NCBI Newsletter

The latest issue of NCBI News is now available online. Short articles on the following are included:

• PubMed's AbstractPlus display - the new default display
• CD Tree - a program for manipulating and analysing conserved domain records
• Cn3D 4.2 - a new version of the 3D structrue viewer
• Whole Genome Shotgun Growth
• New BLAST View Options
• New Genome Builds—Map Viewer

PubMed retrieval glitches - Fixed

Update Tues 19th December - the problem is fixed.

Original post: Today (sic 18th Dec) we have noticed frequent glitches when we try to access records at PubMed. When you have done a search and want either to view more details or change the view for records, then the following error message is appearing:
"id: ######## Error occurred: Document retrieval error: document does not exist".

The id number is unique to each entry in PubMed so in place of ######## there will be an eight digit number.

The library has reported problem to PubMed.

Medline/PubMed End-of year Processing

NLM will be beginning this on 5th November, this will mean there are no new fully indexed Medline records for about 6 weeks. As in previous years this will mean that there will be a temporary halt to alert searches from OVID.

NLM anticipates that all work will be completed by mid-December, so OVID searches should restart late December/early January.

Medline is 35!

The Medline database debuted on 27th Oct 1971.

Evolving from the computer system which was use to produce the printed Index Medicus, it originally covering only 239 journals and limited to 25 simultaneous users via dial-up access. In 1980s a client software (Grateful Med) for pcs was added to make searching from desktop possible. In the 1990s the Internet took off and in response NLM launched Internet Grateful Med (1996), hot on its heals came a new web interface call PubMed - so happy 10th birthday PubMed.

Read more.

PubMed Changes Default Display

The PubMed default display which you see when you click on either the authors or the icon to the left of each citation in the summary list of results has changed. The new default display format is called AbstractPlus. This is also the format that will appear immediately if your search produces a single result.

AbstractPlus is an enhanced Abstract view that shows the first five Related Articles for each PubMed citation. The record starts with a title bar containing the journal citation details, below this are two columns: the left-hand column contains authors, first author address, abstract and PMID (PubMed IDentification) number; in the right-hand column are the 5 papers which share the most cited references in common with the viewed paper.

One downside to this new format is an inconsistency in positioning of the links to full-text.

• The vast majority of links to full-text are appearing as publisher icons in the title bar, at the right hand side next to "Links".
• A few (where icon appears to be too large for titlebar) are appearing at the bottom of the left-hand column below the PMID. This means that if the abstract is extensive the link may not be visible unless you scroll right to bottom of record.

New customization feature in PubMed

When we have searched PubMed we are used to seeing our results presented on 2 tabs: All and Reviews. The technology behind the Reviews tab is a filter. PubMed has now made it possible for you to analyse your results by selecting filters to apply to your search results.

To customise the filters click on the hammer and wrench icon beside the Reviews tab, you will then be prompt to login to your account at MyNCBI (formerly Cubby - accounts are free and easy to set up as you create your own ID and password). Once logged in you are taken to Filter Selections which is broken down into 4 tabs:

• Quick pick list - popular filters such as free full text, last 5 years. Select these by ticking the boxes
• Browse contains a large number of filters in 3 groupings: Linkout, Links, Properties
• Search - the ability to search for a filter by keyword in name or description
• My Selections - the filters you have chosen to apply

The listings within Browse are quite extensive:

• Linkout - options to link to resources provided by external organisations eg Molecular Biology Databases, Literature (includes ability to select by publisher such as Elsevier). As well as selecting to filter by these options you can also add an icon to records to facilitate their recognition in the results list
• Links - options to select records with links to other Entrez databases such as Genes, PubMed Central archive
• Properties - many of these are limit options.

You can set upto a maximum of 5 filters to be applied to your results.

More changes in PubMed

From this month PubMed is changing the order in which authors appear in its records to truly reflect that appearing on the published papers. This change particularly affects Corporate or Group authors.

To summarise how these authors have been handled in the past:
1966-1999 : Corporate author(s) placed at the end of article title, so need to search [ti] field to find them.
2000-Apr 2006: Corporate author(s) entered in separate field and always displayed last in the list of authors. Use field code [cn] to search for these.
May 2006 - : Corporate author(s) entered in separate field and displayed in the order found in the byline of the published article. Use field code [cn] to search for these.

For further details see the article in the NLM Technical Bulletin No 350 : May/June 2006
http://www.nlm.nih.gov/pubs/techbull/mj06/mj06_corp_author.html

PubMed's Search Limits Updated

PubMed have update their Limits page. It is now possible to limit your initial search by:

• Author
• Journal title
• Links to full text available
• Free full text available
• Abstracts available

Other improvements include

• use of tick boxes for selecting items from lists, rather than Ctrl+Click or Apple key+Click
• wider range of date limit options

For further details see the March/April issue of the NLM Technical Bulletin