Tag Archives: medline

Working with Pubmed – Part 5: Setting Filters

Medfilters

PubMed* is an extremely useful resource which allows researchers and clinicians to access biomedical databases. The use of PubMed has been discussed elsewhere on this site (see Appendix). Setting up a MyNCBI account allows you to access more features. By accessing the filters site at MyNCBI, the reader is able to get to the filters page (see screenshot). This is a useful feature that lets you set the default for future searches. Returning only research in humans for instance can be useful depending on the nature of the questions being asked.

Appendix – Related Resources on this Site

Working with PubMed – Part 1: Getting started with a shortcut

Working with PubMed – Part 2: Favoriting abstracts

Working with PubMed – Part 3: Bibliography

How to receive research paper e-mail alerts

A Video Celebrating 10 years of PubMed Central

How to improve your search results with Medline

* This article is not affiliated with NCBI

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

Working with Pubmed – Part 4: Receiving News Updates on PubMed

PubMed is an impressive resource. There are several ways to learn about using PubMed.

A How To Section: This lists ‘How To’ details for different components of PubMed

A Quick Start Section

A YouTube Channel

NCBI Help Manual

MyNCBI Help: You will need to be logged in to access this feature

Training and Tutorials Section

NCBI News: This is updated periodically and gives a broad overview of developments

NLM Technical Bulletin: This is much broader and relates to the National Library of Medicine. However there are many interesting articles such as this one on the new PubMedReader

Appendix – Related Resources on this Site

Working with PubMed – Part 1: Getting started with a shortcut

Working with PubMed – Part 2: Favoriting abstracts

Working with PubMed – Part 3: Bibliography

How to receive research paper e-mail alerts

A Video Celebrating 10 years of PubMed Central

How to improve your search results with Medline

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

Working with Pubmed – Part 3: Bibliography (Updated)

Video Demonstration of My Bibliography Feature

PubMed is a large database of citations maintained by the US National Library of Medicine. You can set up an account with NCBI which I would recommend if your intend to work with NCBI over the longer term. The account is known as a myNCBI lets you do a lot of things you wouldn’t if simply browsing the site. This has been partly covered in previous posts (see Appendix). The video above demonstrates a neat feature of myNCBI which is the ability to store a bibliography. This means that you can select citations of interest and store them in the bibliography. From there you can export to an external database, save as a text file or e-mail them. Using this feature I saved the citation below to the bibliography and e-mailed it to myself before cutting and pasting into this document (changing the format). The bibliography feature is very useful and has many applications.

1: Hietanen H, Pietilä A, Kähönen M, Salomaa V. Ankle blood pressure and dementia: a prospective follow-up study. Blood Press Monit. 2013 Feb;18(1):16-20. doi: 10.1097/MBP.0b013e32835d131c. PubMed PMID: 23275314.


Appendix – Related Resources on this Site

Working with PubMed – Part 1: Getting started with a shortcut

Working with PubMed – Part 2: Favoriting abstracts

How to receive research paper e-mail alerts

A Video Celebrating 10 years of PubMed Central

How to improve your search results with Medline

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

Working with Pubmed – Part 2: Favoriting Abstracts

PubMed is a large database of biomedical citations maintained by the US government. PubMed is globally accessible and aids clinicians and biomedical researchers around the world with their scientific enquiries. There are many very useful features in PubMed for refining search queries. Setting up an account with NCBI is an extremely useful option which helps you to refine, save and modify your searches as well as offering many other possibilities. The video above is another in the series on the NCBINLM (National Library of Medicine) YouTube channel. The video is just over two minutes and takes you through the process of favoriting abstracts that you have retrieved from searches.

Favoriting describes the action of labelling an abstract as a favorite and is fairly self-explanatory. Twitter users will be familiar with this term which is analogous to bookmarking in browsers. If you have entered a search query and looked at the search results the favorite option will not be immediately available (I’m assuming here that you have an account with NCBI and are logged in). As soon as you click on one of the abstracts, the favorite option will appear when the abstract is displayed separately. This makes sense as otherwise you would be favoriting all of the abstracts returned by the search.

This is one of many features available inside the NCBI account and the video illustrates some of the other strategies that this can be combined with.

