know you can now fetch NCBI Gene data programmatically using the NCBI Datasets API or command-line tool?  Quickly retrieve both metadata and gene sequence data for multiple Gene records including transcripts and proteins in one shell command or API request. The API documentation is a good way to get started with programmatic access (Figure 1).

Figure 1. The Datasets API documentation showing a demonstration retrieving Gene metadata using RefSeq mRNA accessions. The API returns a readily processed JSON object.

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NCBI on YouTube: Get the most out of NCBI resources with these videos

Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.

Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips

This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.

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September 12 NCBI Minute: Release Plan for NCBI API Keys

September 12 NCBI Minute: Release Plan for NCBI API Keys

Update: Webinar is now on September 12!

If you already registered for the September 5 date, you are automatically registered for September 12. You do not need to re-register. We welcome anyone else who would like to register.

As previously announced, NCBI has introduced API keys for the E-utilities. You will soon want to start using API Keys in your E-Utilities API calls as these will allow the fastest access to NCBI databases. In this webinar, we will review how API Keys work and will provide you with a schedule of brief testing periods and the timing of the full release of API key functionality.

Date and time: Wed, Sep 12, 2018 12:00 PM – 12:30 PM EDT

Register here: https://bit.ly/2v0wFMl

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

(Webinar re-scheduled to September 12 because the presenter was called away unexpectedly.)

Release Plan for E-utility API Keys

As promised in our post this past spring, we are now announcing the scheduled release of API keys for the E-utilities API. If you’ve missed some of our original discussion of these keys, or have questions about how to get a key, you may want to check out this post.

In this post, we’ll be discussing three things:

  • The current status of API keys
  • Upcoming testing periods in September
  • Final public release on December 1, 2018.

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July 11 NCBI Minute: Five Teaching Examples with NCBI APIs

July 11 NCBI Minute: Five Teaching Examples with NCBI APIs

Next Wednesday, July 11, 2018, NCBI staff will show you a set of simple exercises that use EDirect to explore aspects of a human gene. You can easily incorporate these examples into your undergraduate biology courses.

Date and time: Wed, July 11, 2018 12:00 PM – 12:30 PM EDT

Register here: https://bit.ly/2KmH1yO

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5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more

Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos.

NCBI Minute: Getting the Most out of Web BLAST Tabular Format

The NCBI web BLAST service has several useful download formats, including tabular formats. All formats allow you to easily save your BLAST results for processing, editing, and annotating.

This video will show you how to use basic Unix tools and EDirect to expand and enhance your tabular saved BLAST results. You will also see learn how to add useful information like taxonomy and sequence titles.

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June 20 NCBI Minute: Getting the Genomic Context for BLAST Protein Matches

June 20 NCBI Minute: Getting the Genomic Context for BLAST Protein Matches

Do you ever want to see the flanking genes of a protein match from a BLAST search?  On June 20th, we’ll show you how to see the genomic context of bacterial proteins using the identical protein report and the graphical sequence viewer. You will also learn to use these reports in detail and how to get these genomic contexts in batch for a set of protein matches using the identical proteins report and EDirect .

Date and time: Wed, June 20, 2018 12:00 PM – 12:30 PM EDT

Click to register.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

June 13 NCBI Minute: Using EDirect to Query a Local Installation of PubMed

June 13 NCBI Minute: Using EDirect to Query a Local Installation of PubMed

Next Wednesday, June 13, 2018, we’ll show you how to use EDirect to install PubMed locally and then search and retrieve records from the local instance. You will also see an analysis example that shows the significant speed improvement with the Local Cache and employs some advanced EDirect xtract options to aid with processing records.

Date and time: Wed, June 13, 2018 12:00 PM – 12:30 PM EDT

Click to register.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.