5 ms·

Annotatr - scientific paper commenting done right

28 points by mariuskempe 16y ago

ComSubVie 16y ago
There seems to be a small bug, when I try to search for an author with a german umlaut in the name (for example "Kühn Eva") I get an error ("UnicodeEncodeError: 'ascii' codec can't encode character u'\xfc' in position 9: ordinal not in range(128)"), however searching after "Kuhn Eva" works.
- dmlorenzetti 16y ago
  Another small bug in how author names get scraped. It seems to have to do with colons in paper titles. For example, the paper "Ontologies Are Us: A unified model of social networks and semantics" (by Peter Mika) gets reported as "Ontologies are Us:" (by Unified M. Of).
kenthorvath 16y ago
This would work a lot better if there were social integration with your friends and colleagues - maybe scraped from Facebook?
- mariuskempe 16y ago
  Or if Academia.edu incorporated this feature, or had a login API...
alextp 16y ago
There are loads of duplicate papers. Searching, for example. for "latent dirichlet allocation" shows the same JMLR paper about four times in the top results.
rubidium 16y ago
ah, not quite done right. The search interface really needs to be more like google scholar or web of knowledge (who really wants to type in "author:"einstein a" && year:1905"). Narrowing by field/discipline is a must, esp. for some keywords. Also, just discussing abstracts is pretty lame. The typeface/links to citulike and journal are too small. There's no info on how many times it was cited, or what papers it cited. Not to complain, but I'll wait for the next guy. This won't work.
- crocowhile 16y ago
  Truth is, that even if this was the best interface in the world, scientists would never spend their time discussing papers online. Facultyof1000 tried hard, Plos is trying hard, even nature tried hard to get people to leave comments to papers. It just doesn't work.
  - mariuskempe 16y ago
    Let's hope.
- mariuskempe 16y ago
  You don't have to type in the "author:" etc bits - searches work fine without them. Also, Google Scholar uses the exact same (or possibly a very similar) syntax.
odiroot 16y ago
Sorry guys, I gave you an exception while searching for Polish theses: UnicodeEncodeError: 'ascii' codec can't encode character u'\u0144' in position 14: ordinal not in range(128) EDIT: Also, after navigating to: http://annotatr.appspot.com/citeulike/article/57175 http://annotatr.appspot.com/citeulike/article/57175, I've got: DownloadError: ApplicationError: 5
davi 16y ago
quick wishlist: - interactive refinement of results as I type - ability to restrict results to only papers that have been commented upon - ability to restrict visibility of my comments to friends/colleagues - ability to get notified if a particular abstract gets a threshold number of comments As it stands, this is not a minimum viable product I will return to (though perhaps it would be if everyone else in my field used it). Nice try though, hopefully it will improve with iteration.
mariuskempe 16y ago
I should clarify that I am only a user - the site was made by http://mark.reid.name http://mark.reid.name and http://boscoh.com http://boscoh.com
chapmanb 16y ago
The code is on GitHub: https://github.com/mreid/annotatr https://github.com/mreid/annotatr I remember seeing it last year and it doesn't look to have been worked on recently. A great proof of concept, but it'll be hard to sustain development motivation: there aren't good opportunities for making money, and this type of work unfortunately doesn't generate a lot of recognition amongst scientists.
bhickey 16y ago
There's a persistent cross-site script vulnerability on the front page.
Groxx 16y ago
Searching for nothing causes an error with stack trace: http://annotatr.appspot.com/search/all?q= http://annotatr.appspot.com/search/all?q=
mreid 16y ago
Hi, I'm one of the developers of annotatr. First of all, it's great to see people having a look at it and offering encouragement and constructive feedback. Thanks. Annotatr was more a proof of concept and fun hack than anything else. While Bosco and I did want to offer an alternative to existing commenting systems for scientific papers (Nature, PLoS, CiteULike, etc.) we also realised that a big difficulty is getting continued engagement. Some time after we put it up, I adapted annotatr and turned it into mldiscuss, a site for commenting on papers from ICML 2010: http://mldiscuss.appspot.com/ http://mldiscuss.appspot.com/ Before, during, and after the conference this site had quite a bit of activity but has since died off. I guess the lesson here is that a narrow focus (a single conference) works better than a broad one (scientific papers) -- at least in the short term. I'll likely extend mldiscuss for this year's ICML to see if it can pick up a bit more momentum.
- mariuskempe 16y ago
  Thanks, that's good to know.

