Register to reply

Peer-reviewed biology papers online?

by chipotleaway
Tags: biology, papers, peerreviewed
Share this thread:
Evo
#19
Aug16-13, 06:22 PM
Mentor
Evo's Avatar
P: 26,426
Quote Quote by Pythagorean View Post
I mean in pubmed. The purpose is to have it all in one place when you're doing a literature search (a benefit of Google scholar).

I always use bibtex for both official manuscripts and school papers.
But using google scholar severely limits which papers you can even find, making it a rather useless tool except for high school kids, laymen and undergrads that don't really care, IMO.

You asked what would do bibtex functions for Pubmed so I gave you an option. Professionals use Pubmed for serious research.
Pythagorean
#20
Aug16-13, 06:25 PM
PF Gold
Pythagorean's Avatar
P: 4,262
That goes both ways. Pubmed doesn't have this article from Neurocomputing (thought it has other articles from Neurocomputing):

http://www.sciencedirect.com/science...25231205001049

Google Scholar does.


here's PubMed's result:

http://www.ncbi.nlm.nih.gov/pubmed?t...Morris%20Lecar

and Google Scholar's:

http://scholar.google.ca/scholar?hl=...1%2C5&as_sdtp=
Pythagorean
#21
Aug16-13, 06:29 PM
PF Gold
Pythagorean's Avatar
P: 4,262
here's another paper you can find in Scholar, but not in PubMed:

http://www.sciencedirect.com/science...67278910002617

despite PubMed carrying other Physica D papers.
Pythagorean
#22
Aug16-13, 06:57 PM
PF Gold
Pythagorean's Avatar
P: 4,262
a 2012 study:

CONCLUSIONS:
PubMed searches and Google Scholar searches often identify different articles. In this study, Google Scholar articles were more likely to be classified as relevant, had higher numbers of citations and were published in higher impact factor journals. The identification of frequently cited articles using Google Scholar for searches probably has value for initial literature searches.
http://www.ncbi.nlm.nih.gov/pubmed/22925384




Anyway... the most silly thing you can do is swear yourself to one search engine and eschew another, especially when you want to make sure your claim "this is the first time this phenomena has been found" is true! Just like navigation on the boat, don't rely on just one system.
Evo
#23
Aug16-13, 06:59 PM
Mentor
Evo's Avatar
P: 26,426
Sciencedirect is a web search site that also searches for non-peer reviewed articles, books, etc.

To my knowledge Physica D is not indexed by Medline/PubMed, I would imagine since it primarily would not have papers that fit PubMed.
Pythagorean
#24
Aug16-13, 07:01 PM
PF Gold
Pythagorean's Avatar
P: 4,262
sure it does:

http://www.ncbi.nlm.nih.gov/pubmed?t...2%5BJournal%5D

Nonlinear phenomena is rife with biological applications (that's where my research is)
Evo
#25
Aug16-13, 07:05 PM
Mentor
Evo's Avatar
P: 26,426
Quote Quote by Pythagorean View Post
a 2012 study:



http://www.ncbi.nlm.nih.gov/pubmed/22925384




Anyway... the most silly thing you can do is swear yourself to one search engine and eschew another, especially when you want to make sure your claim "this is the first time this phenomena has been found" is true! Just like navigation on the boat, don't rely on just one system.
LOL, you must have used google scholar, so missed the later 2013 study.

CONCLUSIONS:
Has Google Scholar improved enough to be used alone in searching for systematic reviews? No. GS' constantly-changing content, algorithms and database structure make it a poor choice for systematic reviews. Looking for papers when you know their titles is a far different issue from discovering them initially. Further research is needed to determine when and how (and for what purposes) GS can be used alone. Google should provide details about GS' database coverage and improve its interface (e.g., with semantic search filters, stored searching, etc.). Perhaps then it will be an appropriate choice for systematic reviews.
http://www.ncbi.nlm.nih.gov/pubmed/23923099

No search engine is going to list everything. For biology, which is the subject of this thread, I'd have to go with PubMed to make sure that the results I get are the most current and in an acceptable peer reviewed journal. We have people all of the time posting conference papers and some student's thesis not realizing it's not ever been published in a peer reviewed journal.
Evo
#26
Aug16-13, 07:08 PM
Mentor
Evo's Avatar
P: 26,426
Quote Quote by Pythagorean View Post
sure it does:

http://www.ncbi.nlm.nih.gov/pubmed?t...2%5BJournal%5D

Nonlinear phenomena is rife with biological applications (that's where my research is)
No, they don't.

