Reference
- Key
- Strong Points
- Weak Points
- Ratings
- Excellent
- Very Good
- Good
- Extensive reference collection, links
- Database needed
- Rating
- A-to-I RNA editing
- www.lehigh.edu/%7eswm3/A-to-IRNAeditingwebsite/index.html
- Remember the “good old days” when the central dogma ruled and nucleic acids were largely looked at as giant unalterable cellular blueprints? The more we learn about DNA and RNA, the more this doctrine looks like a quaint convention of a simpler time. Indeed, molecular biology today recognizes not only that RNA information can flow to DNA (reverse transcription), and that eukaryotic genes are usually in pieces in the DNA and must be spliced to make mature (and useful) RNA, but also that RNA itself can be altered in several nonsplicing mechanisms collectively referred to as editing. RNA editing is a phenomenon whose occurrence is now recognized to take place in most eukaryotic organisms. It varies from insertion of bases at specific places in mRNAs (mostly in simple eukaryotes) to chemical modification of bases in most other eukaryotes. The latter process most commonly involves conversion of adenosine to inosine by action of adenosine deaminase. At the A-to-I RNA Editing website, you’ll find everything you need to know about this latter process and gain insights into its significance for the cells that perform it.
- Great idea
- Too much still under construction
- Rating
- Animalbase
- http://www.animalbase.org
- This ambitious and interesting site begins with an apology – “This page is under construction and we apologize for things not yet working perfectly.” While there is still a considerable amount of the site still under construction, there is also a lot currently available. Hosted at the University of Göttingen, Germany, Animalbase is a site that will be embraced by anyone interested in the history of biology. What it provides (or will provide) is free access to digitized images of classic zoological literature dating from the beginning of publishing to 1800 (in the current effort). During the first round, all major works up to 1770 were scanned and provided online. Access to the images is available through either a search engine or by clicking on alphabetical listings of species names. I was disappointed at not being able to find digitizations for the dozen or so publications I searched for, but I did find much peripheral information associated with each book. This one is going to grow over time and it will be interesting to watch it develop.
- Excellent summaries
- Nothing significant
- Rating
- Annual Bibliographies of Significant Advances in Dietary Supplement Research
- ods.od.nih.gov/Research/Annual_Bibliographies.aspx
- I’m always a little cautious reporting on research relating to nutrition because there are so many claims made about supplements and nutrition products that aren’t exactly scientifically established. I figure this interesting set of pages from the NIH ought to be safe, though. In existence since 1999, the site is a simple one. On the opening page, one can click on any of the six annual bibliographic collections and download a PDF covering that year. What is awesome about Annual Bibliographies is the content of these PDFs. Inside each are a summary of every paper representing the 25 most significant findings in the field that year. What an excellent idea! The only question I have is why other disciplines haven’t done the same thing.
- Large number of articles
- Hard to navigate
- Rating
- arXiv.org e-Print archive
- arxiv.org
- It took me a second to realize that the X in the title of this site is to represent a Greek chi, so this is an archive site. Oh—I get it now, but why not just spell the word ’archive’? We are, after all, capable of reading. That’s a pretty petty gripe, however, considering what is available in the archive. Hosted by the Cornell University library, arXiv.org provides free access to over 350,000 ’e-prints’ in physics, mathematics, computer science, and quantitative biology. What’s the catch, you wonder? I can’t seem to find one, save the fact that quantitative biology has the fewest number of headings. Under quantitative biology, topic areas include biomolecules, cell behavior, genomics, and others. Organization is rather higgledy piggledy—mostly focused on dates. The search engine too is formatted for dates, though one can search by words or authors. Papers can be viewed in several graphic formats, including PDF.
- Links, news
- Annoying cursor behavior
- Rating
- BCBLab Yabi – Yet Another Bioinformatics Index
- http://lab.bcb.iastate.edu/yabi/
- I was contacted last year by a group of students at Iowa State University who had created this site as a result of their own initiative and I thought it deserved mention. With an aim to “build the most comprehensive collection of bioinformatics-related links on the web, these folks weren’t fooling around.” Did they succeed? Well, to be honest, the answer is not quite, but the effort is a notable one. First, the site’s plusses include an up-to-date news section, and the YABI part, which has nice hierarchical organizational scheme and a considerable number of listings. What’s not to like? For starters, the section in YABI with hyperlinks has a VERY annoying feature where when the cursor is placed over a hyperlink, a thumbnail view of the link is presented that gets in the way of everything that you do. This is very annoying at best. Second, while the list of links is, indeed, impressive, it is not the most extensive collection I’ve seen, though it is pretty good and it is nicely thought out. A very nice student effort.