28 points by mariuskempe 16y ago

There seems to be a small bug, when I try to search for an author with a german umlaut in the name (for example "Kühn Eva") I get an error ("UnicodeEncodeError: 'ascii' codec can't encode character u'\xfc' in position 9: ordinal not in range(128)"), however searching after "Kuhn Eva" works.

dmlorenzetti 16y ago
Another small bug in how author names get scraped. It seems to have to do with colons in paper titles. For example, the paper "Ontologies Are Us: A unified model of social networks and semantics" (by Peter Mika) gets reported as "Ontologies are Us:" (by Unified M. Of).

kenthorvath 16y ago

This would work a lot better if there were social integration with your friends and colleagues - maybe scraped from Facebook?

mariuskempe 16y ago
Or if Academia.edu incorporated this feature, or had a login API...

alextp 16y ago

There are loads of duplicate papers. Searching, for example. for "latent dirichlet allocation" shows the same JMLR paper about four times in the top results.

rubidium 16y ago

ah, not quite done right. The search interface really needs to be more like google scholar or web of knowledge (who really wants to type in "author:"einstein a" && year:1905"). Narrowing by field/discipline is a must, esp. for some keywords. Also, just discussing abstracts is pretty lame. The typeface/links to citulike and journal are too small. There's no info on how many times it was cited, or what papers it cited. Not to complain, but I'll wait for the next guy. This won't work.

crocowhile 16y ago
Truth is, that even if this was the best interface in the world, scientists would never spend their time discussing papers online. Facultyof1000 tried hard, Plos is trying hard, even nature tried hard to get people to leave comments to papers. It just doesn't work.
- mariuskempe 16y ago
  Let's hope.
mariuskempe 16y ago
You don't have to type in the "author:" etc bits - searches work fine without them. Also, Google Scholar uses the exact same (or possibly a very similar) syntax.

odiroot 16y ago

Sorry guys, I gave you an exception while searching for Polish theses: UnicodeEncodeError: 'ascii' codec can't encode character u'\u0144' in position 14: ordinal not in range(128) EDIT: Also, after navigating to: http://annotatr.appspot.com/citeulike/article/57175 http://annotatr.appspot.com/citeulike/article/57175, I've got: DownloadError: ApplicationError: 5

davi 16y ago

quick wishlist: - interactive refinement of results as I type - ability to restrict results to only papers that have been commented upon - ability to restrict visibility of my comments to friends/colleagues - ability to get notified if a particular abstract gets a threshold number of comments As it stands, this is not a minimum viable product I will return to (though perhaps it would be if everyone else in my field used it). Nice try though, hopefully it will improve with iteration.

mariuskempe 16y ago

I should clarify that I am only a user - the site was made by http://mark.reid.name http://mark.reid.name and http://boscoh.com http://boscoh.com

chapmanb 16y ago

The code is on GitHub: https://github.com/mreid/annotatr https://github.com/mreid/annotatr I remember seeing it last year and it doesn't look to have been worked on recently. A great proof of concept, but it'll be hard to sustain development motivation: there aren't good opportunities for making money, and this type of work unfortunately doesn't generate a lot of recognition amongst scientists.

bhickey 16y ago

There's a persistent cross-site script vulnerability on the front page.

Groxx 16y ago

Searching for nothing causes an error with stack trace: http://annotatr.appspot.com/search/all?q= http://annotatr.appspot.com/search/all?q=

mreid 16y ago

Hi, I'm one of the developers of annotatr. First of all, it's great to see people having a look at it and offering encouragement and constructive feedback. Thanks. Annotatr was more a proof of concept and fun hack than anything else. While Bosco and I did want to offer an alternative to existing commenting systems for scientific papers (Nature, PLoS, CiteULike, etc.) we also realised that a big difficulty is getting continued engagement. Some time after we put it up, I adapted annotatr and turned it into mldiscuss, a site for commenting on papers from ICML 2010: http://mldiscuss.appspot.com/ http://mldiscuss.appspot.com/ Before, during, and after the conference this site had quite a bit of activity but has since died off. I guess the lesson here is that a narrow focus (a single conference) works better than a broad one (scientific papers) -- at least in the short term. I'll likely extend mldiscuss for this year's ICML to see if it can pick up a bit more momentum.

mariuskempe 16y ago
Thanks, that's good to know.