Tuesday, September 30, 2008

Genome of Penicillium chrysogenum

The genome of the fungus that produces penicillin has been sequenced, according to a report on the BBC (discovered via the BBC Health feed that I get in Twitter). The genome has been published as an advance online publication in Nature Biotechnology and may lead to the discovery of new antibiotics, according to the BBC report.

If you are University of Leicester but off campus, try this link instead -login with CFS username and password when prompted. If any problems, of course, contact me.

Friday, September 26, 2008

New features in My NCBI - My Bibliography - updated

The My NCBI feature of PubMed has had some enhancements. There is an announcement about this, and yesterday afternoon (UK time) there was an announcement on PubMed that My NCBI would be missing for some hours while the changes were made.

The changes are there this morning (UK time!). My NCBI has a new look (and a new feel, doubtless). There is a "I forgot my password" feature, and you can elect to have your password remembered or to remain signed in at all times. The features that were there before are still there - saved searches, collections, filters - but there is now a "My Bibliography" feature, which appears with the collections and saved searches under "My Saved Data".

My Bibliography enables you to gather PubMed citations to your own publications. I tried this, for my own publications (all 2 of them!). You can choose more than one name, if you appear in more than one form, and the search box fills itself in, in the same way that the index boxes do, in PubMed itself, so you can see what forms of name exist within PubMed. You can apply filters - year of publication, grant number, and so on - and you could search by PMID. Once you have put your citations into My Bibliography, you can sort that list by title, first author and date, and you can remove citations.

You can add Other Citations to My Bibliography, this only searches PubMed and is designed to give you a place to collect other citations, not your own. This seems to suggest that there is no way to add citations that are not included in PubMed. There also seems to be no way to output the citations in My Bibliography into lists. There also seems to be no way to export from My Bibliography into things like EndNote, but since you can export from PubMed into EndNote, that seems not to matter a lot.

New bit - Laika Spoetnik has a posting about what happens if you try to save a search in My NCBI and that search has a line like #1 AND #2 in it. Read the posting if you have problems - and Laika suggests contacting the PubMed helpdesk as well, in case this is a bug.

Thursday, September 25, 2008

EndNote X1 tips

This posting is to augment the information at http://www.le.ac.uk/li/research/bibliographic.html and I shall add to it as I realise things. What is on this page applies only to University of Leicester members.

Updated - 1. EndNote 9 has now gone from CFS. You must download EndNote X1. Instructions for doing this are on the link above. Exporting from Web of Science into EndNote (using the "Save to EndNote..." button) appears to fail if you have not installed EndNote X1.

2. You then need to install the EndNote X1 toolbar - go to Start - All Programs - CFS Software 2 - EndNote X1 - Install Word toolbar. Note that Word 2007 has its own referencing facilities (on the References tab) - I personally think this will be too limited for the sort of use we want to make. This References tab is nothing to do with EndNote. If you had EndNote 9 and Word 2007, EndNote appeared on the Add-Ins tab. Once you have installed the EndNote X1 toolbar, it will appear on its very own tab.

3. You can delete the old EndNote 9 toolbar and custom menu, by right clicking them. I can't see a way to uninstall EndNote as such. I have seen the installation of the EndNote X1 toolbar bring up a dialog box asking if you want to uninstall the EndNote 9 toolbar. I don't think this happened to me when I installed X1.

4. You might also have spotted that Word 2007 has a "references" tab. This is Word's own citation tool, which looks to work quite well, but is very basic, only having a very small number of unalterable styles, and it seems that you have to add all your references manually. I'm teaching the Word referencing tool soon so will have more structured thoughts soon.

Tuesday, September 23, 2008

Accessing full text journals via PubMed

This may be of interest to University of Leicester members. If you are at a different institution, then your access to resources may be different and you need to talk to your library.

Leicester now has a proxy server, which makes off campus access to databases and journals easier. PubMed, however, is not behind the proxy server.

What this means is:

- if you are on campus, and follow a link from PubMed to full text, that link will work if we have on campus access to the journal in question.