- Powerful searches of the literature
- Cumbersome to use
- Rating
- BioMinT
- biomint.pharmadm.com
- BioMinT is a page with a purpose. Aimed at researchers hoping to mine the text of biomedical articles, the search engine takes an interesting approach. Focusing on PubMed/Medline, its claim to fame is that it presents the most relevant articles first and can also extract relevant sentences from abstracts. To use the service (at least for the most meaningful part of it), you’ll need to register, but after that, everything is free. I did a search on insulin in Drosophila and turned up 425 hits after I was given a multitude of options for selecting them. My searches generally aren’t too sophisticated, so I may not be a good judge. I must wonder, though, how much time this approach saves. The engine was not particularly speedy in its work, and navigation was not exactly what I would call intuitive. I can’t complain about the results, though, and the price (free) certainly won’t get anyone’s hackles up. Probably worth a look-see if you do much searching of the literature.
- Superb coverage of subject
- None
- Rating
- Brain Blog
- http://neuropsychological.blogspot.com
- I almost hate to say it, but my brain hurt while reading through these pages. It wasn’t that the material was too dense or complicated, but, like the feeling we get when we see someone being hurt in a movie, my brain ached for the sufferers of HIV whose brains were described in the opening article on the site (at presstime) as being damaged/destroyed by the HIV virus. That’s only one of many interesting brain-related articles to be found on this informative blog. Other recent topics included coverage of computer-generated skulls for designing better helmets, Losing Betsy – A Journey Through Dementia, genetic risk factors for multiple sclerosis, and channelrhodopsin-2 – a fascinating photosensitive protein. Archives from the site are available and date back to September, 2004. Unlike many blogs which focus on raving and ranting of the creator, BrainBlog stays, shall we say, cerebrally focused on its subject and in the process delivers the most informative collection of brain-related information that I’ve come across on the Web. An excellent way to kill a couple of hours.
- Clever approach to common problem
- Success requires work from users
- Rating
- CBioC
- cbioc.eas.asu.edu
- From Arizona State University comes the Collaborative Bio Curation (CBioC) project, which attempts to get a handle on the enormous volume of biomedical articles currently flooding the scientific community. Consider, for example, that from 1994–2004, almost 3,000,000 biomedical articles were published in the U.S. and Europe on top of the 15,000,000 articles already in PubMed. Managing this material is no small job, but that is what CBioC is aimed at doing—providing automated information extraction by a novel approach, mass collaboration. In this method, the community of researchers reading the material contributes to the curation process. This is a sort of a combination of a Wiki and an open-source blog, and it gets my thumbs up for its creative approach as well as a practical way to deal with a problem. As one might imagine, hiring curators is expensive, and automated approaches to curation are not yet perfect, so this may be the best way to handle the information deluge at the present time.
- Excellent free idea
- None
- Rating
- Connotea: Online Reference Management
- www.connotea.org
- If you’ve ever used information-sharing sites like Delicious (http://del.icio.us) or Flickr (www.flickr.com), you’ll be familiar with the idea behind Connotea. If you aren’t, then read on. Connotea is an information sharing service (free, free, free) for “researchers, clinicians, and scientists” that provides online storage, access, and sharing of references for use in bibliographies. Imagine, for example you are on the road and need to access references for a talk you are giving. If you had stored references at Connotea, they would be available to you wherever you can get Web access whenever you want. How does it work, you ask? Simple – you have to register. This provide you with account space and after that, you simple click on references to add them to Connotea. Ideally, you add keywords to them so you can retrieve them later when you need them. Simple is good and easy access is even better. Connotea scores big time with this valuable tool for scientists.
- Eclectic
- Needs more focus
- Rating
- Element List—Science Links for Scientists
- www.elementlist.com
- A curious site with a curious name, Element List describes itself as science links for scientists, but that’s a bit simplistic. To start, the site has a blog section that is a bit odd and is focused mainly on the news. Second, science forums provide opportunities for registered members to chat. Third, there is a section entitled “Science Jobs” that seemed (at press time) mostly focused on positions relating to math or that require strong math skills. The links section of the site contains a nice hierarchical design led by main categories, such as Research Labs, News/Journals, Science & Society, Science Education, and Research Opportunities, among others. Each of these contains numerous sub-headings that were unlinked, for some reason, but each main heading led to additional, useful sites. The linked sites were eclectic and, in most cases, interesting and informative. A mixed bag overall.
