The way in which scientific publications appear online is going to become increasingly important. How literacy research is conducted is changing rapidly. People are turning to online resources rather than utilizing libraries. Publications that haven’t been made available on the internet may be overlooked. This could result in your paper not being referenced as often, or worse, your research may be repeated.
The number of citations a paper receives helps to determine the impact of the research within that paper. Even if your research is excellent, if no one finds the paper it won’t be cited.
The probability of your paper being read increases the closer it is to the number one search result.
So how do you become the #1 publication in search results?
SEO (search engine optimization) is a field that studies how search engines are influenced by content. The basis for this work is that it is believed that search engines are not perfectly efficient. Therefore with a little tweaking, you may be able to give your publication the boost it needs to be noticed and deemed an appropriate match by search engines. Just to be clear, papers should not be poorly written in an attempt to gain search ranking and in the end content will have a much great impact than SEO.
There are many factors a search engine considers when assembling a results page. The scientist in me cringes a bit at presenting this information since the search algorithms are kept secret making it very difficult to know exactly how search results can be influenced.
Today, we are going to focus on the two items that you can control.
1) Paper Title
2) Keyword Density
Paper Title:
The basics of SEO of titles is that your keywords (the search terms that you people may use to find your paper) should be contained within your title. Although opinions are mixed it is also thought that keywords placed near the beginning have a higher influence than those at the end.
Here’s a great example of how a title should be written for SEO from Acta D:
‘Eukaryotic expression: developments for structural proteomics’
An example of a disadvantageous title would be:
‘The 1.6 Å resolution crystal structure of a mutant plastocyanin bearing a 21-25 engineered disulfide bridge’
The problem here is the resolution of the structure is listed first in the title. More than likely, this paper is going to rank higher for the term ‘1.6 Å’ rather than, for example, ‘mutant plastocyanin’.
If you were the author of this paper and thought each word in that title was critical, it would be more beneficial to arrange the words as follows:
‘Mutant plastocyanin a 1.6 Angstrom crystal structure bearing a 21-25 engineered disulfide bridge’
This tweaked title would be ideal if you were looking to rank for ‘mutant plastocyanin’.
Keywords:
Of course, your paper should be written for humans, but it may help to keep search engines in mind. Although not as influential as in the past increasing the keyword percentage in your document should also help. For example, if you wanted to keyword for ‘protein crystallization’ think about if you can increase the number of times the term is being used.
Again, I don’t have direct proof of how much influence these changes make, but many top brands have excellent top keyword density (percent that term is used on their site) and my feeling is that it wasn’t by accident:
Zappos: shoe (8.33%), shoes (7.78%), zappos (5.00%)
Visa: visa (25.00%), card (10.61%), cards (4.55%), credit (3.03%)
JCrew: crew (6.77%), clothing (3.59%), dresses (3.19%)
Take some time and really think about the title of your paper and what keywords are important. You may find that the one thing standing between you and the first page of Google scholar……is a little tweaking.
A year ago today this site was created.
P212121 has been more successful than I would have ever imagined. My primary goal has been to help someone in the field of macromolecular crystallography. I hoped that by bring together resources, creating tutorials and answering questions that this website would be helpful.
I also need to say thank you. I have had many readers contribute so much time and effort answering my questions and sharing their experiences. My friends that have share with me more than I given with a comment here, thank you.
If you like numbers, the current RSS count here considering only Google is at 140 as a (probably bad) reference point Acta Crystallographica Section D is at 93.
The blogging community has been wonderful and for fear of leaving someone off of a list, I hope a general thanks will suffice.
A number of crystallographic companies have shown their link love:
Emerald Biosystems
Hampton Research
Microlytic
Rigaku
This site was also recently included in the science Alltop, which is cool resource for finding science information.
What’s next? I have a lot in the pipeline, but before we get there I would love to hear from you. Have an idea or suggestion to make this site better? If we have spent the last couple of months together and haven’t met just a Hi or Happy Birthday 
would be great.
Thanks again.
At the beginning of the year, we discussed whether the CCP4bb should become a forum. Initially, BioKlatch.com was created by Matt Harrington – the site is now being redirected to MajorGroove.org.
The site is based on StackExchange, which is a new website designed around a simple question and answer format. It will be interesting to see if the pricing changes once the site is out of beta. The site includes a number of community features. On example: the ability to earn badges by performing various activities, from filling out your profile to posing a good question.
The discussions are still kept on the CCP4bb, but the answers/responses are then posted on MajorGroove.org. If the system works well, it should provide an extensive selection of Q&A that have previously been addressed on the CCP4bb.
Are you excited about this new resource? Is this just one more place to visit? I have joined, will you?