- if you are off campus, there is no way that the journal will be able to identify you as University of Leicester, and so very probably the link will not work...

...unless you do this...

- go to the Leicester Digital Library at http://www.le.ac.uk/library/digital/index.html and click the Login to electronic resources link.
- login with your CFS username and password
- you will then be taken to the A-Z list of databases
- go to P and choose PubMed
- follow the links as you would normally do. Now you are identifiable as University of Leicester, and so full text ought to work.

If you have any problems, tell me! Leave a comment on the blog or email me.

Monday, September 22, 2008

Link between antibiotics in pregnancy and cerebral palsy

This Lancet study was picked up by the press last Thursday - it looks at the development of children born to mothers who were administered antibiotics in premature labour. The antibiotics were being given to delay premature birth, and the Department of Health is advising that they only be given in the event of infection.

The Society for General Microbiology news page has a summary and links to the story in four national newspapers. The Lancet article is here, with links to several related things.

(Note: the SGM news page link may cease to work when there is later news - you need to navigate to the news for the 18 September. The Lancet link uses the DOI and whether it will work for University users off campus I am not exactly sure. If you find out, please let me know by leaving a comment).

Asthma in the Lancet

The Lancet for 20-26 September, 372(9643) is full of articles about asthma. This includes original research and commentaries of one sort or another. The research includes a paper on paracetamol and asthma, which I think was picked up in the press (I heard it mentioned by someone at a party at the weekend - they could of course be avid Lancet readers).

University of Leicester members can access the Lancet via ScienceDirect.

MetaBase: database of biological databases

I read somewhere of Ecoliwiki, a wiki about E. coli (not a surprise), and this led me to MetaBase, a user contributed list of biological databases. The initial data comes from the database issue of Nucleic Acids Research, and there are conditions of use (see http://biodatabase.org/index.php/Help:About#Database_Description)

You can search it, or browse it by category. I searched for "human genome", and found no page matches, but got links through to title matches. Some of the links to those titles appear to be faulty, and need another click to get to the correct resource. Once you have the details of a resource, though, you get a database description, a link to the database itself, and contact details if they are known.

Ecoliwiki's details are here. There is also a guide to using MetaBase.

Friday, September 12, 2008

Protocol for handling research misconduct

The BMJ also carries a news item on this - a draft protocol from the UK Research Integrity Office - UKRIO offers advice to universities and research organisations on research conduct. The document (downloadable from the link above) contains the P-word (plagiarism, not peanuts!), without going into detail about what it is, just including it as one of the examples of misconduct.

BMJ news item here.

Coffee creamer used as infant food

Obviously, anything to do with infant feeding is close to my heart at the moment, although I am very much a minor player. So, my eye was caught by a study in the BMJ, looking at a popular brand of coffee creamer available in Laos, and whether it is used as an infant food or not. The creamer logo portrays a baby bear in an apparently breastfeeding position.

Most of the paediatricians surveyed said that they were aware of parents who had used the creamer as infant milk, and most of the adults surveyed said they thought it contained milk (which I assume it does not, although I could be wrong). The creamer does have a warning on the can about not using it to feed babies , which 80% of people surveyed had not read.

Read the article here.

Which prompts me to check - is there still a boycott of a well known food manufacturer because of its policies on promoting (real) baby milk? Yes, there is.

Saturday, September 06, 2008

NIH takes down two open access genetic databases

My eye was caught by a report in Biotechniques news that the NIH had removed access to two genetic databases following research that indicated that you could extract an individual's data from a set of pooled data.

I had not been able to work out exactly which databases - see below for something I have just read that might shed light.

**Later note** - this story is discussed in Science, whose report suggests that it is not whole databases that have been pulled, but some data from within particular databases. Some data has been pulled by the NIH from dbGAP, and from a cancer genetics database called CGEMS (http://cgems.cancer.gov/, which is currently displaying a news item saying that some data is temporarily unavailable for public posting). The Wellcome Trust has pulled data too - the Science report does not give details.

The story is also reported in the LA Times, Peter Suber's Open Access News, and (mentioned by Suber) Nature News. The research itself is in PLoS Genetics.