[Victor:] Completing our trinity of Community Liaison Goodness, may I introduce Brandon King! He is a Ph.D. student in neuroscience at Brown University, doing fascinating research on brain-computer interfaces (so don’t mess with him, or his army of cyborgs will come and get you. No, I just made that up. He’s as nice and funny as they come). We’re excited to have him on our team! Here’s his introduction in his own words:
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I graduated college 2001, the year that journals were just beginning to become available online. So, for the vast majority of my undergraduate existence, I was forced to do the unthinkable: go to libraries and pull articles from the stacks. “I don’t get it. I’m looking for small bits of constantly updated text, so for my uses, the whole library could be replaced by a web page and a search box.” Of course, this was back when saying you read something on the internet was akin to citing facts from a fictional work.
After spending five years in ‘industry’, I decided to return to academia to continue research on brain-computer interfaces. When I discovered that I could download almost any paper on any topic I could imagine, I was like a kid in a candy store. I could hear my Windows machine cry when the indexer hit my “Papers” folder. As I honed in on my eventual project/thesis topic, I began to amass a big collection of PDFs. “No problem,” I thought. “I’ll just sit down for a whole day at some point and organize it all!”
That was when my papers were numbering around 200. After discovering RSS feeds and launching a blog, that number quickly ballooned up into the thousands. As I type this, there are ~3,700 papers in my library. Yes, it is impossible for me to have read them all, but having read at least the abstracts from each, the interplay of all these ideas and the trends in topics over time have played a major role in shaping my understanding of my field of interest.
Did I mention that none of these PDFs have file names? Well, they didn’t, unless you consider sdarticle(122).pdf to be a useful identifier.
As I started working on my project proposal, I knew I had to find some way to keep this mountain of information in order. It should be easy enough to spend a couple hours tediously searching for each paper in one of those ‘reference manager’ programs, right? Or someone must have come up with a really snazzy web app to take care of references, right? Wrong and wrong. At least that’s what I thought until a member of the Mendeley team brought their program to my attention.
Maybe I dismissed it at first because of the beta moniker or the funny name, but as soon as I installed Mendeley and started to play with it, I was hooked. The hours, nay, days, it saved me made it instantly one of my ‘must have’ programs.
I saw huge potential in Mendeley, and started submitting suggestions and bug reports (it was in version 0.5 at the time) and when Victor came to the States to talk with university librarians, we arranged to meet. I walked away thinking Mendeley could easily be a game changer in the same way online journal access changed research.
We came up with the idea of adding the position I am now starting at because realizing the potential of this awesome tool is only possible by engaging the people that are going to use it. Each lab, each researcher, and each student has their own system of compensating for the near Paleolithic Era reference management tools they have access to. To make Mendeley the most useful program out there, we have to get your feedback on how we can better adapt Mendeley to the way YOU work while at the same time gently nudging people away from the status quo in which reference managing is tedious but necessary. I want to make Mendeley as much a source for creating ideas and new connections between ideas as it is for simply managing references. I think one of the unspoken lessons of research is that you have to stop looking at papers as files or a limited set of ideas, and understand instead how the work fits into the topic of interest as a whole. My hope is that Mendeley will allow researchers to bridge old ideas, inspire new ones, and provide a platform for sharing the information that led them to a novel insight. You know. Small goals, like change everything.
Mendeley Blog 
What a cool guy. I feel like I could have written the exact same thing about my own thoughts on Mendeley’s ongoing evolution. Best wishes to you, Brandon! We’ll keep sending in the bug reports and suggestions – you keep working on ways to make mendeley a social-enabled tool. Here are some wild ideas for the road.
**Create a feature in Mendeley which allows you to “string” papers into a chronological sequence. This goes with next suggestion which is:
**Create an importance field where you can personally rank a paper from -2 (cheapens the literature) to +2 (important step) with a special flag for “landmark” article.
**Once you’ve got those two, social network the stuff. I’ve got three papers on statin therapy in heart attacks strung together in a chain. Mendeley suggests that others with similar chains have also had the 4S and WOSCOPS studies flagged as landmark importance.
If it someday becomes possible to abstract the bibliography data of papers,
**Allow a user to assemble a chain of X papers and find out what studies are frequently cited in each – these must then be the seminal papers in that field.
**Have a feature in Mendeley where it reproduces the bibliography of the paper you’re looking at in a pane, with every paper you’ve already got in your library hotlinked in one color, and every paper that you don’t have, but that the author has made available in another. One click and bam – you’re looking at the next link in the chain.
We can’t thank you enough for the continued feedback and great ideas, John! So please keep them coming – they’re greatly appreciated…
John, that’s precisely the kind of thing I’ve had on my mind, too. There are a variety of algorithms for measuring or ranking a paper’s scientific impact, and of those, user-behavior based metric tend to be the best, although network analysis a la eigenfactor works well, too.
Thanks for the kind words John. I totally agree with your ideas on the social networking possibilities of Mendeley. Look at Google Scholar. It’s been around a couple years only, and just by making searching a little more intuitive and using ‘modern techniques’ to pull together information, it’s quickly becoming the place to go to find papers.