Not currently indexed for MEDLINE.Only articles related to space life sciences were indexed.
http://www.ncbi.nlm.nih.gov/nlmcatal...rch&querykey=2

They only pick up a few papers. They do not index the entire journal AFAIK. Of course now someone will find where they have added the journal.
Pythagorean
#27
Aug16-13, 07:15 PM
PF Gold
Pythagorean's Avatar
P: 4,262
Your link doesn't work (I don't have your cookies). I'll take your word for it.

I wonder how this one was indexed then:

[PubMed - indexed for MEDLINE]
http://www.ncbi.nlm.nih.gov/pubmed/11540720
Pythagorean
#28
Aug16-13, 07:17 PM
PF Gold
Pythagorean's Avatar
P: 4,262
Quote Quote by Evo View Post
LOL, you must have used google scholar, so missed the later 2013 study.



http://www.ncbi.nlm.nih.gov/pubmed/23923099

No search engine is going to list everything. For biology, which is the subject of this thread, I'd have to go with PubMed to make sure that the results I get are the most current and in an acceptable peer reviewed journal. We have people all of the time posting conference papers and some student's thesis not realizing it's not ever been published in a peer reviewed journal.

naw, they're just saying two different things. In fact, your paper is saying exactly what I said. Don't use it alone. As I've demonstrated, you don't want to use PubMed alone either, at least not for computational/mathematical/theoretical neuroscience. That's a general rule any professional should follow.

Biology is too big of a subject to say, "go with this, go with that". You have to know more specifics.
Evo
#29
Aug16-13, 07:21 PM
Mentor
Evo's Avatar
P: 26,426
Quote Quote by Pythagorean View Post
Your link doesn't work (I don't have your cookies). I'll take your word for it.

I wonder how this one was indexed then:

[PubMed - indexed for MEDLINE]
http://www.ncbi.nlm.nih.gov/pubmed/11540720
I searched on their journal list. It could be that they only pick up papers that meet their criteria, I don't know.
Evo
#30
Aug16-13, 08:20 PM
Mentor
Evo's Avatar
P: 26,426
It's because of the specific needs of the OP that I believe searching in PubMed would be best for his needs. If you just want to throw out a net and catch anything on a particular topic, then no need to care about the search source. But he's a first year undergrad that specifically needs current and peer reviewed sources, the best source for that would be PubMed. They don't need to worry if it's a paper in a proper peer reviewed journal, or if they are accessing current papers, it's already sorted for them.

My example earlier of searching on a specific topic in google scholar, yeah, they returned the most highly cited papers...that were 20 years old and cited 20 years ago and new technology and research has made many of those papers obsolete. But you wouldn't know that there were newer studies using google scholar, the newest paper in the first few pages was from 1996. Oh, but very highly cited.

So, if you are just doing blanket searches for anything topic related and have plenty of time, using multiple searches will find the most papers. For this thread OP's specific situation, I've got to go with PubMed.
Pythagorean
#31
Aug16-13, 08:34 PM
PF Gold
Pythagorean's Avatar
P: 4,262
It's one click in Scholar to look at recent papers. A click and some keyboard taps to specify a date range.

Highly cited is good though. Ideally, you want something about 2-3 years old but heavily cited. This is very easy to do with Google Scholar, since you can see all its citing papers and do a search only within it's citing papers. If you look at something just published yesterday and you're an undergrad, you don't get to see the critiques of it. But if you look at something with a couple years between now and then, you can see what other people said.

As an example: An unknowing undergrad could pull up a peer-reviewed paper on the quantum brain that was published yesterday, and thus had no citations. Story over, he cites it in his paper because he wasn't familiar with the field. It would be more helpful to see one published a couple years ago and then be able to see all the citing papers so he can see how heavily the paper is criticized and rebuked. The buck doesn't stop at peer-reviewed. That's what's great about Google Scholar's "cited by" function.

Of course, you could use Web of Knowledge too, but there have been cases with my adviser where I demonstrated Google Scholar showed more (valid) "cited by" sources than Web of Knowledge did. In one case, Web of Knowledge showed 1 citing article and GS showed 100+ (ok, I only checked the first five... but they were all peer-reviewed journals that cited the article in question).
Evo
#32
Aug16-13, 09:10 PM
Mentor
Evo's Avatar
P: 26,426
I was just going to edit my last post to say, if it wasn't evident, that I agreed with you on checking multiple sources, for those that can sort the wheat from the chaff, as I know you can. But you've already responded.