- Useful, interesting analysis tools
- None
- Rating
- eTBlast Search
- invention.swmed.edu/etblast/etblast.shtml
- Staying on top of the literature is no small effort for scientists today. Not surprisingly, there are dozens of online tools for managing this vast body of information, and eTBlast is one of the more interesting attempts. Describing itself as “a unique search engine for searching biomedical literature,” eTBlast is probably best described as a similarity searcher, rather than a keyword searcher. At the site, visitors can upload a paragraph of text and the search engine will try to identify Medline entries that best match it. The idea is to reduce the “noise” that arises often in keyword searches. Does it work? Yes, and surprisingly well. I pasted in the text from the bone marrow program above and, to my pleasant surprise, the search engine listed as the top “hit” an article about the NMDP program. Other features at the site include TRITE (precomputed Medline similarities), eTSNAP (identify related information in a body of text), FRISC (faculty research interest comparator), RIC (compare one’s research interests with MEDLINE abstracts), ARGH (world’s largest catalog of biomedical acronyms), and more on the way. A winner for anyone hoping to pull more out of references.
- Automation
- Could be more informative
- Rating
- GeneWays
- geneways.genomecenter.columbia.edu
- The expansion of scientific information is occurring at a pace faster than it is being efficiently managed. Consequently, the development of tools for handling and even identifying this data are as important if not more so than the data itself. Toward this end comes GeneWays, a tool that uses natural language processing (NLP) to scan thousands of research articles in order to automatically extract relevant molecular knowledge. Well, they certainly caught my attention, so I read on – “GeneWays' architecture combines various modules designed to automatically gather knowledge on signal transduction pathways from online scientific journals.” The approach has most recently been detailed in Scientific American. Note that the dataset can be downloaded, so the best thing to do with the site is to check it out.
- Clever idea
- Not appropriate for all searches
- Rating
- GoPubMed
- www.gopubmed.com
- “Give me a ‘G’, give me an ‘O’, give me a ‘PubMed’ too. Roll it all together. Make something new. GoPubMed, GoPubMed, GoPubMeddddddddd.” OK, the spirit moved me, which may be what also happened when the designers of this site came up with the idea for it. Simply put, GoPubMed takes input, makes PubMed inquiries, and then sorts the results. It may sound trivial, but it’s not. I used my name “Ahern” as a search term and quickly retrieved over 900 hits. Making sense of those hits was made easier by the fact that a panel on the left side organized the results according to topic, author name, journal published, and time of publication. If I wanted to bring up all of the hits for M. Ahern, it was a simple click. Similarly, getting a list of all articles in 2003 was another click. This is one of the best ways I’ve seen to wade through the sometimes massive results of a PubMed search.
- Formatting options
- Lack of bulk exporting
- Rating
- HubMed
- www.hubmed.org
- Speaking of PubMed, we now come to HubMed, a site that describes itself as “an alternative to the PubMed medical literature database” and “The Swiss Army knife of PubMed interfaces.” That Swiss army knife metaphor is getting a little tired, to the point of being a cliché, so I was a bit skeptical about the offerings here. The upshot? There’s a lot to like at this site. One can perform PubMed searches and export citations in several formats, including RIS, BibTeX, RDF, MODS, and RefWorks. One can also unzip the site’s import filter to allow importing directly into Endnote. The RIS format also allows for direct imports to ProCite, RemMan, and others. This is a great way for users to not only search PubMed but also to format results into popular reference managing software. There wasn’t much of a downside except that I didn’t see any simple way of exporting the complete results of a search without having to individually click on each retrieved entry. Given that most searches won’t have a large number of desired hits, I suppose this isn’t a big deal, but it would be nice to see it as an option.
- Publication links
- Not clear what the numbers were for
- Rating
- Institutional Archives Registry
- archives.eprints.org
- With a name that sounds like it houses ancient personnel files, buried in the basement of a dusty university building, Institutional Archives Registry has a bit of PR work cut out for it self in the name department. On the site’s About page, one learns that the registry tracks the number and size of open access eprint archives. With this archiving, authors of scientific papers can self-archive the full text of the entire work and make it available for everyone to see. At the site, one can view plots of publication numbers in over 500 publications/databases currently archived. Hyperlinks to each publication make access easy. Indeed, it is the hyperlinks to these publications that seem to be the primary advantage of the site. I had a hard time understanding why the numerical plots were of use.
- Number of translations
- Poorly organized
- Rating
- Online Dictionaries and Translators
- www.word2word.com/dictionary.html
- There are a zillion online dictionaries on the Web, so when I saw the title of this site, I wasn’t exactly overjoyed. It always pays to look a little deeper, and such was the case here. What I discovered at Online Dictionaries and Translators was the incredible compilation of translators for languages from all corners of the world. We’re not talking just Germanic tongues here! Need to translate between English and Inupiaq? How about between Malagasy and French? You’ll find engines here for doing just that. On the downside, the translators are great for words, but aren’t really set up for phrases. In addition, the organization is decidedly poor. Visitors click on a language, which brings up a long table that has links to many languages besides the one requested. Yes, this could be improved, but the price (free) is hard to beat.
