My NCBI, My Tuesday, My Time-warp.

I don’t know how you start your Tuesdays, but I start mine with literature. And coffee. This morning, though, I wasn’t sure I had enough coffee.

Every Monday evening NCBI runs some searches for me and sends me the results. I have several saved searches set up in the My NCBI system (a lot of alliteration…). I have a search that sends me papers that match keywords such as “bioinformatics” and “distance learning” among others. It is one of the ways I keep up with new resources. I find new genomics resources, and I find papers where people have used resources to analyze the data. Both are important to me.

But today in my results I found a species that I hadn’t heard of before, Pristionchus pacificus. And the title told me that I would learn about the genetics and genomics of this species, so I went to look at the abstract–it is linked right from my email, so I can hop over to NCBI.

From the abstract, I could go right to the full text site for the article. I started to read the WormBook. WormBook As I was reading, I was finding phrases such as: “….will be completed in late 2006.” As I am struggling to write 2008 on my checks and my notes these last few days, I thought I had read that wrong. But it turns out this was a paper dated 2006. I poured more coffee and tried to figure out what was up.

WormBase I don’t know how it popped up in today’s literature search–I have had this search in place for a long time. It was rather timely, though, as we are about to complete a tutorial on WormBase! It was time for me to review some worm data anyway. But how did NCBI know? Are they checking my email??

If you haven’t used My NCBI saved searches, try them out. You can set them up to be very simple or very complex with Booleans and phrases and all the other standard tools of literature searching from NCBI. You can customize the results with various amounts of data, highlighting of key terms, and set the searches to run at different frequency. I learn something new every week. Now I know that there is a WikiOnchus. I didn’t know that yesterday.

But it is a little spooky. I’m still not sure how NCBI knew I needed to brush up on worms this week. Excuse me while I get some more coffee….

UPDATE:  I was just reading our RSS feed of WormBase news, and the news is that WormBook chapters are now indexed in PubMed.  That explains Tuesday.

WormBook chapters now indexed in PubMed

The WormBook team is pleased to announce that chapters are now indexed in PubMed. See, for example, the PubMed entry for “The sensory cilia of Caenorhabditis elegans“. Abstracts are linked directly to the full text at WormBook.



2 thoughts on “My NCBI, My Tuesday, My Time-warp.

  1. Pingback: Navigating the literature | The OpenHelix Blog

  2. Pingback: ‘Bioinformatics: Gone in 2012’ | The OpenHelix Blog

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