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Old Sep 13, 2012, 12:01 PM   #1
jojoba
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researchers: which apps do you use to organise your literature review notes?

I've been using excel a lot so far, but I'm looking into alternatives that will provide with me an enhanced version of the excel sheet format in the attached screen shot. In other words, I am looking for a program that will allow me to portray notes that I have made for lots of different journal articles side by side, so I can quickly analyse them across for certain factors (e.g. theoretical approach, research questions, journal of publication etc). (I am not looking for a general pdf management or writing tool).
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Old Sep 13, 2012, 02:13 PM   #2
sigamy
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Are these apps what you are looking for?

http://www.mekentosj.com/papers/

http://www.devontechnologies.com/pro.../overview.html
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Old Sep 13, 2012, 04:13 PM   #3
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Papers 2 by mekentosj (http://www.mekentosj.com/papers/) as mentioned above is definitely the way to go.

Excellent software to keep your papers organized and cite them, while writing manuscripts. There is also an iPhone / iPad app and the library can be synched via Dropbox. Has made my life writing papers a lot easier.
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Old Sep 13, 2012, 08:18 PM   #4
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I use Sente both Mac and iPad. I currently have just under 2000 references in Sente, a large proportion including the pdf (mostly downloaded and attached to a reference as I mine the reference from one of the academic databases--Sente is quite smart about importing and attaching these).

An interesting blog that hits on this and other useful topics on thesis writing, publication, etc is Organizing Creativity by Daniel Wessel. See his very interesting approach using Circus Ponies Notebook for Academic Writing at
http://www.organizingcreativity.com/...hesis-writing/

Wessel also discusses a number of other software tools for academic use (e.g., Sente, DevonThink,...) and a variety of approaches to academic work. One of the blogs I keep revisiting. You can also get a pdf of his book Organizing Creativity.

Here is an academic workflow by Kerry Magruder using Sente, DevonThink, Scrivener, and Pages (note: this is an archived web page, the original has disappeared from the net)
http://www.icyte.com/system/snapshot...f28/index.html
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Old Sep 14, 2012, 07:39 AM   #5
jojoba
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Thanks everyone!

I use Papers, Sente (mostly Sente these days rather than Papers) and DevonThink. Sente is primarily for reference management and annotation, and DevonThink I've so far used for other kinds of projects I'm working on (e.g. gathering and sorting information on a future book project, plus a lot of personal admin goes into DT).

What I'm missing with those apps (but perhaps this function exists somewhere in there and I haven't found it) is the opportunity to display selected elements (e.g. research question, theoretical approach, key findings) from a number of different texts side by side. I've currently been doing it in excel (see snapshot attached for example), but I'm looking to see if there are other/better ways of doing about that. Those links MathRulz posted had several ideas that were new to me, so I'm going to look more in depth at that to see if some of that could be usefully integrated into my work flow.
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Old Sep 14, 2012, 08:45 AM   #6
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Quote:
Originally Posted by jojoba View Post
What I'm missing with those apps (but perhaps this function exists somewhere in there and I haven't found it) is the opportunity to display selected elements (e.g. research question, theoretical approach, key findings) from a number of different texts side by side. I've currently been doing it in excel (see snapshot attached for example), but I'm looking to see if there are other/better ways of doing about that.
Hi

This is exactly what I was looking for for a long time.

I'm currently using Scrivener for citation and knowledge management. The main purpose of Scrivener is to write novels or papers but I found it to be very helpful for my needs in knowledge management.

I have a folder with all my texts as subfolders where I'm saving indiviual citations. Besides that I have a folder "topics" with different topics in subfolders. I copy individual citations of the papers to the different topic subfolders. By doing so, I can see either all citations of an individual paper (in folder "texts") or I can see citations/elements from different papers side by side (in folder "topics"). The disadvantage of Scrivener is that it doesn't feature reference management (auto-import of reference metadata etc.)

I would prefer using Citavi for it's brilliant integration of reference and citation/knowledge management. But unfortunately it's only available for Windows (even in the future).

I also suggest looking into those free apps:

- Zotero (as Firefox Addon or as standalone app)
- Mendeley
- Colwiz

Regards

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Old Sep 14, 2012, 11:46 AM   #7
MathRulz
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Quote:
Originally Posted by jojoba View Post

What I'm missing with those apps (but perhaps this function exists somewhere in there and I haven't found it) is the opportunity to display selected elements (e.g. research question, theoretical approach, key findings) from a number of different texts side by side. I've currently been doing it in excel (see snapshot attached for example), but I'm looking to see if there are other/better ways of doing about that.
Thanks for that screenshot. That helps clarify what you seek. I use OmniOutliner Pro for this and similar purposes. Much better for this purpose than excel. OO has educational pricing.
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Last edited by MathRulz; Sep 14, 2012 at 12:36 PM.
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Old Sep 16, 2012, 07:14 AM   #8
jojoba
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Quote:
Originally Posted by cntwtfrmynwmbp View Post
Hi

I'm currently using Scrivener for citation and knowledge management. The main purpose of Scrivener is to write novels or papers but I found it to be very helpful for my needs in knowledge management.

