Lenus, the Irish Health Repository

LENUS is an online repository of health-related reports, research and official publications from 1960 compiled by the HSE Regional Library & Information Service in Dublin. LENUS includes policy documents, official publications, clinical research, theses and statistics. Authors can also submit their original research to the repository. LENUS includes documents from the former Irish Health Boards, the Health Service Executive and Department of Health and Children. It is an important resource for health professionals, policy makers, academics, librarians, students and the general public.

Paul

NCBI Biosystems Database

The NCBI Biosystems database has now gone public. The NCBI BioSystems Database currently contains biological pathways from two source databases, KEGG and the EcoCyc subset of BioCyc. It uses the same search interface as other NCBI databases as pubmed and Entrez Gene.

Use the database to list genes, proteins, and small molecules that are involved in a biological pathway. More

• Find the pathways in which a given gene or protein is involved. More
• Find the pathways in which a specific small molecule is involved. More
• Retrieve 3D structures for proteins involved in a biosystem. More

Paul

Paying open access publication charges - a report

The Research Information Network have published the following report on open access publication charges:

"Paying for open access publication charges. Guidance for higher education and research institutions, publishers and authors. A report by Universities UK and the Research Information Network"

Publication charges are the fees levied by some journals (such as BioMed Central) to publish articles and make them available free of charge to the reader. This report provides advice and guidance on the arrangements for paying open access publication fees and is aimed at research institutions, research funders, publishers and authors.

The report is available in the Mercer and Beaumont Hospital libraries. Alternatively you can view the full report by clicking on the link below
http://www.rin.ac.uk/files/Paying_open_access_charges_guide_March_2009.pdf

RCSI repository for research and scholarly output - e-publications@RCSI

The Library has set up a repository for RCSI research and scholarly output called http://epubs.rcsi.ie/

What is e-publications@RCSI?
e-publications@RCSI (http://epubs.rcsi.ie/) is an open access repository of the research and scholarly output of the Royal College of Surgeons in Ireland. The service is in development and is maintained and managed by RCSI Library.

Whose research is in it?
Material can be deposited by RCSI staff and students.

Where is it?
You can find it at http://epubs.rcsi.ie/ or link to it from the RCSI Library web pages.

How do I deposit my research?
Contact the repository administrators at epubs@rcsi.ie. We will contact you with further information on how to submit.

What can it do for me?

• Help make your academic work freely available on the internet
• Increase worldwide access to your work (in just 4 weeks people have downloaded RCSI research from 16 different countries)
• Provide a central archive of your work
• Many Irish funding bodies, including SFI, the HEA, the HRB and IRCSET, require researchers to submit published work funded by them to an open access repository

What do I need to do?
Keep pre- and post-prints of all your publications!
If possible we will use the publisher version of your publications. However, many publishers do not allow use of their final version. They usually allow use of pre-prints (this is the version of the paper pre-refereeing/pre-peer review) and/or post-prints (this is the final draft post-refereeing/post-peer review).

Find it@RCSI Library

1. I have found the abstract (summary) of a really good article and I have the full reference (volume and page numbers) – where do I go to find the full text?

2. I have to find information on the overuse of medication, which database should I use to find articles on the topic?

3. Google gives me loads of irrelevant sites – biased, commercial – is there an alternative?


Looking for answers to these or similar questions?

Ask us at the Service Desks in the Mercer and Beaumont Hospital Libraries

Email us at library@rcsi.ie

Explore the Library’s website :

• Ejournal portal to link through to the full-text of articles


• Databases page to find articles on a topic


• Ebooks page for the full text of a large range of electronic textbooks and digests


• Library guide for opening hours and staff contacts

Sign up to the Information & Library Skills section on Moodle for lots of support on searching the web, using databases to find articles, doing literature reviews and using citation styles

Keep an eye on the Library blog for lots of information

Answers:
1. Use the Ejournal Portal on the Library’s website
2. The Medline and Embase databases include articles on biomedical and healthcare topics – see the databases page on the Library’s website
3. Try using Scirus – a search engine which focuses on government, healthcare, technical websites

Searching PubMed & using subject headings

The previous posting dealt with checking how PubMed has interpreted the words you typed. A typical “translation” includes searching for those words (separately and as phrases) as well as a subject heading search.

But what are subject headings?

· Subject headings are added by indexers to the record when it is added to the database. The record describes the article: author, title, journal details, abstract and subject headings. The indexers read the article, identify the principal topics and add the standard subject headings to the record.

· They describe articles in a standardised way – eg, pressure sores, pressure ulcers, bed sores, bed ulcers are all described as decubitus ulcers

· Therefore a subject heading search for decubitus ulcers will pick up all the variations in the way the authors describe pressure sores, bed sores etc

· The words you type are translated into the appropriate subject heading. If you are unhappy with the subject heading, try a new search but describe the it in a different way

· PubMed explodes the subject heading: it searches for articles with the selected heading as well as articles with more specific headings on the same subject

· Click on the heading and you will see the tree (categories), which displays the narrower headings (more specific). For example, exploding Bereavement includes Grief in your search

· Use the MeSH Database in PubMed to carry out a subject heading search alone (ie excluding the word searches)


Use subject headings to:
· make your search more relevant – a subject heading will only be added if it is an important topic
· pick up the variations in describing the topic – the subject headings are standard
· gather narrower, related subjects into your search – when the subject heading is exploded

Be careful:
· In PubMed, the most recent articles don’t yet have subject headings, so you need to do word searches as well (default search)
· While subject headings are standardised, there can be differences in interpretation. For example, the topic “do not resuscitate” can be found with subject headings of “Resuscitation Orders”, “Refusal to Treat” and “ Withdrawal of Treatment”

More information on subject headings from the PubMed tutorial and the Information Seeking & Library Skills section on Moodle.

Do you know what PubMed is doing for you?

PubMed is an intuitive and sophisticated database. When you type in your keywords, it translates them into a complex search. You need to be sure that the system is interpreting them appropriately.


After each search, click on the DETAILS tab to find out.

You type deep vein thrombosis and PubMed translates it into the following searches:

Venous Thrombosis (MeSH – subject heading search)
OR
venous and thrombosis (searches for the words, but not necessarily together or in that order)
OR
“venous thrombosis” (searches for the phrase)
OR
deep and vein and thrombosis (searches for the words, but not necessarily together or in that order)
OR
“deep vein thrombosis” (search for the phrase)

Checking Details after each search allows you to keep track of the searches PubMed carries out on your behalf.

More information from PubMed or see the Information & Library Skills section on Moodle for lots of support material on searching PubMed.