Writing Research Papers, Presentations and Blogs With Google Docs

The advent of cloud-based office suites like Google Docs, have changed the collaborative process of research writing.  Google Docs allows you and your collaborators to work on the same document at the same time.  No more sending versions of a document back and forth as each person works on a particular section, followed by a bunch of editing at the end to give the paper a cohesive voice.

Recently, Google added the “Research” tool to make reference management easier.  To get started, create a new document in Google Docs, and select Tools/Research.  A Research panel will appear to the right of your document as shown below.

gdocs

A search field at the top of the panel lets you search for assets (images, articles from Google Scholar, posts from your Google + account, quotations and dictionary words) to include in your article.  In my case, I’m interested in adding citations on “pancreatic cancer genomics” to my paper, so I enter the search terms, select Google Scholar, and view the results.

As you hover over each search result, a link will appear that will take you to the original paper.  You can insert the paper as a footnote, or insert the citation at your current cursor location.  The citation can be formatted using MLA, APA, or Chicago Style formatting.  No support yet for other citation formats like ACS.  The only other fly in the ointment seems to be getting Google Docs to use end notes instead of footnotes.  Which limits its usefulness when writing papers for publication.

On the other hand you can use the Research tool in Google Docs presentations as well as papers.  Presentations will often include both a footnote at the bottom of a slide, if there is a quotation, or other citation on the slide, and the final slide will include the all of the References along with links to PubMed, or other websites.  You still have to go through all of your slides and collect all of the references manually.  It would be nice if all citations were tracked in the Google Docs Presentation, and automatically added to the final slide or to a designated “References” slide.

Lastly, I wanted to mention that you can use Google Docs to compose blog entries.  In fact, I often find it easier to use than WordPress’s editor.  Wordpress tries to provide similar functionality for finding useful additions (like images, and related articles) to blog postings but I often find the results too limiting, and the Research tool does a more comprehensive job of finding citations.

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ClinVar – A database of mutations and their clinical relevance

One of the key pieces of the drug discovery puzzle involves determining the clinical relevance of the target.  Over the past few years big pharma have been pulling back from this critical part of the drug discovery process and ceding this territory to biotech startups and academia.  Until recently, the only major database that could provide this type of information was OMIM (Johns Hopkins Online Mendelian Inheritance In Man).  However, the focus at OMIM was more on providing a wide-angle view of the genes involved in particular diseases.

Moreover, if you wanted to understand a disease and all potential targets for that disease, the most you could expect from an OMIM record was the Reader’s Digest perspective.  You have only to compare the OMIM record for pancreatic cancer, with the NCBI’s eBook on the same subject to get an idea of the difference in the depth of coverage of the subject.

Recently, the NCBI began work on the ClinVar project. The purpose of ClinVar is to “provide a freely accessible, public archive of reports of the relationships among human variations and phenotypes along with supporting evidence”.  This YouTube video gives you an overview of ClinVar.  The data in ClinVar includes records found in OMIM, but also data from dbSNP and other data sources.

One caveat about ClinVar, the database is still a work-in-progress. A simple search for “pancreatic cancer” yields hits for hereditary pancreatitis, whereas a search for “pancreatic adenocarcinoma” yields a much more targeted set of hits.  The results are also incomplete, since you won’t find any references for the KRASG12D mutation found in the majority of pancreatic cancers, nor will you find reference to mutations in TP53 (found in approximately 50% of patients), or BRCA2 mutations.

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Blogging and Google Reader: The Missing Link

Image representing Google Reader as depicted i...

Image via CrunchBase

In my previous post I talked about the impending shutdown of Google Reader in July and I listed some of the features that I’d like to see in a Google Reader replacement.  One of the major missing pieces in the puzzle has always been getting articles that you’ve saved into a blog posting.

WordPress has a useful feature using Zemanta that identifies related blog postings and lets you add them to the bottom of your blog posting.  And while that’s useful it really doesn’t go far enough.

I’d like to be able to select a number of search hits, or articles from my RSS feed and add them to my post.  If the articles are journal articles, then I’d like to see them formatted with the appropriate PubMed ID and link, and I’d like a mouseover that let’s me see the abstract of the article. It would also be useful to be able to format those for use in the references section of a journal article.

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What’s On Your Google Reader Wishlist?

Image representing Google Reader as depicted i...

Image via CrunchBase

This week Google announced that by July, their Google Reader service will be a memory. A number of companies have stepped up to the plate with announcements of services.  This includes companies like Digg and Feedly.  My current RSS reader service is Feedly, primarily because I like the magazine layout which makes it easy to read in Chrome, on my tablet and on my phone.