At our university we are required to give a literature presentation. The presentation is 1 hour including time for questions. The goal of this exercise is to help students develop various skills that are valuable in a scientific career such as presenting, evaluating literature and answering questions. Good stuff.
I did my presentation and it really well except to one professor. According to my evaluation, I had confidently fabricated an answer and misled an entire audience. Fair enough, I make mistakes, but in this case I was right and had the literature to back it up. My scores were fine despite this one professor, but I wanted to discuss the issue. I was curious if the book and papers that supported my view were wrong. I wanted to learn.
I went to the head of session and asked who gave this evaluation. I was then told that the feedback was anonymous and they were not allowed to tell me. I then asked if he could ask the professor to contact me so that I could visit their office and discuss the evaluation. The head of session said that would be fine and sent out an email, but the professor never got in touch.
From this experience, I have also decided to no longer give anonymous feedback. I don’t want to hide. If the person who is getting my feedback disagrees, wants clarification, suggestions then great, let’s talk.
Scientific dialogue is invaluable and is reflected in our numerous publications and conferences.
I asked a faculty member of nearly 30 years why the policy existed and was told ‘this is the way we have always done it.’
Does your department give anonymous feedback? Do you find it helpful? Do you know why they keep that policy?
When giving presentations, scientists typically don’t have trouble making their complicated work seem…well, complicated. The challenge is in making your message clear and audience appropriate.
Example:
How does life expectancy at birth and the number of children a woman has change by country over a period of one hundred years?
I felt a table with 8 point font coming on, but instead was amazed by this.
Hint: Hit play
Would making a graph like this be helpful in crystallography? Perhaps showing PDB entries by country over the last 60 years? I realize this tool may not be the most useful to our community, but it’s helpful in the sense that it inspires creativity. I now find myself contemplating how I can present research in a way that is clear, concise and creative. How can I help my data tell a story?
We were able to put together a compilation of 36 resources that publish articles related to macromolecular crystallography. The result is a RSS feed that contains about 1500 articles and is constantly being updated. (what is a rss feed?) If the average article is 10 pages then this feed is currently at 15,000 pages — that’s a lot to sift through!
Fortunately, yahoo pipes allows a RSS to be filtered and only send you those that contain information of interest. In an effort to save you time, I am going to set up a customized feed for you. Consider it my way of saying ‘thanks for reading’.
What do you need to do?
Simply leave a comment with the keyword(s) that must be included within the journal article.
For example:
Sean
Keyword(s): hiv protease, crystallography, crystallization
How does this work?
I will then create a customized pipe from the 26 resources to your keywords and then reduce the number of entries to the 10 most recent articles. I will reply to your comment with a link that will generate your RSS feed. You can then copy/paste that link into your RSS feeder.
I am going to offer this help for the next 48 hours and then close the comment section.
I have a good feeling about how cancer changes lives. My mother, aunt, uncle, grandmother and both grandfathers have had cancer.
The cost of cancer research is mind blowing, at least billions.
I have complete respect for the people that are raising money for cancer research (Bill and Melinda Gates Foundation, Lance Armstrong Foundation, Susan G. Komen, @drewfromtv). The people and organizations that are willing to fund cancer research are critical, but money alone does not fix the problem, people do. Scientists do.
I am missing a hero in my life. This hero is dedicating their life toward curing cancer.
I mean really working on it. Not some buzz word on an intro slide.
Who is your favorite scientist involved in cancer research? Who is the person that will fill Madison Square Garden with a science talk?
I thought the enzyme catalytic mechanisms (ECM) database would be a nice follow up from yesterday.
The amazing part about this database is not the number of entries (720), but in the details. The ECM has devised a classification of enzymatic reactions which are as follows:
R: Basic Reaction
L: Ligand group involved in catalysis
C: Catalysis type
P: Residues/cofactors located on Proteins.
This classification system creates a hierarchy that is then search able by the user. The hydrolysis classification even has pictures of the general mechanisms. Here is an example of a Pepsin-like mechanism and Trypsin-like mechanism. If you or your students are learning general mechanisms a number of these illustrations could serve as excellent real world examples.
The search page contains a number of unique inputs.
For example, ECM utilizes the KEGG pathway database to generate a reference pathway.
Note: use the bottom search button not the top, which is (above the fold) if you do not have a DB code input.
BenchflyTM has videos of protocols, tips and teachings some of which are quite relevant to macromolecular crystallography. The video quality is excellent. I will look forward to watching their future productions even though the buzz intro gives me the creeps.
How to Calibrate Pipettors
Timesaving miniprep tips
Nucleic acid absorbance to concentration
How to remove static from a scale (not for kids)
How to perform colony PCR
Pouring and running an agarose gel
Tip for loading many gel samples quickly
Molarity Tip