I have a folder with all my texts as subfolders where I'm saving indiviual citations. Besides that I have a folder "topics" with different topics in subfolders. I copy individual citations of the papers to the different topic subfolders. By doing so, I can see either all citations of an individual paper (in folder "texts") or I can see citations/elements from different papers side by side (in folder "topics"). The disadvantage of Scrivener is that it doesn't feature reference management (auto-import of reference metadata etc.)
I also use Scrivener and I think it's a great app, I do all my drafting in it, and keep all the literature notes relevant for a specific publication available there. I haven't used it for general pdf management and literature review, though, I just import the review notes I need for a particular publication.


Quote:
Originally Posted by MathRulz View Post
Thanks for that screenshot. That helps clarify what you seek. I use OmniOutliner Pro for this and similar purposes. Much better for this purpose than excel. OO has educational pricing.
Thanks for this tip, I'm looking at the trial version now. One question: One thing I really like about excel is that I can rearrange all the information based on different columns. So, for example, I might rearrange everything according to journal published, or according to date of publication. I was trying to do this in OmniOutliner Pro but couldn't get the sort number function to work for year of publication. When I do it for journal names, for some reason some of the entries are changed around and others are not, but they don't end up alphabetical This is a key function for me. I otherwise like the look of OmniOutliner, but if it can't do this I would probably stick with excel.
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Old Sep 16, 2012, 08:31 AM   #9
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Quote:
Originally Posted by Coltaine View Post
Papers 2 by mekentosj (http://www.mekentosj.com/papers/) as mentioned above is definitely the way to go.
Same.

Since you can write notes and use keywords, I think it will get the OP a long way.
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Old Sep 16, 2012, 08:45 AM   #10
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Quote:
Originally Posted by jojoba View Post
So, for example, I might rearrange everything according to journal published, or according to date of publication. I was trying to do this in OmniOutliner Pro but couldn't get the sort number function to work for year of publication. When I do it for journal names, for some reason some of the entries are changed around and others are not, but they don't end up alphabetical This is a key function for me. I otherwise like the look of OmniOutliner, but if it can't do this I would probably stick with excel.
Did you select "date" for the type of column that contains the year of publication?
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Old Sep 16, 2012, 09:21 AM   #11
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Take a look at these:

CP Notebook and Scrivener

Scrivener: Perfect for Dissertation

CP Notebook: Structured Creative Writing
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Old Sep 16, 2012, 11:19 AM   #12
jojoba
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Quote:
Originally Posted by steveoc View Post
Did you select "date" for the type of column that contains the year of publication?
Yes, but still nothing happens.

Thanks for those links. I do use CPN and Scrivener for my academic work, I just don't feel they give me the kind of comparative overview of literature that the excel sheet example I posted above provides. I might just stick with excel for that purpose, I was just curious if there were other things around. I'm still checking out OmniOutliner, though.
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Old Sep 16, 2012, 11:49 AM   #13
thasan
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mmm....endnote...it serves me well. handles more than 4k references with pdf i have in my lib with ease. and i sync it through dropbox, can open it in pcs.
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Old Sep 16, 2012, 12:42 PM   #14
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Thanks, thasan. I like endnote for cite while you write functionality, but it doesn't really serve the purpose I'm looking for here. I realise the original wording of my OP was very vague, so I have added some text to it now.
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Old Sep 16, 2012, 12:42 PM   #15
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jojoba,

Re: Sorting dates/numbers in OO Pro

Quote:
Originally Posted by jojoba View Post
Yes, but still nothing happens.
I'm not sure what the problem is. I have no trouble doing this in OO Pro with my files. FYI--I usually use date with a custom format (via the inspector) to just give me year.

I created a test file with the date column as just the year and another column with year as a number (no decimals). My test file had ten rows and five columns. I had no issues sorting my test file with either the custom date or with number. Everything ended up where it should have. I have attached a window grab showing this.
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File Type: pdf Test Sort.pdf (52.4 KB, 63 views)
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Old Sep 16, 2012, 01:21 PM   #16
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Originally Posted by MathRulz View Post
jojoba,

Re: Sorting dates/numbers in OO Pro



I'm not sure what the problem is. I have no trouble doing this in OO Pro with my files. FYI--I usually use date with a custom format (via the inspector) to just give me year.

I created a test file with the date column as just the year and another column with year as a number (no decimals). My test file had ten rows and five columns. I had no issues sorting my test file with either the custom date or with number. Everything ended up where it should have. I have attached a window grab showing this.
Thanks, MathRulz, appreciated. So there must be something I'm not getting right and I'm sure I can figure this out - the important thing is knowing that this function is available as long as I can get it right. The other tip was useful as well (I was wondering how to get rid of the year and month).

