Just throwing it into the mix, what would it take to convince Google to stop indexing the content of journal articles from closed-access journals? Surely without search, the articles are siloed; both journals and authors get a taste of the importance of opening access.
UK chemist on Elsevier's ban on textmining
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Re: UK chemist on Elsevier's ban on textmining
#22Re: UK chemist on Elsevier's ban on textmining
#23You should take the time to discuss a bit with your librarian. As I did my PhD in Denmark (DTU), I naively wrote a robot to download the issues of a well known chemical data journal. In about a week of balanced usage, I went to discuss with our librarian. He had seen my usage, was nice not to talk about it, but told me this: I downloaded more than the entire university in a year… and it was not a lot. It means that at that time, they paid a bit less than the $35 per article price.
What is really important to notice is that Elsevier are not selling knowledge for most of the scientific communities but influence. That is, you are published, cited, you get ranking and your university reward you. This is what we need to address if we want to have really open access. We need a better way to “sell” influence to the university researchers and deans.
As I am building Cheméo http://chemeo.com a chemical data search engine, I suffer too. It is maybe time to unit and propose a legal, efficient and rewarding way for the researchers to publish their papers. We can do that on the side and let our influence grow.
Additional notes for HN readers as yeah, we are a bit more on the programming side. What we basically need is a parallel DOI system easy to use, able to load all the open repositories and able to accept "direct" submissions.
We are not going to solve the problem in a year, this is an influence issue, it will take time, years, to really address it, be it by our own work or by "law".
Re: UK chemist on Elsevier's ban on textmining
#24To make more a available and searchable I actually uploaded everything to academia.edu. I hope they don't get sued by Wiley and/or Elsevier for what the service they offer. If anyone wants to check out some chemistry you can check out what I have here http://unlv.academia.edu/AlexiNedeltchev
Few side thoughts: I think there are many things that can be improved in the science publishing: 1. Articles could be more interactive by providing discussion /commenting section. 2. Currently, if you want to see if the article you are checking out is worth reading you have to refer to the overall rating of the journal (this is known was impact factor). I think every article should have separate ratings. That way you can tell which are high impact articles and which are not. Btw the impact factors is calculated based on how many articles referred the article in hand. Does that sound familiar? It's the same concept as a webpage SEO. The more links pointing in the higher the rank. 3. Publishing process is every inefficient. It takes months to get something published since it was to be peer-reviewed. This obsolete approach that begs to be improved. Any ideas?
Re: UK chemist on Elsevier's ban on textmining
#25After it's all been mined stop submitting to Elsvier.
Re: UK chemist on Elsevier's ban on textmining
#26Re: UK chemist on Elsevier's ban on textmining
#27I'm not sure how a tool to read some text and display a diagram of the chemical reaction described falls under the "law" of the quoted passage. Copyright law certainly allows for this, so all the journals can do is say, "you don't get to buy our feed anymore if you run your program on our articles," but surely this is a game of chicken because no company wants to lose tens of thousands of dollars a year for no reason…
Second: as it stands, this looks more to be a contractual than copyright matter (Elsevier is contractually banning use of automated text processing by subscribers), though it might possibly attempt to put teeth into this by asserting copyright. The remedy sought by Elsevier would be not to allege infringement, but to cancel future subscriptions. It might be nice for, say, a large collection of institutions to call Elsevier's bluff.
Third: Copyright law as it exists (and particularly in the US where I understand it reasonably well) is very mechanical: it governs the making of copies of an expressive work. Copyright does NOT govern facts, it does not apply to works which are not expressive, it does not apply to works which are functional in nature.
The real test here would be to put this (and possibly other) contract claims to test in a court. Unfortunately, contracts are governed (in the US) under state, not federal law, and while there's some uniformity of language, it would probably take several such cases (and appeals to at least the Federal Circuit) to establish reasonable case law.
Otherwise, what's significant about this to me is that, once again, it's a case far less about the availability and copying of information (journal articles are routinely copied), than it is about power and control within an information market. This is an area in which conventional economics is far too often lacking (though it's also an area in which much interesting work is starting to happen).
Re: UK chemist on Elsevier's ban on textmining
#28Repost of my comment on the blog (because waiting in the queue and not approved). You should take the time to discuss a bit with your librarian. As I did my PhD in Denmark (DTU), I naively wrote a robot to download the issues of a well known chemical data journal. In about a week of balanced usage, I went to discuss with our librarian. He had seen my usage, was nice not to talk about it, but told me this: I downloade…
Re: UK chemist on Elsevier's ban on textmining
#29Repost of my comment on the blog (because waiting in the queue and not approved). You should take the time to discuss a bit with your librarian. As I did my PhD in Denmark (DTU), I naively wrote a robot to download the issues of a well known chemical data journal. In about a week of balanced usage, I went to discuss with our librarian. He had seen my usage, was nice not to talk about it, but told me this: I downloade…
How come your search system doesn't appear to know chemistry? That is, I searched for "CCO" and found ethyl alcohol, but I searched for "OCC" and found nothing. Are you only doing a text search on the SMILES rather than a canonicalization first?
Nothing very complicated, but it needs to be well done to be of any use.
Thanks for the feedback!
Re: UK chemist on Elsevier's ban on textmining
#30Earlier quoted context omitted.
How come your search system doesn't appear to know chemistry? That is, I searched for "CCO" and found ethyl alcohol, but I searched for "OCC" and found nothing. Are you only doing a text search on the SMILES rather than a canonicalization first?
Good point, this is on the way. The problem is more to do it right, that is, you want for each "word" to detect if this is a word, a chemical formula or a SMILES. Then, if SMILES, you then need to canonicalize it and search. Nothing very complicated, but it needs to be well done to be of any use. Thanks for the feedback!
If you want a SMILES detector, you can use my opensmiles-ragel grammar to detect if a word is syntactically correct. (Not grammatically correct; it will allow "c1C" unless you write code to require balanced parentheses and matching ring counts.)
This would be much faster than passing it to any of the cheminformatics toolkits to do the first level detection.
If you're doing similarity searches, you might be interested in my chemfp project.