The announcements started me thinking though about what I’d like to see in a replacement service (beyond what Feedly currently provides).  Here’s the list I came up with:

  • The ability to search for RSS feeds.  Prior to using Google Reader I had to search web sites for their RSS feeds, and subscribe to each one individually.  Or use the JournalTOCs site to find journal-related RSS feeds. With Google Reader I could simply enter a search term and find all feeds that contained relevant content. Or use an existing RSS feed to help me “find more feeds like this one”.
  • The ability to subscribe to searches.  I’d like a button in the Google/Google Scholar/PubMed search results that let’s me subscribe to the search.
  • Google News integration.  I currently use Google News to keep up-to-date on a variety of topics.  For example, I have a search called “Mutation” that finds news articles about discoveries where a mutation was found to be involved.  It’s useful when  the etiology of so many diseases involve a genetic mutation.  Whenever I open my Google News page, there’s a Mutation channel that contains the latest news articles.  I’d like to be able to subscribe to that channel as an RSS feed.
  • Browser integration.  Any time I click on an RSS feed, I want my browser to automatically add it to my collection of feeds, and let me categorize the feed.
  • Share With Multiple Social Networks.  Right now, sharing is unnecessarily complex.  To share an article, you have to click on each service, and provide a comment and tag.  If you want to share on 4 different services, you have to repeat that process 4 times.  I’d like to click on an article, select the services I want to send the article to, and craft a short message.  When I click submit, I want to article to be shared on all of the services simultaneously, or select a time when I want the article to be shared.  This last requirement would allow me to target times when I know specific readers are most likely to pickup on the content.  For example, if you send content to Twitter subscribers who haven’t woken up yet, you’re not likely to get much of a response.
  • Filter Feed Content.  There are a lot of journal feeds that contain content I’m not interested in.  I’d like to filter those feeds to only show me relevant content.  I would be able to switch back and forth between the filtered and unfiltered content to see what I’ve missed.
  • Saving Content.  I’d like to be able to tag and star content.  This will let me create collections of articles with a particular theme.  It should also be smart enough to be able to extract tags from the RSS’s article element, and mine the abstract or content of the article for tags that I’ve previously used.  For example, if I’ve tagged an article with #KRAS, then if this new article also contains the term KRAS, I want the service to automatically apply that tag.  It should also automatically apply tags for terms found in ontologies — in particular terms having to do with genes, diseases, and drugs.
  • Creating & Sharing RSS Bundles.  One of the really useful features in Google Reader was the ability to bundle RSS feeds and share those bundles.  This made it easy for me to share my journal RSS feeds with friends.  It would be great if we could share those RSS bundles with Google Plus Communities.
  • Find Content From Social Network.  Let me find articles, and RSS feeds that people in my social network have recommended, starred, or tagged.
  • Use Any Kind of News Reader.  There are so many news reader applications out there, and everyone has their favorite.  I want to be able to export my RSS feed collection as an OPML file.  Whenever I launch my RSS reader it would simply sync with the OPML file.
  • Smart PubMed integration.  I often find myself doing PubMed searches and sharing the results in Mendeley or Google Plus:
    • it would be useful if I could see a histogram of the journals that contained my search results.  Those journals that contained the most hits are most likely to be the ones I should be paying attention to, and the ones whose RSS feeds I would most likely subscribe to.
    • I’d also like to see a histogram of authors to help me find the experts in a particular area.
    • I’d like to tag or save articles in a collection, and then do a “find more articles like this” search.
    • Show me a tag cloud of common terms in the articles of search result, or in a collection, and let me turn any of those terms into a new subscribable search.

What would you like to see in a Google Reader replacement?

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Latest Pancreatic Cancer Articles

Image representing Celgene as depicted in Crun...

Image via CrunchBase

During the recent ASCO GI conference, the big news was the release of the results of the Abraxane trials.  The data show that the lives of pancreatic cancer patients can be extended by two months when adding Abraxane into the standard gemcitabine treatment regimen.

Sally Church at the PharmaStrategy blog gave a good overview of the conference, and included an interview with Dr. Hedy Lee Kindler who gave us the clinicians perspective on the Abraxane results.

In addition to this Congress signed off on the Recalcitrant Cancer Research Act which provides funding for traditionally under funded diseases like Pancreatic Cancer.

News

Articles

Here are the latest additions to the Mendeley Pancreatic Cancer Genomics collection.

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Latest Pancreatic Cancer News & Articles

Micrograph of pancreatic ductal adenocarcinoma...

Micrograph of pancreatic ductal adenocarcinoma (the most common type of pancreatic cancer). H&E stain. (Photo credit: Wikipedia)

News

In this weeks news:

Articles

Here are the latest additions to the Mendeley Pancreatic Cancer Genomics collection.

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Pancreatic Cancer News & Articles

News

In this weeks news:

Articles

Here are the latest additions to the Mendeley Pancreatic Cancer Genomics collection.

Posted in Uncategorized | Tagged , , | Leave a comment