I'm still a bit on the fence about purchase - from your perspective, has this app been a good investment for you in relation to your research work?
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Old Sep 16, 2012, 04:31 PM   #17
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I'm still a bit on the fence about purchase - from your perspective, has this app been a good investment for you in relation to your research work?
Yes, I have it on both iMac and iPad. I am doing historical research in higher education for my dissertation. I have one OO file that is by year from 1801 to 2001 by decade with each year indented under the decade. Then columns of notes about key items for each year.
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Old Sep 16, 2012, 04:37 PM   #18
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Originally Posted by MathRulz View Post
Yes, I have it on both iMac and iPad. I am doing historical research in higher education for my dissertation. I have one OO file that is by year from 1801 to 2001 by decade with each year indented under the decade. Then columns of notes about key items for each year.
I see, sounds smart. I'll keep exploring the app for the duration of the trial period, and revisit my excel sheets as well (they've been dormant for a while). I have colleagues also working on the history of higher education - I'm based at a dept of education.
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Old Sep 17, 2012, 03:52 AM   #19
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I just discovered that there is no real sync feature for OmniOutliner I'm going to pass on that app until that's sorted out (seems like it's been an ongoing issue for a while judging by their forums). I work in a windows environment so I need my iPad versions of docs to be easily synced because I don't always have my Air with me. Excel addresses the cross platform issue (although not great on the iPad) better for me at the moment than OO, even if OO looks better in many ways.
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Old Sep 17, 2012, 09:29 AM   #20
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Quote:
Originally Posted by jojoba View Post
I just discovered that there is no real sync feature for OmniOutliner I'm going to pass on that app until that's sorted out (seems like it's been an ongoing issue for a while judging by their forums). I work in a windows environment so I need my iPad versions of docs to be easily synced because I don't always have my Air with me. Excel addresses the cross platform issue (although not great on the iPad) better for me at the moment than OO, even if OO looks better in many ways.
Yes, sync is currently the biggest issue for OO, Mac<-->iPad. Unlike the effortless, always in sync OmniFocus, which I also use, OO requires manual intervention. OmniGroup is working on it but has not given an ETA for that feature.
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Old Sep 21, 2012, 09:40 PM   #21
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Citavi in VMware Fusion. I'm not thrilled with the arrangement, but there's no comparable solution for OS X right now.
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Old Sep 25, 2012, 01:03 PM   #22
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Originally Posted by MathRulz View Post
Yes, sync is currently the biggest issue for OO, Mac<-->iPad. Unlike the effortless, always in sync OmniFocus, which I also use, OO requires manual intervention. OmniGroup is working on it but has not given an ETA for that feature.
I'm back to trying out OO again, but I can't find a quick way of navigating back and forth between the different rows in my document (I'm doing a first round of data sorting, so the document is quite wide and tall). Any tips? I'm looking through the manual but haven't found anything yet. I first thought the 'utilities' button for was that, but that just shows me weird lines that I don't know what I'm supposed to do with
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Old Sep 26, 2012, 07:01 PM   #23
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nvALT in Combination with Elements or PlainText for iPhone is what I use for my notes database.for my notes database.
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Old Sep 29, 2012, 10:58 PM   #24
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Originally Posted by jojoba View Post
I'm back to trying out OO again, but I can't find a quick way of navigating back and forth between the different rows in my document (I'm doing a first round of data sorting, so the document is quite wide and tall). Any tips? I'm looking through the manual but haven't found anything yet. I first thought the 'utilities' button for was that, but that just shows me weird lines that I don't know what I'm supposed to do with
I am not really sure what you are trying to do. As I recall you had one big document with no sections. I primarily use the 'Utilities' jump capability in documents with sections. For example, my outline with notes by year (1801--2001) is organized by decade. Years within a decade are indented and the decade can be collapsed to not show the individual years. If I have the whole outline expanded, Utilities is a quick way to jump between sections. It pops out to the side with the sections listed. Clicking on one just shows that decade so that I can focus on it. To go back to full view, I click on the outline title (file name) at the top of the Utilites listing.

I don't recall that your document has sections. In that case Utilities just shows every line of the outline with whatever is listed in the first column.
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Old Oct 1, 2012, 01:45 AM   #25
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Originally Posted by MathRulz View Post
I am not really sure what you are trying to do. As I recall you had one big document with no sections. I primarily use the 'Utilities' jump capability in documents with sections. For example, my outline with notes by year (1801--2001) is organized by decade. Years within a decade are indented and the decade can be collapsed to not show the individual years. If I have the whole outline expanded, Utilities is a quick way to jump between sections. It pops out to the side with the sections listed. Clicking on one just shows that decade so that I can focus on it. To go back to full view, I click on the outline title (file name) at the top of the Utilites listing.

I don't recall that your document has sections. In that case Utilities just shows every line of the outline with whatever is listed in the first column.
Thanks, MR, that clarified it for me!
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