So I’d collected a cast number of citations in Zotero, but needed to export them in a custom format to a .csv if I wanted to upload them into another database. I was also a little put-off that Zotero’s search wasn’t more powerful (that’s just me being picky- Zotero is awesome and anyone who says otherwise will get an earful from me).

A little Googling led me to this post by Royce Kimmons that discusses how to query Zotero’s SQLite database.

(This post is largely a short summary of Mr. Kimmons’- but it is such a neat trick that I wanted to share it.)

Zotero’s database is SQLite. For me, the database was located here:

C:\Users\[UserID]\AppData\Roaming\Mozilla\Firefox\Profiles\[random string].default\zotero\zotero.sqlite

In your OS, it may be elsewhere. According to Zotero’s support documentation,  ”[t]he quickest and most reliable way to find your Zotero data directory is through the “Show Data Directory” button in the Advanced tab of your Zotero window.”

Once you find it, COPY it somewhere else to work with it. Don’t monkey with your original database.

Then you need a tool for working with the copied database. Kimmons recommends SQLite Manager, a Firefox plugin, but I ended up using SQLiteStudio (free, portable application that requires no installation) and found it much more pleasant to work with.

Even knowing next to nothing about Zotero’s data model, I could modify Kimmons’ query to get just the data I wanted, exactly how I wanted it.

Another option is to export the SQLite as SQL and run your searches using your favorite database tool (even MS Access).

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I’ve been slowing realizing over the last several months that neither Liz nor I religiously check our home answering machine. This is bad, because there may be important messages.

We both, however, check our email religiously. I was convinced there was a better way for us to manage the calls to our home that we missed. Eventually, I realized that Google Voice would work quite nicely. Here’s what I did:

In Google services:

1. Set up a new Gmail account.

2. Signed up for Google Voice and chose a number that is local for us.

3. In Settings > Phones, I turned OFF all phones (DEselected the check boxes)…so that none of the phones associated with the account would ring when this number was called. This means that all calls to this number would, by default, go straight to voicemail.

4. In Settings > Voicemail & Text, I recorded a new greeting appropriate for our home phone and set it as the default greeting for all calls.

5. In Settings > Voicemail & Text >Voicemail Notifications, I set notifications to be sent to the account’s Gmail address.

6. I also elected on this screen to have voicemails transcribed. These transcriptions are far from perfect, but they often provide enough information to let us know what should be done with the message.

With my home phone service provider:
(Our home phone provider is Time Warner Cable- they have a VoiceZone service you can sign into to manage these settings yourself. Your provider may or may not have something similar- call them and ask!)

I set calls to forward to my new Google Voice number if we did not answer after four rings:

Back to the new Gmail account:

7. Now that this new Gmail account was receiving emails from Gvoice with the date/time, number, the machine transcription of the message and a link to play the audio, it was time to make sure that Liz and I both got them.

First, I set up all emails from this account to be forwarded to my main email account. Next, I set up a filter to make sure all such emails were forwarded to Liz’s main email account.

So now we were each getting the email when someone called our home phone and left a message.

8. Lastly, I wanted to make sure that neither Liz nor I would accidentally overlook such voicemail-containing emails when we received them, so I made one more filter for each of us that slaps on a big red label:

So here’s what it looks like in my inbox when someone calls our home phone number and leaves a message:

The email contains a link to a Web-based audio player through which either one of us can listen to the message if the machine-transcription is insufficient (as it often is).

Results:

1. We can’t fail to notice that we have messages (as we sometimes do now with the little blinking red light on our answering machine).

2. We no longer have to worry about whether one of us or the other has heard a particular message and wonder if it can safely be deleted. We can manage our own listening as we would our own reading. It is as if we are both “cc’d” on voicemails left on our home phone.

3. Neither of us can accidentally delete old messages.

4. We can both easily access our messages anywhere.

5. We’re throwing out our answering machine without having to pay anyone for voicemail service.

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“I wonder if you have found a free add-on for Word 2003 that includes medical terms in the spell check feature and is secure enough for me to recommend to my users at the hospital?”

This is such a great question and something that has come up at my place of work previously. Out of the box, Microsoft Office Word doesn’t recognize a whole lot of the specialized medical vocabulary that people at our hospital use every day. The result of this is that Word frequently fails to recognize clinical terms and underlines them in red, essentially making them false positives for spelling errors.

Only one employee in my department has Stedman’s medical dictionary installed in her copy of Word 2003 because paying a license for each copy used in an entire hospital would add up to an unmanageable sum quite quickly.

Among the books made available to all employees through our hospital’s intranet is a medical dictionary- and that’s okay for the kinds of people who don’t mind stopping what they’re doing to look up a word, but it would be so much faster and easier for Word to be able to spell-check and correct spelling issues with medical terms.

So I promised the friend I’d think it over and come up with some recommendations.

In MS Word, a “dictionary” is just a list of words.

That’s all. Nothing on pronunciation, etymology, or definition.

