Re: Literature documentation software
I use and recommend Zotero: https://www.zotero.org/ , I think it meets all of your requirements. It was originally a firefox extension but now runs standalone and will interface with most browsers. It will automatically obtain the bibliographical information and save the pdf from most journal web sites, and interfaces nicely with word / openoffice to generate citations / bibliographies (and will export to bibtex if you prefer) You can attach notes to your entries (I use this to write my article summaries) You can search your articles (including the full text if you like, it extracts it using pdftotext) It is open source and runs on linux, osx and windows. It will also sync across different computers, and if you like you can share your library (but not the pdfs) online via the zotero web site. Jason On Mon, Apr 29, 2013 at 8:09 AM, Steve G. wrote: > I am preparing to do a (scientific) literature review, in which I am going > to look for articles on a topic, read them, and summarize their important > content. > > I would like to do it electronically, in an organized fashion, so I can > also search and retrieve information later on. Right now, I print the > articles, read and mark important parts, and then write up the content in a > text document. > > My ideal program would have fields for the article name, source (journal, > web address, etc.), authors, link to original article (i.e. the pdf file I > will save or either a link or a copy of the web page in case of an html > page) and summary/comments which I will enter. > > There should be some searchable record keeping system, where all the > articles will be listed and be searchable by field (say, all articles from > Washington Post, or Lancet, etc.). > > If it is online, it would be nice to be able to share access to a document. > > Can you recommend a program that does that, on Linux or online? > > Thanks, > > Z. > > ___ > Linux-il mailing list > Linux-il@cs.huji.ac.il > http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il > > -- Jason Friedman, PhD Department of Physical Therapy Tel Aviv University email: write.to.ja...@gmail.com web: http://curiousjason.com ___ Linux-il mailing list Linux-il@cs.huji.ac.il http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il
Re: Literature documentation software
Micha Feigin writes: > There is jabref which is a bibtex management program and can probably > be abused for your purpose - i.e you can use the review entry for your > notes I was going to suggest BibTeX or some derivative. I am not familiar with jabref, but even raw BibTeX knows how to ignore any field that is not required or optional, so you can put your notes into some field, e.g., "comment", of your own. I don't know of an off-the-shelf tool that would do all you want havng BibTeX as input, but a bit of scripting may take you a very long way. There ar some open source tools that may be useful for your purposes, e.g., bibtex2html. > I don't know if there is a linux supported pdf markup program that > will work with it as well, I think that the KDE one or something like > that should work (they have notes on their site. Okular certainly has notes. -- Oleg Goldshmidt | p...@goldshmidt.org ___ Linux-il mailing list Linux-il@cs.huji.ac.il http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il
Re: Literature documentation software
There is jabref which is a bibtex management program and can probably be abused for your purpose - i.e you can use the review entry for your notes I like using docear, which is a scientific oriented mindmap program with strong support for paper management. Personally I use it under windows along with acrobat pro to make notes in the paper, it then can automatically find documents in given directories and extract all notes from the papers. I don't know if there is a linux supported pdf markup program that will work with it as well, I think that the KDE one or something like that should work (they have notes on their site. Both of these are written in java so work under linux (acrobat pro unfortunately has no linux version and I couldn't run it under wine either). On 4/29/2013 01:09, Steve G. wrote: I am preparing to do a (scientific) literature review, in which I am going to look for articles on a topic, read them, and summarize their important content. I would like to do it electronically, in an organized fashion, so I can also search and retrieve information later on. Right now, I print the articles, read and mark important parts, and then write up the content in a text document. My ideal program would have fields for the article name, source (journal, web address, etc.), authors, link to original article (i.e. the pdf file I will save or either a link or a copy of the web page in case of an html page) and summary/comments which I will enter. There should be some searchable record keeping system, where all the articles will be listed and be searchable by field (say, all articles from Washington Post, or Lancet, etc.). If it is online, it would be nice to be able to share access to a document. Can you recommend a program that does that, on Linux or online? Thanks, Z. ___ Linux-il mailing list Linux-il@cs.huji.ac.il http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il ___ Linux-il mailing list Linux-il@cs.huji.ac.il http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il
Re: Literature documentation software
I'm not sure how relevant it is to your question, but I'm using org-mode in emacs for all my documentation needs. Computers are so fast these days, so that there is almost impossible for a single person to generate more data in e.g. a year than may be found quickly enough by brute force search. I.e. for a database like you propose, one or more linked text files in org-mode should be more than sufficient. org-mode also comes with advanced search options, though I have not yet used them: See: - http://orgmode.org/ - http://orgmode.org/worg/org-tutorials/advanced-searching.html Regards, Dov On Mon, Apr 29, 2013 at 8:09 AM, Steve G. wrote: > I am preparing to do a (scientific) literature review, in which I am going > to look for articles on a topic, read them, and summarize their important > content. > > I would like to do it electronically, in an organized fashion, so I can > also search and retrieve information later on. Right now, I print the > articles, read and mark important parts, and then write up the content in a > text document. > > My ideal program would have fields for the article name, source (journal, > web address, etc.), authors, link to original article (i.e. the pdf file I > will save or either a link or a copy of the web page in case of an html > page) and summary/comments which I will enter. > > There should be some searchable record keeping system, where all the > articles will be listed and be searchable by field (say, all articles from > Washington Post, or Lancet, etc.). > > If it is online, it would be nice to be able to share access to a document. > > Can you recommend a program that does that, on Linux or online? > > Thanks, > > Z. > > ___ > Linux-il mailing list > Linux-il@cs.huji.ac.il > http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il > > ___ Linux-il mailing list Linux-il@cs.huji.ac.il http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il
Literature documentation software
I am preparing to do a (scientific) literature review, in which I am going to look for articles on a topic, read them, and summarize their important content. I would like to do it electronically, in an organized fashion, so I can also search and retrieve information later on. Right now, I print the articles, read and mark important parts, and then write up the content in a text document. My ideal program would have fields for the article name, source (journal, web address, etc.), authors, link to original article (i.e. the pdf file I will save or either a link or a copy of the web page in case of an html page) and summary/comments which I will enter. There should be some searchable record keeping system, where all the articles will be listed and be searchable by field (say, all articles from Washington Post, or Lancet, etc.). If it is online, it would be nice to be able to share access to a document. Can you recommend a program that does that, on Linux or online? Thanks, Z. ___ Linux-il mailing list Linux-il@cs.huji.ac.il http://mailman.cs.huji.ac.il/mailman/listinfo/linux-il
