Peer-reviewed biology papers online?

[chipotleaway]

I am taking a first year molecular/cell biology course and the lab reports I write all require references to peer-reviewed and (preferably) up-to-date papers. Does anyone have suggestions for websites where I can find such papers, and 'how' to search for them?

One problem I'm encountering is that most too specialized for my needs. For example this first report I have to do is on a practical we did involving enzymes from fruits, basically we looked at the effects of pH and temperature on enzyme function. Now in talking about the theory of enzymes in the introduction, it would be easy to reference the prescribed textbook but I'm not allowed to - it has to be directly from published papers.

Thanks

 

[Ygggdrasil]

PubMed (http://www.ncbi.nlm.nih.gov/pubmed) is the site most biology researchers use to search through the scientific literature.

You may also consider seeing if you textbook cites the primary literature as many provide a list of papers for further reading at the ends of their chapters.

 

[JonMoulton]

PubMed will give citations and abstracts for both open-access and pay-walled papers. You can visit http://www.plos.org/ to see some open-access journals only. Try PLoS Biology and PLoS one.

 

[atyy]

Some recent papers (those covered by the public access policy of the NIH of the United States of America) on PubMed are available free in their final accepted form, even though the nicely formatted journal version is behind a paywall. These papers appear in PubMed Central within 12 months after their appearance in the journal. When you search PubMed, a link to the free version appears at the top right of the page (not sure if this feature is in the Mobile version).

Here's an example http://www.ncbi.nlm.nih.gov/pubmed/22499176

As usual, just because it's published doesn't mean it's right, so read the peer-reviewed literature as critically as you would any other.

Ygggdrasil suggested looking at the references to original papers that are available in some textbooks. PubMed also makes some textbooks available free http://www.ncbi.nlm.nih.gov/books

Many journals allow authors to post the final accepted manuscript on their website or other free archive, so googling can often bring those free versions up, even if they are not on PubMed Central.

You can email (addresses are usually available from the journal's website) the authors of papers for a copy if you need to read a paper that your library privileges don't give you access to. They are not obliged to reply, but in many cases authors will be delighted with a short and courteous email in which you say why you are interested in their paper, eg. for a school project.

 

[Monique]

Well, if you require paper citations than PubMed is the way to go. For more general papers you can filter for reviews, but if you are citing a specific example it is always better to cite the original/best study. I never search in a limited set of journals, like JonMoulton suggests. If pay walls are an issue that can not be overcome (in my opinion they always should be overcome), you can filter for free full-texts.

You should learn how to use the Field Descriptions and Tags:
http://www.ncbi.nlm.nih.gov/books/NBK3827/#_pubmedhelp_Search_Field_Descrip_
Useful ones are [ti] or [tiab], to search for keywords in titles or including abstracts only (thus giving more relevant results).

 

[chipotleaway]

Thanks very much everyone!

 

[aroc91]

Don't forget about Google scholar.

 

[Monique]

What advantage does Google scholar have over Pubmed?

 

[Pythagorean]

What advantage does Google scholar have over Pubmed?

My experience with pubmed is limited, and I've never reigstered an NCBI account, but here's what I notice with my shallow pubmed experience:

1) google scholar presents multiple versions, often including free manuscripts marked with [PDF] (so you know it's not just another intermediate paywall).

2) 'cited by' function right in the search results immediately tells you the impact the article and links you right to the citing articles, making citation tracking fast and easy.

3) wider scope. this can be an advantage and a disadvantage as it includes non-peer-reviewed resources like books. Not limited to biomedical.

4) "cite" function automatically gives the article citation to you in your choice of format including bibtex, endnote, etc for us LaTeX users.

 

[Monique]

1) Pubmed as well
2) not in Pubmed, can be useful, I use Web of Knowledge to track citations
3) not useful for biomed literature research
4) PubMed as well

I'm not convinced

Can one use field descriptions and tags in Google Scholar, like in PubMed?
Search limiting to reviews?
Display full abstracts?

 

[Ygggdrasil]

PubMed displays results chronologically, so the first results are the most recent papers matching your search but not necessarily the most relevant. Google scholar, on the other hand, sorts by relevance so it may do a better job at finding the most relevant articles more quickly. I don't know if I trust the Google Scholar results to be as comprehensive as PubMed, however.

If you are looking for the most recent papers on a topic, PubMed is probably the tool to use. If you are looking for all of the papers published by a particular author, PubMed is probably the tool to use. However, if you're looking for a set of important papers on a particular topic, maybe here, Google Scholar has an advantage.

 

[Monique]

I find it dangerous when a search engine determines what is the most relevant paper. I rather have a chronological order and know how the research progressed on a topic. I do see how it can be useful for a quick paper find.

 

[Evo]

I find it dangerous when a search engine determines what is the most relevant paper. I rather have a chronological order and know how the research progressed on a topic. I do see how it can be useful for a quick paper find.

I don't know if or how many of the problems concerning google scholar have been fixed since this report.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1324783/

I just did a simple search for the same topic and google scholar's most recent paper was from 1996, while PubMed had dozens starting in 2013. Chipotle, since one of the preferences stated is that you use the more current studies, you might want to stick with PubMed.

 

[Monique]

Great find, thanks Evo!

 

[Pythagorean]

how do you get bibtex out of pubmed?

 

[Pythagorean]

also, how do you do 1)?

 

[Evo]

how do you get bibtex out of pubmed?

For the rare times someone might want it.

http://www.hubmed.org/

 

[Pythagorean]

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.

 

[Evo]

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]

That goes both ways. Pubmed doesn't have this article from Neurocomputing (thought it has other articles from Neurocomputing):

http://www.sciencedirect.com/science/article/pii/S0925231205001049

Google Scholar does.


here's PubMed's result:

http://www.ncbi.nlm.nih.gov/pubmed?term=(Tsumoto[Author]) AND Bifurcation Morris Lecar

and Google Scholar's:

http://scholar.google.ca/scholar?hl=en&q=Bifurcations+Morris+Lec+ar&btnG=&as_sdt=1,5&as_sdtp=

 

[Pythagorean]

here's another paper you can find in Scholar, but not in PubMed:

http://www.sciencedirect.com/science/article/pii/S0167278910002617

despite PubMed carrying other Physica D papers.

 

[Pythagorean]

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]

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]

sure it does:

http://www.ncbi.nlm.nih.gov/pubmed?term="Physica D"[Journal]

Nonlinear phenomena is rife with biological applications (that's where my research is)

 

[Evo]

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]

sure it does:

http://www.ncbi.nlm.nih.gov/pubmed?term="Physica D"[Journal]

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/nlmcatalog?cmd=historysearch&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]

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]

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]

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]

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]

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]

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]

how do you get bibtex out of pubmed?

You can "send to" and there different options.

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.

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]

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?term=(Krahe[Author]) AND Burst firing in sensory systems

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

http://scholar.google.ca/scholar?cluster=10932066625886224407&hl=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]

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?term=(Krahe[Author]) AND Burst firing in sensory systems

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

http://scholar.google.ca/scholar?cluster=10932066625886224407&hl=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.