Again, I am just thinking of the OP, and his/her specific needs, I don't know how familiar they are with scientific journals, if they know about how to check for journals http://ip-science.thomsonreuters.com/mjl/, and even that list contains journals we don't accept and it has even added pop-science magazines!!

I'm reminded of an assignment I had in my freshman year in college (before the internet) and a not too bright student in my class was leaving the library, I assumed he'd given up, I figured I would ask if I could help him look for things and he said "nope, I'm finished". Of course I didn't believe him, but looking at what he had, he certainly had enough references. I asked him how he managed so quickly, he said that the librarian had noticed he was lost and asked him what he was looking for, and she went off and got him everything, he did nothing.

Moral of the story, librarians are a tremendous, often overlooked resource. I could've kicked myself for not using the most precious asset I had available to me. Now with the internet, they are maybe even more helpful. Don't forget to use the librarian to assist you in your searches.
Monique
#33
Aug17-13, 03:10 AM
Emeritus
Sci Advisor
PF Gold
Monique's Avatar
P: 4,642
Quote Quote by Pythagorean View Post
how do you get bibtex out of pubmed?
You can "send to" and there different options.

Quote Quote by Pythagorean View Post
also, how do you do 1)?
PubMed shows multiple sources for papers, like here: http://www.ncbi.nlm.nih.gov/pubmed/23874428 In a search one can filter for free full text. I'm sure that feature was included for developing countries that don't have the resources to subscribe to journals.

Quote Quote by Pythagorean View Post
Highly cited is good though. Ideally, you want something about 2-3 years old but heavily cited. This is very easy to do with Google Scholar, since you can see all its citing papers and do a search only within it's citing papers. If you look at something just published yesterday and you're an undergrad, you don't get to see the critiques of it. But if you look at something with a couple years between now and then, you can see what other people said.
An undergrad should learn that one has to judge an article on its content, when one cites it. It is not sufficient to rely on the impact factor of a journal, or the number of citations, or a citation in another publication.

The student should read a paper and judge whether it's an appropriate citation. Having thought about it, I am against listing the number of citations in PubMed. It does no justice to emerging research. Impact factor of journals is also not listed in PubMed, exactly because it prejudices people to only cite certain studies, it's the content of the article that should count.
Pythagorean
#34
Aug17-13, 10:45 AM
PF Gold
Pythagorean's Avatar
P: 4,262
Quote Quote by Monique View Post
You can "send to" and there different options.
none of which are bibtex, though.

PubMed shows multiple sources for papers, like here: http://www.ncbi.nlm.nih.gov/pubmed/23874428 In a search one can filter for free full text. I'm sure that feature was included for developing countries that don't have the resources to subscribe to journals.
Here's an example where pubmed only lists one restricted version:

"To read this article in full you may need to log in, make a payment or gain access through a site license (see right)."
http://www.ncbi.nlm.nih.gov/pubmed?t...sory%20systems

whereas Scholar gives several versions (14 in fact!), including free manuscripts:

http://scholar.google.ca/scholar?clu...=en&as_sdt=0,5

This has also been useful for me when authors have several different versions with different scales of content for the same named paper.

An undergrad should learn that one has to judge an article on its content, when one cites it. It is not sufficient to rely on the impact factor of a journal, or the number of citations, or a citation in another publication..
There's nothing in Scholar's terms and agreements that prevents you from reading the article and judging for yourself. If you want to speculate about how it affects perceptions, that's fine, but it's not a very solid argument for completely eschewing Scholar.
Monique
#35
Aug18-13, 05:07 AM
Emeritus
Sci Advisor
PF Gold
Monique's Avatar
P: 4,642
Quote Quote by Pythagorean View Post
Here's an example where pubmed only lists one restricted version:

"To read this article in full you may need to log in, make a payment or gain access through a site license (see right)."
http://www.ncbi.nlm.nih.gov/pubmed?t...sory%20systems

whereas Scholar gives several versions (14 in fact!), including free manuscripts:

http://scholar.google.ca/scholar?clu...=en&as_sdt=0,5

This has also been useful for me when authors have several different versions with different scales of content for the same named paper.
The versions scholar finds are illegal, one can't blame PubMed for not indexing illegal content.

Then there should only be one published version. What a mess when people are using in-between-versions for their work! A new version is made for a reason, for instance to correct mistakes.


Register to reply

Related Discussions
Few questions about getting peer reviewed Academic Guidance 5
Peer reviewed global cooling Earth 68
Reference to a peer reviewed paper Quantum Physics 0
Peer review reviewed General Discussion 5