7 ms·

When I read papers, I often write short notes to myself about them, as I imagine most people do. I could imagine these notes as also being comments on a site li

When I read papers, I often write short notes to myself about them, as I imagine most people do. I could imagine these notes as also being comments on a site like this, particularly if it's all open and community-run. However, if the paper I'm reading is some 10 year old paper in some niche subfield, which ultimately is the majority of what scientists end up reading, I'm just going to be talking to myself there, so what's the point? I'm not going to submit a paper there that I know no other readers will care about. How do you overcome that barrier? It's not even network effects alone, it's like extreme network effects because the tail is so long in science. I guess it's really the barrier between being high-level discussion about only the latest big-name science news in certain fields, and being a central hub for all kinds of relatively short comments on scientific papers. Seems like a difficult problem to solve. Have you thought about maybe pre-populating your database with all papers, ready for discussion, rather than having it as a Reddit-like discussion of only recently submitted things? Or is there some other kind of grand vision for where this will go?

jayunit 14y ago
Not to speak for Mek, but one hope I have is that these small personal notes automatically make their way onto places like OpenJournal and start to seed conversations. Something like a cross between ScienceBlogs and Twitter, with enough mini metadata to tie to the paper and paragraph. Do you use a library management tool like Zotero or Mendeley for notetaking, or writing on printouts, or something else?
- mekarpeles 14y ago
  I'm a fan of plaus, academia, and mendley, etc. I wish there was more of an outlet/community for people to contribute their own research (in a way that made the research repeatable and improvable)
- streptomycin 14y ago
  I used to use plain text files. Recently I started using Mendeley because it's so damn convenient and it has a very nice UI, but my problems with Mendeley are (1) comments are private and (2) it's proprietary. http://www.researchblogging.org/ http://www.researchblogging.org/ is a great website that aggregates more long-form posts about papers, but it has a really shitty UI and it doesn't do anything for short comments on random papers by random non-bloggers.
  - MrGunn 14y ago
    Research blogging is great, but just to clear up the misunderstanding, comments are only private on Mendeley if you make them in a private group. Public groups are open to the web.
  - mekarpeles 14y ago
    Let's see what inspiration we can draw from researchblogging.org -- I've read a bunch of data driven / research oriented blogs (or blogs about [understanding] research) and found them helpful.
- jamesjporter 14y ago
  I use zotero to manage my paper library and its wonderful. One of my favorite features is tag search. If I find a paper where they measure, say, the strength of a particular protein-DNA interaction that I'm interested in, but I know I'm never going to remember the title, I can just tag it with "Pnt binding strength" or something, and then search for it later.
  - mekarpeles 14y ago
    Thanks James, tag / faceted search is something I've envisioned for openjournal. I'll start working on the feature.
mekarpeles 14y ago
One of my buddies (michael) is doing something similar with annotations and social reading @ pen.fm. I'll see how we may be able to incorporate some of these ideas. I do have around 450k papers from JSTOR (released legally via archive.org). I have these papers indexed and can expose them via openjournal. Also, as I mentioned in my previous post, a few guys from Berkeley (Tony Chen et al) are work on peer library which will be a more complete non profit academic search engine. Good points about the 'barrier'. I'm hoping people will contribute their own papers (even if they are no published). My ultimate vision would be for people to write their papers within a git repo and then upload/submit their .tex source (along with unit tests). I'm in the process of building some of these features. Also, experimenting with some ocr and pdf analysis to scrape as much useful contextual information as I can from the papers contributed (for the great benefit of our users) Thanks for taking the time to respond, streptomycin!
- streptomycin 14y ago
  I do have around 450k papers from JSTOR (released legally via archive.org). I have these papers indexed and can expose them via openjournal. PubMed would be another obvious datasource, if you were going to go that route.
kanzure 14y ago
> When I read papers, I often write short notes to myself about > them, as I imagine most people do. I picked up a strange habit because of a high school biology teacher.. the vast majority of homework that he assigned was inevitably content creation based on source material. As a consequence, when I read papers now, I compulsively: * re-draw diagrams in different styles * make tables for data that wasn't presented as a table * categorize which claims are associated with which citations * make lists, lots of lists! You can never have enough lists. Gunkel said so: http://ideonomy.mit.edu/gunkel.html http://ideonomy.mit.edu/gunkel.html * change the way information is displayed * demonstrate equations, or at least attempt to work through them * make up summaries of content * paste direct excerpts.. which over time deteriorate in usefulness. So far, every "annotation solution" I have tried just impedes my work, so I always resort to using some HTTP file server to host my files, or write HTML when I want to add markup to my notes.