A quick search reveals that these “dictionaries” (word lists) are stored as .dic files.

Microsoft even tells you how to MAKE a custom dictionary.

So, what we really need is a list of words to turn into a custom dictionary.

OpenMedSpel is pretty awesome.
Free, open source, and released under a GPL license, OpenMedSpel includes nearly 50,000 medical terms. This is all looks great, but while they have a plug-in for OpenOffice, there doesn’t seem to be one for MS Word.

No problem, though. I took apart a .dic file, and it is pretty much a .txt file with a word on each line, renamed with a “.dic” file extension. This means we can just download the .txt version (in the .zip fail available here) and rename it from OpenMedSpel 100.txt to OpenMedSpel 100.dic and save it to our computer.¹

To add this .dic file to Word (2003 or 2007), we just follow these instructions from Microsoft:

1. Start Word.
2. In Microsoft Office Word 2003 and in earlier versions of Word, click Options on the Tools menu.

   In Microsoft Office Word 2007, click the Microsoft Office Button, and then click Word Options.

3. In Word 2003 and in earlier versions of Word, click Custom Dictionaries on the Spelling & Grammar tab.

   In Word 2007, click Proofing, and then click Custom Dictionaries under When correcting spelling in Microsoft Office programs.

4. Click New to create a new custom dictionary.
5. In the File name box, type a name for the
   new custom dictionary, and then click Save.

   The custom dictionary is added to the Dictionary list.

6. In the Custom Dictionaries dialog box, click OK, and then click OK in the Options dialog box.

That’s it. You have medical term spell-checking in Word 2003 or Word 2007.

PLEASE NOTE: I would not hesitate to recommend this solution to my hospital’s CIO and could demonstrate to him why there is absolutely no security risk in adding this .dic file- but I wouldn’t go around setting it up on other employees’ computers without his go-ahead.

Want to go with a bigger word list?

The MTHerald blog has built on the OpenMedSpel list to one that contains almost 100,000 terms. I downloaded and checked it out and will recommend it as a harmless, malware-free .dic file- but as with any file I don’t host myself, I can’t promise that’ll be true tomorrow.

There are a number of other sources for lists of medical terms or abbreviations you can find online and add to your .dic file as suits you.

Know of any other especially good sources? Please advise in the comments.

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[via: http://liblog.mayo.edu/2009/10/13/video-tutorial-my-ncbi-custom-filters-and-sharing-collections/]

Melissa rules.

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The Mayo Clinic Libraries’ Liblog has a screencast by Melissa Rethlefsen on PubMed’s new Advanced Search features that you can embed on your own page:

In case I have not mentioned it recently: Melissa is awesome.

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Yay!

You can buy a copy from:
Springer Publishing

or here:

I’m looking forward to eventually seeing it in WorldCat.

Congratulations to Melissa Rethlefsen (who wrote a heck of a lot more than I did)! You should really go email Melissa now and tell her how much she rocks.

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So I subscribe to lists using a Gmail account. Here’s why:

• Separating list emails into a separate account allows me to treat them, as a whole, in a different manner than emails from higher-priority senders (patrons, co-workers, etc.). This lets me keep my attention focused where it needs to be.
• Because list emails are in a separate account, I also never have to annoy other list subscribers with “out-of-office” messages that get sent to whole list- because there’s never need to turn on an “out-of-office” message for this account.
• Threaded conversation: Instead of having one line per each email received, Gmail inboxes have one line for each conversation. That means that my Gmail lists inbox doesn’t get as cluttered. It also lets me efficiently manage whole conversations instead of individual emails, even if a particular email is sent to multiple lists I subscribe to. Example image below shows that all (23) emails on the topic of “abortion” being made a stopword in POPLINE are one (expandable) line item in my Gmail inbox:
  
• Mute function: If there’s a particular conversation(/thread) that I’m not interested in continuing to follow, I can “mute” the conversation and not need to see any further emails in that thread.
  
• Gmail’s search capabilities are awesome. If I want to find a MEDLIB-L email I remember was sent by Michelle Kraft about OvidSP, I can search for label:medlib-l from:Kraft OvidSP and find it really, really quickly.
• Gmail’s filters are powerful and easy to use.
  • Assigning labels: You can set up your Gmail filters to automatically assign colorful labels based on information that lets you scan your email quickly. For example, you could set your account up to automatically assign colored labels based on which list the conversation is from.
    
  • Forwarding based on content: You can combine Gmail’s great searching and filtering to monitor your list subscriptions. Say you subscribe to multiple lists, but only really want to pay attention if Young Adult services are mentioned. I can create a filter from the search for young OR youth OR “YA” and set any hits from that search to be automatically forwarded to my primary email address so it comes to my attention. Imagine the time saved by not having to manually look through all those emails for mentions of the topic I want to follow.

Bonus tip: Would you rather read your list email information in your feed aggregator? Set your lists Gmail account to forward the emails to MailBucket, and MailBucket will give you the content in an RSS feed.

