Converting Lots of GI Numbers to Accession.version

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As you may have read in previous posts, NCBI is in the process of changing the way we handle GI numbers for sequence records. In short, we are moving to a time when accession.version identifiers, rather than GI numbers, will be the primary identifiers for sequence records.

In a previous post, we outlined a method for converting GI numbers (used to identify sequence records) to accession.version identifiers. That method used the E-utility EFetch and is capable of handling cases where you have no more than a few thousand GI numbers to convert.

What if you have more?

We now have a bulk conversion resource that will allow you to handle very large jobs. The resource consists of a Python script coupled with a database file (about 40 GB uncompressed). You’ll need to download both of these files (gi2accession.py and gi2acc_lmdb.gz) to local disk, and then you can process as needed.

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Converting GI Numbers to Accession.version

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As you may have read in previous posts, NCBI is in the process of changing the way we handle GI numbers for sequence records.

In short, we are moving to a time when accession.version identifiers, rather than GI numbers, will be the primary identifiers for sequence records.

As part of this transition, an obvious question for any of you currently using GI numbers is how to convert a GI number to an accession.version, so that you can make appropriate updates. The good news is that it’s pretty easy if you have no more than a few thousand GIs to convert.

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Identifying and Correlating Chemical Names & Synonyms

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This blog post is intended for people who refer to chemical names/symbols and synonyms in databases like PubMed and PubChem, or in their own scientific papers. There is a similar post for gene symbols and names.

During the research and publishing process, scientists need to refer to their chemicals-of-interest. While there are standardized nomenclatures (IUPAC, SMILES, InChITM, etc.), different labs sometimes use different names for the same chemical.

The NCBI PubChem project has set up a system to identify and correlate these various names as well as ‘alias’, ‘synonym’, or ‘also known as’ terms that have been used in the literature.

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Clearing Up Confusion with Human Gene Symbols & Names Using NCBI Gene Data

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This blog post is intended for people who refer to gene symbols or names in databases such as Gene, ClinVar, or PubMed. There is a similar post for chemical names and symbols.

During the research and publishing process, scientists need to refer to their genes-of-interest. However, different labs sometimes use different gene symbols to refer to the same gene. As you can imagine, this leads to confusion.

To standardize the use of terms, the HUGO Gene Nomenclature Committee (HGNC) sets official gene symbols and names. The NCBI Gene resource reports these official gene symbols and names, as well as additional symbols and names that are included on related sequence records for the same gene or from submitted GeneRIFs.

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NLM In Focus blog profiles Dr. Kim Pruitt, NCBI Staff Scientist

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The inaugural article in NLM In Focus’s new series on NLM scientists features Kim Pruitt, PhD. Dr. Pruitt is a staff scientist at NCBI; she heads the Reference Sequence Database, better known as RefSeq.

In the article, Dr. Pruitt shares her career trajectory as well as pearls of wisdom for young scientists.

Click through to read NLM's profile on Kim Pruitt, PhD.

Click on the picture to read NLM’s profile on Kim Pruitt, PhD.

Introducing Magic-BLAST

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Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Magic-BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available on the FTP site.

Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-Seq, locating the candidate introns and adding up the score of all exons. Sequencing reads can be provided as NCBI SRA accessions, FASTA or SRA files.

Magic-BLAST implements ideas developed in the NCBI Magic pipeline using the NCBI BLAST libraries. Magic-BLAST is under active development, and we expect the next few releases to occur on a monthly basis. Read more about Magic BLAST on the FTP site.

NCBI’s Bryant and Bolton receive 2016 Herman Skolnik Award for PubChem database

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On August 23, Drs. Stephen Bryant and Evan Bolton received the American Chemical Society (ACS) 2016 Herman Skolnik Award for their work in developing, maintaining, and expanding the National Center for Biotechnology Information’s PubChem database of chemical substances and their biological activities. The award was presented at the ACS 252nd National Meeting & Exposition in Philadelphia.

Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.

Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.

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Second Round of HTTPS Tests

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NCBI has scheduled the next round of HTTPS tests, following up from the initial tests performed on September 15.

The schedule for these tests is as follows (all times are EDT):

Thursday, Sept 22
8:00 AM – 12:00 PM : redirect web pages from HTTP to HTTPS, same as the first test on Sept 15.
8:00 AM – 9:00 AM : redirect CGI’s and API calls to HTTPS where possible, reject where not possible

Monday, Sept 26
8:00 AM – 10:00 AM : redirect web pages from HTTP to HTTPS with HSTS activated using a 1-hour expiration
10:00 AM – 12:00 PM : redirect web pages from HTTP to HTTPS without HSTS

Tuesday, Sept 27
8:00 AM : Start continually redirecting web pages from HTTP to HTTPS

If you use NCBI APIs, please see https://go.usa.gov/xKf8H

For more detailed information about these tests, please see https://go.usa.gov/xKH6Y

Important considerations:

  • If you develop software that depends on NCBI APIs or toolkits (e.g. SRA or C++), please target the 8-9 AM window on Sept 22 for testing, as we expect any problems with HTTPS to result in failures of affected applications during this test.
  • Some browsers may cache the HTTPS pages viewed during the test periods, and so may continue to request pages over HTTPS once the tests are complete. If this causes problems, clearing the browser’s cache and cookies will restore access over HTTP.
  • We will be running additional tests on CGI applications once we analyze the results of the tests on September 22.

NCBI Begins HTTPS Tests

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You may have heard that NCBI, along with the rest of the Federal Government, is switching to HTTPS-only access. To help prepare for this, NCBI is beginning a series of tests. During these tests, all traffic to NCBI will be redirected from HTTP to HTTPS to simulate our system’s behavior once the HTTPS transition is complete.

The first test will be Thursday, September 15, from 8:00-9:00 AM EDT.

If you experience problems with any NCBI site or service during that hour, please see our Secure Website Tests plan for advice on how to proceed.

If you use software that accesses NCBI data, and you experience problems with that software, we recommend that you contact the software vendor, as they may need to update their products to work over HTTPS.

If you use proxies to access NCBI (for example, EZProxy) and you experience problems during this period, we also recommend that you contact the proxy service to ensure that your service is ready for HTTPS.

If you develop software that accesses NCBI services or that depends on NCBI APIs (such as the E-utilities) or toolkits (such as the SRA or C++ toolkits), these tests are a great opportunity for you to see how your software will function over HTTPS.

If you have other questions or concerns, please contact us at info@ncbi.nlm.nih.gov.

The Future of Existing GI Numbers at NCBI

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NCBI has announced that we will be changing the way we handle GI numbers for sequence records in September 2016. (Read more, in case you missed it).

In this post, we’ll address a key question:

What is the future of existing GI numbers?

The short answer is that nothing is happening to these GI numbers.

If a nucleotide or protein record already has a GI, it will continue to have that GI indefinitely. You will also be able to retrieve such a record using its GI either on the NCBI web site or using the E-utilities.

Moreover, GIs will remain part of the XML and ASN.1 formats of sequence records.

If not GIs, then what?

Accession.version identifiers. All sequence records, both new and old, will have a unique accession.version identifier.

Existing records will keep the accessions they already have; new sequences will only receive an accession.version identifier.

So what’s all the fuss about?

Two things:

Stay tuned for additional posts about this topic, and please contact us if you have questions.