Saturday, May 20, 2006

Back Again, proposal of a new project

Dear ISEEPI-South Asia Members, the following is an outline of a project I thought that might be of use to all of us who regularly use literature sources and search for them on the web.

Project Name: ISEEPI-SA Bibliography Project

Aim of the project
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The project aims to build a database of online/offline repository of literature, that is peer-reviewed and available over the web using a common search algorithm (one or several search algorithms) where we can access and download. The literature repository may be of different topical areas, including for example indoor and outdoor air pollution, arsenic toxicity, lead poisoning, benzene toxicity and so on. We can restrict the repository only for research that has been conducted in South Asia

How do we build the repository
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Using search engines like Pubmed and social bookmarklets and programs like Connotea (www.connotea.org), we can quickly build a large repository of articles that can then be downloaded, edited, or accessed. Some articles will have free full-text online access, and we can mark them as such. For others, some of us may have full-text copies that we can then distribute among our members whoever requests them. That way, we can build up a large effective repository of articles and literature database sources that can come handy for our personal research or for writing research reports, working on theses, and working on writing grants, etc.

What's needed at the time
--------------------------

As you may understand, this is a large project. With different topics that we need to consider, it is not possible to be conducted by one person. We need a group of us to collaborate and work on it. If any of you are interested in participating in this project, please email me off-list (arin.basu@gmail.com).

How much time will you need for the project?
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Very little really. If you do regular internet searches for your articles on the web, it will not take much time to contribute to the growing collection at all. Further, as the collection grows, you need not do extensive search for articles for your research from pubmed or other bibliographic repositories, since our ISEEPI repository of articles will already be available to you.

Thus, if you can spend five minutes a day say now, (or even less, if you already have endnote libraries available that you want to upload), you will save yourself weeks to months over time. Think about it.

What will you have to do if you want to participate in the project?
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All you have to do at the time is to visit http://www.connotea.org
and start adding your bookmarks. The process is very simple. If you already have a collection of references, say in Endnote, you can convert them to "file.ris" format (where file = name of the file you want it to give) and then upload them directly to connotea. That way, you can later access all your articles and bookmarks for your later use. That's all. You can also use
http://www.hubmed.org
for your literature search (as opposed to http://www.pubmed.com), although you can also save your bookmarks from pubmed search as well.

In subsequent posts, I will try to cover the topics of using connotea or other social bookmarking programs and Hubmed to work on this. For the time being, let's stick to connotea and build it up. Later on, we can build our own database.

Is there something I can see?
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Yes, for the time, if you want to see how the database looks like, you can check out my database on arsenic toxicity that I am building, here:

http://www.connotea.org/user/arin

Here, I got seven entries. But the library is being built, and we can literally have thousands of entries. Once we build the literature database (unlike pubmed, which is a vast repository, this will be a repository that contains the literature and other sources that "we" want to use), we can then export whole or part of it to our hard disks for using. You can access the repository for all types of machines, all you need is an internet connection.

What next?
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If you are interested to build the extensive repository of articles, please write to me at arin.basu@gmail.com, and we can take it from there.

Thursday, January 26, 2006

List of ICD-10 codes: Information From Answers.com

ICD-10 codes: a listing

Anyone interested in health outcomes will find the following website invaluable in terms of what they have achieved. In a simple web based format, they have archived the ICD-10 codes with appropriate listing. Wish someone had listed the clinical modifications as well.

List of ICD-10 codes: Information From Answers.com

Wednesday, January 25, 2006

pdf text table conversion free - Google Search

Pdf to text table converter programs

Ondine (ove@berkeley.edu) asked this evening if I knew some online or other tools to convert pdf tables to text files. A quick googling led me to several good software. Some free, others were not, kind of shareware. Here are the results of the google search.

pdf text table conversion free - Google Search

There are programs of course, for converting text files to PDF. I use latex and that come bundled with macros for doing it. Openoffice, available at http://www.openoffice.org is the other one. You can save all your office files as PDFs.
How to create RSS feeds from pubmed search

Introduction

RSS stands for really simple syndication. What this means is, you can get updated contents of websites into a reader (called a feed reader), and read the contents as you wish. The contents will be readily updated and be delivered to your feed reader. Practically, then, if you searched Pubmed for your research topic, you could then have a list of your updated topics every day or every week with least effort. You do not need to retype your search algorithm; set up the search algorithm once and you get the feeds every week, updated and you see new articles get added to your search terms. Also, if you read your feeds with a feed reader, you do not clog your mail boxes.

Methods

What will you require

1. An RSS reader. You can download RSSReader from any of the following site:

http://www.rssreader.com
Download and Install the Rss reader on your computer

2. An Internet connection to access pubmed and a browser
(If you use Mozilla Thunderbird, then you do not need an RSS reader.)

How to do it
For pubmed

1. Go to Pubmed (http://www.pubmed.com),
2. Type your search term in the search box and then,
3. In the selection box, select "send to rss feed" option
4. In the next page, click on the "create feed" button
5. Click the button that says, "XML" (orange color):
6. Click the XML button -- this will open a new window
7. Copy the URL (the website address that you see on the top of your browser)

For RSS READER

8. Fire up the RSS Reader
9. Click the "Add" button on the RSS reader
10. The website URL will be automatically entered. If not, paste the URL
11. Enjoy the feeds from the site.
12. When you need updates, click "Get" and it will get the headlines for you.

Discussion

This was the simplest way to set up RSS for your pubmed search. There are several other ways as well. If you do not want to install a new software or do not know how to do that, use the Google's reader service (for this you have to create an account at Google) at http://reader.google.com
Finally, I hope to write a script that will take your queries on pubmed and will get you emails every week on the updates. But that's not coming any sooner.

References

Will be added later.