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• Added a feed from Google Blog Search (which uses a fairly narrow search) to the Superfeed.
• Added filters to the Superfeed to screen out a handful of false positives.
• Embedded Grazr widget (see end of post)

[/edit]

[edit2]
Wouter has made the Superfeed available in Dutch.
[/edit2]

To make sure I don’t miss any online chatter about Computers in Libraries 2008 (which starts next Monday), I’m subscribed to the following feeds:

• LibWorm
  [LibWorm feed]
• Feed for Twitter “CIL2008″
  http://twitter.com/statuses/user_timeline/10313522.rss
• This feed aggregates all tweets from CIL08 and from various CIL-related searches in tweetscan.com:
  http://feeds.feedburner.com/AllCil2008Tweets
• CIL 2008 Wiki feed
  http://cil2008.pbwiki.com/rss2.php
• Technorati tag: CIL2008
  http://feeds.technorati.com/tag/CIL2008
• del.icio.us tag: CIL2008
  http://del.icio.us/rss/tag/cil2008
• YouTube: CIL2008
  http://www.youtube.com/rss/search/CIL2008.rss
• SlideShare tag: CIL2008
  http://www.slideshare.net/rss/tag/cil2008
• Flickr tag: CIL2008
  http://api.flickr.com/services/feeds/photos_public.gne?tags=cil2008&lang=en-us&format=rss_200

If you’re like me, you’d rather subscribe to one feed than several, so all the feeds above are included in the feed below:

Single feed that combines all of the above:
http://feeds.feedburner.com/Cil2008Superfeed

Grazr widget below will let you browse the Superfeed contents:

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The idea behind ReadBurner is that it aggregates counts of items that are frequently shared in Google Reader.

First a point of clarification: ReadBurner doesn’t get its data directly from Google Reader in aggregate via an API- it gets the data from the RSS feeds of public linkblogs fed by Google Reader. This is explained on ReadBurner’s About page:

“ReadBurner aggregates items that are shared on the Google Reader.

This works by constantly updating RSS feeds of currently several hundred linkblogs. In order to filter out the best stuff ReadBurner counts, whenever an item is shared by multiple persons.”

ReadBurner’s creator, Alexander Marktl, allows users to submit new linkblogs (or does he?), but he can’t ever gather all of them…so I suspect that ReadBurner won’t ever really represent the sharing habits of Google Reader users. Further, I find it hard to believe that Google would not be working on a similar project that actually will have access to all the sharing data from Google Reader users in its entirety…at which point ReadBurner will stop being interesting.

In the meanwhile, ReadBurner is still pretty neat. The features I’d most like to see added are search and to have searches outputted as RSS feeds. I’ve had no luck getting ReadBurner to output the feeds I want, but I have managed to make it filter for just the stuff I want.

I really wanted a form so I could search and, for instance, see if any posts at this blog were being frequently shared. Sadly, no such search form exists at ReaderBurner.

Fortunately, we can make it search in a limited fashion even without a form by messing with the URL a bit.

The back end of ReadBurner is PHP/MySQL, a combination I gained some familiarity with through working on LibWorm with Frankie Dolan (and by using WordPress to power this blog).

All our little hacks will start from this URL:
http://www.readburner.com/index.php?

From here, we can play with two parameters, r and a.

r = The name of the source the item came from
a = The name of the author of the item

So if we wanted to see items in ReadBurner that were shared from davidrothman.net, we just need to tack r=davidrothman.net onto the end of http://www.readburner.com/index.php? like so:
http://www.readburner.com/index.php?r=davidrothman.net

For another example, shared items from Boing Boing could be found like so:
http://www.readburner.com/index.php?r=boing%20boing

But what if we want only to see shared items items from Boing Boing which were authored by Cory Doctorow?

To our existing http://www.readburner.com/index.php?r=boing%20boing, we’ll tack on &a=Cory%20Doctorow¹, giving us:
http://www.readburner.com/index.php?r=boing%20boing&a=Cory%20Doctorow

Marktl himself shows how to tweak the URL of ReadBurner to filter for language and for a minimum number of shares.

Of course, there are easier ways to get this kind of info from ReadBurner. Once could subscribe to the feed for the recently submitted items and then filter using Yahoo! Pipes or one of the other free tools for filtering RSS feeds…but that’s not as much fun.

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Check it out: Noted biblioblogger Steven Cohen is one of the top sharers on ReadBurner.

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Connie Schardt pointed out that it could be useful for finding handouts, tutorials and other teaching materials. Here are some ideas on how this might be done.

• Say you’re looking for PowerPoint presentations about Evidence based medicine. You’d want to seach for “Evidence Based” or “EBM” or “EBP” where the file type is .ppt or .pps, right? To perform this search in the Medical Library search engine, just enter:
  (”evidence based”|EBM|EBP) (filetype:ppt OR filetype:pps)
• If you’re looking for handouts about PubMed:
  handout pubmed (filetype:doc OR filetype:pdf)

Your turn: What other searches would be useful?

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