jayunit 14y ago

Not to speak for Mek, but one hope I have is that these small personal notes automatically make their way onto places like OpenJournal and start to seed conversations. Something like a cross between ScienceBlogs and Twitter, with enough mini metadata to tie to the paper and paragraph. Do you use a library management tool like Zotero or Mendeley for notetaking, or writing on printouts, or something else?

mekarpeles 14y ago
I'm a fan of plaus, academia, and mendley, etc. I wish there was more of an outlet/community for people to contribute their own research (in a way that made the research repeatable and improvable)
streptomycin 14y ago
I used to use plain text files. Recently I started using Mendeley because it's so damn convenient and it has a very nice UI, but my problems with Mendeley are (1) comments are private and (2) it's proprietary. http://www.researchblogging.org/ http://www.researchblogging.org/ is a great website that aggregates more long-form posts about papers, but it has a really shitty UI and it doesn't do anything for short comments on random papers by random non-bloggers.
- MrGunn 14y ago
  Research blogging is great, but just to clear up the misunderstanding, comments are only private on Mendeley if you make them in a private group. Public groups are open to the web.
- mekarpeles 14y ago
  Let's see what inspiration we can draw from researchblogging.org -- I've read a bunch of data driven / research oriented blogs (or blogs about [understanding] research) and found them helpful.
jamesjporter 14y ago
I use zotero to manage my paper library and its wonderful. One of my favorite features is tag search. If I find a paper where they measure, say, the strength of a particular protein-DNA interaction that I'm interested in, but I know I'm never going to remember the title, I can just tag it with "Pnt binding strength" or something, and then search for it later.
- mekarpeles 14y ago
  Thanks James, tag / faceted search is something I've envisioned for openjournal. I'll start working on the feature.

mekarpeles 14y ago

One of my buddies (michael) is doing something similar with annotations and social reading @ pen.fm. I'll see how we may be able to incorporate some of these ideas. I do have around 450k papers from JSTOR (released legally via archive.org). I have these papers indexed and can expose them via openjournal. Also, as I mentioned in my previous post, a few guys from Berkeley (Tony Chen et al) are work on peer library which will be a more complete non profit academic search engine. Good points about the 'barrier'. I'm hoping people will contribute their own papers (even if they are no published). My ultimate vision would be for people to write their papers within a git repo and then upload/submit their .tex source (along with unit tests). I'm in the process of building some of these features. Also, experimenting with some ocr and pdf analysis to scrape as much useful contextual information as I can from the papers contributed (for the great benefit of our users) Thanks for taking the time to respond, streptomycin!

streptomycin 14y ago
I do have around 450k papers from JSTOR (released legally via archive.org). I have these papers indexed and can expose them via openjournal. PubMed would be another obvious datasource, if you were going to go that route.

kanzure 14y ago

> When I read papers, I often write short notes to myself about > them, as I imagine most people do. I picked up a strange habit because of a high school biology teacher.. the vast majority of homework that he assigned was inevitably content creation based on source material. As a consequence, when I read papers now, I compulsively: * re-draw diagrams in different styles * make tables for data that wasn't presented as a table * categorize which claims are associated with which citations * make lists, lots of lists! You can never have enough lists. Gunkel said so: http://ideonomy.mit.edu/gunkel.html http://ideonomy.mit.edu/gunkel.html * change the way information is displayed * demonstrate equations, or at least attempt to work through them * make up summaries of content * paste direct excerpts.. which over time deteriorate in usefulness. So far, every "annotation solution" I have tried just impedes my work, so I always resort to using some HTTP file server to host my files, or write HTML when I want to add markup to my notes.