databases

By @finchtalk (Todd Smith)

In 2014 and beyond Finchtalk will be contributing to Digitalbio’s blog at this site. We kick off 2014 with Finchtalk’s traditional post on the annual database issue from Nucleic Acids Research (NAR).

Biological data and databases are ever expanding. This year was no exception as the number of databases tracked by NAR grew from 1512 to 1552. In the leadoff introduction [1] the authors summarize this year’s issue and the status of the NAR index. The 21st issue includes 185 articles with 58 new databases and 123 updates. In the 1552 database repository ... Read more

by Todd Smith


Biological data and databases are ever expanding. This year was no exception as the number of databases tracked by Nucleic Acids Research (NAR) grew from 1512 to 1552. In the leadoff introduction [1] the authors summarize this year’s issue and the status of the NAR index. The 21st issue includes 185 articles with 58 new databases and 123 updates. In the 1552 database repository, 193 had their URLs corrected and 24 were removed because they were deemed obsolete.


In the leadoff introduction [1] the authors ... Read more

One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.

One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As ... Read more

Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I'm staring out my window watching the rain. Inspiration hit! What about searching for August?

i-15229e4ef21ba40ef0a2aa526c93f358-HFQ_protein.gifFolks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term 'August'.

HFQ is a lovely ... Read more

or is it just an idea that's ahead of the curve?

Last week, I was stunned to discover at least 31 papers in an NCBI Gene database entry that were in the entry for the wrong gene. I wrote about this here, here, here, and here.

Now, an oversight like this is a little understandable. The ... Read more

In a recent post, I wrote about an article that I read in Science magazine on the genetics of learning.

One of things about the article that surprised me quite a bit was a mistake the authors made in placing the polymorphism in the wrong gene. I wrote about that yesterday. The other thing that surprised me was something that I found at the NCBI. ... Read more