The only thing I would be cautious about with social networking is, well, first how rivalries are handled and real experts are given a rightfully earned, higher priority place (Google Knowl style), and secondly how to protect the system from infiltration (ala-buying Digg front page stories). I think the first step is to get the ‘underlings’ – students, science writers, other non-primary literature producers – integrated and then introduce paper rankings and more features allowing what amounts to critiquing as more influential mentor/PI/professor types begin to move in. The one thing the current paper review system has right is the need for experts who have earned their titles as experts. I mean, imagine if we threw open the doors to voting on papers submitted by users and the first ‘school’ to really bombard the system was some Creationist, Flat-Earth, Mystical, Loch Ness Monster institution… It would be a mess!
Absolutely, Brandon. That’ why it’s key that Mendeley never actually rank a paper for you. At its absolute most autonomous, the best it should ever do is suggest a rating (ala Netflix) for what it thinks a paper merits. Want to really have fun? Create a proprietary algorithm for medicine based on some weighting of: 1) published in AIM (abbreviated index medicus – a library of only the most important publications in medicine) 2) cited by other papers > x times 3) ranked by other mendeley users as +2 or landmark y times, and then subtract OUT people who consistently vote against the trend (ala Google and PageRank, Amazon and user reviews). You can get a whole group of people working on Mendeley optimization 🙂 J/K.
I think the conclusion that I keep arriving at over and over again for myself is that EndNote is a product of necessary evil. I’m writing a manuscript for publication right now, and hate every minute of setting up the library in X2. But for Mendely to make its first inroads into acceptance, it has to help rapidly set up a library. EVERY OTHER FEATURE is entirely secondary to the ease with which people can get papers into the library in the first place. I just spent literally 3 hours looking up the PMIDs for all these papers I want to import, and there’s only 40 cites so far. It’s maddening.
That’s why I sound like a broken record urging you guys to focus first on combining algoriths for recognition with some sort of social networking with fingerprinting so that I only have to do this once for the rest of my life – less if someone else has identified the paper once before. Get that done, and polish the word plugin so that it can at least use NEJM citation style or NLM citation style and you’ll be golden from medicine. The rest is gravy.
Can’t wait to see the new betas. In the meantime, back to End-of-me-Note. Have a great weekend!
OK – Decided I wasn’t being as helpful as I could be. Some further suggestions, tempered with the realization that yes, I represent only one segment of the audience Mendeley will eventually work for.
What I did is to take the entire library of articles I’m using for this journal paper and auto-extract them into Mendeley. Not bad – it’s getting better, but there’s still not one that I can leave untouched. Here’s the process I’m going through…
Sometimes it’s finding the DOI, which is AWESOME and it’s pulling that data. But in medicine the DOI lookup contains far less data (and is far-less correctly proofed) than the PMID dataset. So I’ve got a browser window open to PubMed, I’m simply copy/pasting the DOI number into the PubMed search field, hitting enter, and it’s giving me the record every time. From that, I copy the PMID back to Mendeley, hit search, and we’re doing great so far, with a couple of minor annoyances (doesn’t copy DOI back into Mendeley, not getting as many fields as it could). Honestly, I think you need a button next to the PMID field in addition to lookup called “Lookup PMID via DOI.” Seriously. PMID >> DOI.
Other times, it hasn’t been able to find the DOI but is almost always getting the journal title correct. In this case, I’m just copying the journal title into PubMed and hitting search, and it’s giving me usually just one, sometimes up to 4 hits. But it’s easy to get the PMID from that list, which again, I just paste back into Mendeley.
Now here’s where it almost hurts to see potential missed. Once you have a PMID, you can pull some phenomenally useful stuff straight off the tubes. See what I mean by going to http://www.pubmed.com, just put “17492789” in the search field and hit enter. You’ll get an article by Karlsson and Breall on stent thrombosis. But down at the bottom of the page, there’s a drop-down list called “Display.” Change that from “AbstractPlus” to MEDLINE. See how it separates 1st and second authors? MH stands for MESH terms – things metasites like OVID use as keywords (hint). It also gives you the correct abbreviation for the paper for use in citations/biblios/footnotes (the TA field) and (hugely important) the complete abstract (the AB field).
OK, now scroll down again to Display and change to XML – that’s for the import filter if you’re not already using that to get PubMed import data. It’s killing me that when I import via PMID, it doesn’t also fetch the DOI, btw. Please – use all this data. It’s going to be necessary down the road. If nothing else, have Mendeley fetch all the data with field codes then map the field codes to Mendeley in the program. That way, if you’re not using the AB field today, at least you can build it in as a feature tomorrow without me having to re-lookup all my PMIDs 😦
Now here’s the one where it gets REALLY useful. One more time to Display and change to “related articles.” When I was talking earlier about suggesting papers, here’s an easy way to make it work. Get the related papers list for everything you have in a specific “playlist” of articles, rank them by how many times each appears, then color code the ones that are already in the user’s library (green), then color code all the ones that free full text is avail for, either via pubmed or the Mendeley social service (blue) then those that there is no full text avail (black or red). Holy cow! Now I know which papers are highly likely to be cited by my audience and demanded by my critics.
OK – enough with the thought exercise. I hope this helps! All my best to you guys… You have unlimited potential with this program. Keep working hard. This is the part of development that separates the Googles of the world from the Infoseeks and Lycoses. You’re going to be great.
If it’s helpful, I’ll keep giving my feedback. Just think of me fondly when your commercial version costs $500 and no researcher can live without it 🙂