Appendix – Related Resources on this Site

Working with PubMed – Part 1: Getting started with a shortcut

How to receive research paper e-mail alerts

A Video Celebrating 10 years of PubMed Central

How to improve your search results with Medline

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

Working with PubMed – Part 1: Getting Started with a Shortcut

Figure 1 – Preferences Page in NCBI

 

This is the first in a series on using PubMed. PubMed is the gateway for several important biomedical databases including Medline. Being able to work with PubMed is a very useful skill in the life sciences. In the first part the reader will need to set up an account with the National Center for Biotechnology Information. I will assume that the reader has done this. The first lesson is very simple and focuses on preferences. As someone that uses PubMed frequently I find shortcuts really useful. The shortcut i’m going to discuss here is one used in searches. The first step is to go to the preferences page once you’re logged into your NCBI account. Then under PubMed Preferences click on ‘Result Display Settings’. Finally select abstract, 200 and Pub Date under preferences. Every time you log into your NCBI account and use this to access PubMed, these preferences will be used automatically.

So what does all this mean? Well firstly the ‘abstract’ preference simply means that all returned results will be displayed with the abstract. This enables you to get a quick overview of the paper without needing to click on a hypertext link to get to the abstract. The second preference ‘200’ means that each page will feature 200 results per page. The default is 20 which means you have to click 10 times to see all of the results. The only drawback is that you need appropriate resources on your computer to avoid a sluggish response. Finally the ‘Pub Date’ preferences means that the articles will be displayed in chronological order. This is especially useful if your interested in the most recent papers in the field.

So that’s the lesson – brief and simple and you’ll see the benefits after using the saved preferences on just a few occasions. Of course if your needs are different then you can just adjust the preferences accordingly.

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

The Growth Of PTSD in Anxiety Research

The article reviewed here is a brief report – original research by Mark Boschen who is based at the School of Psychology, Griffith University, Southport, Australia.

The idea is a neat one and fairly easy to replicate – as it involves looking at research articles on Medline. Indeed Boschen has submitted or published a number of other articles using this approach. Boschen cites various pieces of research which suggest a trend towards a greater coverage of anxiety disorders in the psychiatric literature.

Boschen selects a number of terms related to anxiety including agoraphobia, OCD, acute stress disorder and of course PTSD before entering these as search queries into the medline database. The number of articles obtained each year are counted and also retrieved to ensure they are relevant. Boschen found that there was a trend to a linear increase in the number of articles produced per year (linear regression analysis showed r = 0.97 with p < 0.001). PTSD articles increased from 16.3% of the total number of ‘anxiety articles’ to 38% in 2001-2005.

However there are a few cautions in interpreting these results. I’ve been interested in this area myself and have been involved in some preliminary research. The first point is that the software for accessing Medline was not mentioned. There are numerous interfaces for searching the Medline database and the software itself is important in determining the results. It is difficult to anticipate how the different interfaces might bias the results.

The next point is that a small number of anxiety disorders are explicitly mentioned and these do not include terms such as neurasthenia, dissociative disorder or specific phobias such as acrophobia or arachnophobia. Thus it is more than likely that the proportion of articles represented by PTSD was overestimated.

Another point is that there are numerous publications that are not cited in the Index Medicus which forms the basis for the medline database. Thus there is a substantial amount of literature on PTSD and anxiety disorders which will not have been identified from this search. If there is a trend towards increasing PTSD research in established journals then perhaps research bucking this trend will find a home elsewhere and PTSD research will have been overestimated as a proportion!

A more tricky issue is that of nomenclature. Thus within the MeSH headings of medline abstracts – tags which help to identify articles more easily – there are occasional changes in categorisation. This means that PTSD may have been ‘filed’ with anxiety disorders initially. There is no mention in the paper of the year in which PTSD was created as a MeSH heading. This means that PTSD research could have been underestimated in the earlier years examined in the study. It would have been nice to see some graphs of the other anxiety disorders mentioned to (superficially) examine some of these issues.

Nonetheless, it is difficult to argue with the conclusion that the number of PTSD studies has increased. Regardless of whether all articles are included, the results most likely represent a trend in the overall literature. Boschen has clearly put a lot of hard work into this study and done so single-handedly and the results are valuable.

What is remarkable is that if these trends continue, by 2010 there will be over 400 articles per year. This is an exciting area for research as it points to the overall process of doing research from a strategic perspective.

Disclaimer

The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.