PubMed searches

[cortig]

Hi All,

 

I just created a simple workflow for performing searches on PubMed (biomedical literature searches).

It’s right here (zipped archive).

 

          Corentin

 

 

==-==-==

Update (Feb 1st): I updated the version on the same link with the modification “hankydysplasia” submitted belowe just in case people don't read down the thread and miss his link. Now includes an option for searching for MESH terms witht he Alt key down (and a nicer-looking icon).

[hankydysplasia]

Thanks.  FYI you can do this in the custom searches list.  To make it more workflowy, I've added MeSH search with ALT.  I've also made the logo transparent instead of white so that it looks better with themed backgrounds.

 

https://dl.dropbox.com/u/417808/Search%20PubMed.alfredworkflow

[phyllisstein]

How inspirationally nifty! I'll have to see if I can't do something similar with JSTOR one of these days.

[cortig]

Thanks.  FYI you can do this in the custom searches list.  To make it more workflowy, I've added MeSH search with ALT.  I've also made the logo transparent instead of white so that it looks better with themed backgrounds.

 

https://dl.dropbox.com/u/417808/Search%20PubMed.alfredworkflow

 

Very nice! I clearly didn't think about MESH terms.

 

 

          Corentin

 

[cortig]

Thanks.  FYI you can do this in the custom searches list. 

 

 

On that note, I thought about a custom search, but I'm not sure how you can share a custom search…

Sharing and installing a workflow is easy and I suspected some users might either not figure out the syntax for the custom search for PubMed (I know it's easy with the current PubMed syntax, but some users are *not* all that tech savy).

 

 

          Corentin

 

[Filoumino]

Wow, great! Thanks!

[cortig]

How inspirationally nifty! I'll have to see if I can't do something similar with JSTOR one of these days.

 

The search link is easy:

 

http://www.jstor.org/action/doBasicSearch?Query={query}

(obviously {query} is the query term). You can create an easy custom search for it as “hankydysplasia” mentioned, but if you want, I can create a workflow for you that will do the same thing.

You could even take the PubMed workflow and edit the link and keyword in there to search JSTOR instead.

 

 

          Corentin

 

[cortig]

How inspirationally nifty! I'll have to see if I can't do something similar with JSTOR one of these days.

 

Well, I just created a workflow for JSTOR: http://www.alfredforum.com/topic/501-jstor-searches/

The workflow uses modifier keys to restric the searches to different subgroups.

 

 

          Corentin

 

[GamerChase]

As a nursing student, this could be absolutely incredible with one alteration... the ability to choose search results within Alfred, similar to what's seen in simonbs's search IMDB workflow, so that it takes you directly to the PubMed Health article you desire.  Is this a possibility?

 

...please please please...   

[cortig]

As a nursing student, this could be absolutely incredible with one alteration... the ability to choose search results within Alfred, similar to what's seen in simonbs's search IMDB workflow, so that it takes you directly to the PubMed Health article you desire.  Is this a possibility?

 

...please please please...   

 

 

It's not just an alteration… It's a whole project onto itself. You'd need to parse the results from the HTML result page while maintaining the links to the corresponding articles, and the selecting one of the results would open up the corresponding new page in your web browser anyway.

In addition, I see a lot of disadvantages:

• You can't narrow down the search by adding terms
• You can't see more than a few results
• You can't perform any action for the search (like generating an RSS stream for the saved search)

…and after all that, you still have to open the web page.

It sounds like a lot of work for close to no gain

 

 

          Corentin

 

[GamerChase]

It's not just an alteration… It's a whole project onto itself. You'd need to parse the results from the HTML result page while maintaining the links to the corresponding articles, and the selecting one of the results would open up the corresponding new page in your web browser anyway.

In addition, I see a lot of disadvantages:

• You can't narrow down the search by adding terms
• You can't see more than a few results
• You can't perform any action for the search (like generating an RSS stream for the saved search)

…and after all that, you still have to open the web page.

It sounds like a lot of work for close to no gain

 

 

          Corentin

 

 

Understand, I know almost nothing about how the complicated stuff works. I get that it's guaranteed to be more complicated than I think, but I figured it was worth checking.  

[cortig]

Understand, I know almost nothing about how the complicated stuff works. I get that it's guaranteed to be more complicated than I think, but I figured it was worth checking.  

 

 

In addition, I don't think there is even enough space in the Alfred UI to display everything you'd need for each result (list of authors, title, journal, volume, year, pages, etc).

 

 

          Corentin

 

[phyllisstein]

The search link is easy:

 

http://www.jstor.org/action/doBasicSearch?Query={query}

(obviously {query} is the query term). You can create an easy custom search for it as “hankydysplasia” mentioned, but if you want, I can create a workflow for you that will do the same thing.

You could even take the PubMed workflow and edit the link and keyword in there to search JSTOR instead.

 

 

          Corentin

 

 

I'll have to check out your JSTOR workflow! I had in mind scraping the results for a PDF link, rather than just doing a custom search.

[hankydysplasia]

David Ferguson created this one here which blows the results back into Alfred:

http://www.alfredforum.com/topic/488-easy-way-to-create-web-searches-with-results-in-alfred/?p=2296

[ctwise]

This intrigued me so I came at it in two different ways. One script filter looks up the term being entered and provides a list of articles with titles, dates and authors. Choosing one of the entries takes you directly to the summary page.

 

The other script filter does an autocomplete for search terms, e.g., 'diabetes' gives you options like 'diabetes mellitus'. Choosing one of the entries takes you to a search page for that search query.

 

Pick your poison.

 

 

http://tedwi.se/u/d5

 

[cortig]

Impressive work!!

 

 

          Corentin

 

[jrmargelidon]

This intrigued me so I came at it in two different ways. One script filter looks up the term being entered and provides a list of articles with titles, dates and authors. Choosing one of the entries takes you directly to the summary page.

 

The other script filter does an autocomplete for search terms, e.g., 'diabetes' gives you options like 'diabetes mellitus'. Choosing one of the entries takes you to a search page for that search query.

 

Pick your poison.

 

 

http://tedwi.se/u/d5

it's really a good one

 

I've found a strange behavior. if you type "pubmed rochebro" you wait and it gives you the articles linked to the authors. this if fine.

 

But you add more letters to finish the author name (the complete name is rochebrochard) and / or delete some, at some point you have the search google /  amazon / wikipedia for "pubmed xxx"

 

It looks like a bug, bug I'm not sure if it's Alfred's or not.

[ctwise]

it's really a good one

 

I've found a strange behavior. if you type "pubmed rochebro" you wait and it gives you the articles linked to the authors. this if fine.

 

But you add more letters to finish the author name (the complete name is rochebrochard) and / or delete some, at some point you have the search google /  amazon / wikipedia for "pubmed xxx"

 

It looks like a bug, bug I'm not sure if it's Alfred's or not.

 

It's a bug in the workflow, due to UTF-8 encoding. Fixed and a new version was uploaded.