- Functions well at several levels
- None
- Rating
- Orphanet
- www.orpha.net/consor/cgi-bin/home.php?Lng=GB
- The problem of rare diseases and orphan drugs is an important one. Our profit-driven health care system has its faults, as we all recognize, but these are magnified even more if you suffer from a rare disease or disorder for which drug developers aren’t willing to create drugs due to a limited market. There is probably more information on Orphanet than there is for some of the rare diseases described therein. Information is available that is targeted at medical professionals, patients, support groups, industrialists, and the general public. Articles are well-written and easy-to-understand. What more could one ask of a site?
- Links to RNA sites
- Not totally focused on RNA
- Rating
- paRNAss
- bibiserv.techfak.uni-bielefeld.de/parnass
- RNA folding is yet another amazing aspect of this oft-overlooked nucleic acid. Let’s face it, RNA is a pretty complex set of molecules. The potential of RNAs to form numerous secondary structures has been known at least as long as the sequence of rRNAs and tRNAs has been available. RNAs can make unusual base pairings, so predicting their occurrence is only a partially-solved problem in many cases. As seen at the paRNAss opening page, a single RNA can assume multiple secondary structures. Hence, understanding their potential has biological relevance. At the paRNAss site, the RNA folding problem (actually an RNA base-pairing problem) is the prime objective. Visitors will discover a wide-ranging and useful collection of links to RNA-related webpages within the RNA Studio section. Curiously as well as distractingly, the site also links to numerous sites totally unrelated to RNA folding, including some covering genome comparison, alignments, primer design, and evolutionary relationships. While these are all important topics, I must ask why they are included in a site focused on RNA folding.
- Aggressive approach
- Nothing significant
- Rating
- Patent Lens Home
- www.patentlens.net/daisy/patentlens/patentlens.html
- I like the opening page of the Patent Lens Home. Prominently displayed at the top of the page are symbols that resemble both the number 101 (as in the numbers of an elementary college course) and the letters IOI (as in the Initiative for Open Innovation). It is the latter that the site’s designers are referring to and it is effective. The Patent Lens site has a sort of “plain Jane” interface on the opening page with only a simple text-box entry providing access to a search engine. Under the hood, however, there are mountains of information free for access. They include search technologies that are independent of language; protein/DNA sequence searching (over 51,000,000 sequences in worldwide patent databases); free PDF downloads for all U.S., Australian, PCT, and European patent documents; and searches for lapsed/expired/abandoned U.S. patents. The aim of the site is to make patent claims both transparent and navigable and provide users with understanding of freedom to operate with respect to patents. Is it effective? You be the judge.
- Organization, types of documents available
- Limited number of sources, some documents not translated to English
- Rating
- Scitopia.org
- www.scitopia.org/scitopia/search.html
- For research scientists, PubMed is as essential as oxygen—a necessary portal to the publications
of others. Yet, probably fewer people are aware of the search portal Scitopia.org, which, similar in some respects to PubMed, offers unique advantages and resources of its own. Queries are searched against 24 sources, 18 scientific society sources and 6 government information sources. Abstracts from society documents are free to read, but the article itself must be purchased unless one is a member of that particular society (much like the system employed by PubMed and its various journals). Particularly useful on this site are the other two types of search results: patents and government documents. Complete patents from the U.S., European, and Japanese patent offices
are downloadable, although a warning—the Japanese patents are only written in Japanese. The “government documents” category seems only inclusive of the U.S., but perhaps that will change
in the future. Across all categories, results can be clustered by subtopic or author. The site is nicely organized, easy to maneuver, and contains pertinent information from a variety of sources.
- Abundance of information
- Nothing significant
- Rating
- SpringerLink Home-Main
- www.springerlink.com/home/main.mpx
- SpringerLink, according to the opening page on this site, is “one of the world’s leading interactive databases for high-quality STM journals, book series, books, reference works, and the Online Archives Collection.” The amount of info housed here is not trivial; there are (gulp) over 3 million documents that can be accessed. Full access requires free registration, but even without registering, one can view abstracts and summaries of articles. To be sure, not all of the content is for scientists (for example, architecture, business/economics, humanities), but there is a lot here for biologists/behavioral science (75,000+ articles), biomedical/life sciences (829,000+), chemistry/material sciences (589,000+), earth/environmental science (300,000+), and medicine (650,000+). A site definitely worth a look-see, SpringerLink is packed to the gills.
- Exellent coverage
- Mainly for nerds
- Rating
- The Arrowsmith Project Homepage
- arrowsmith.psych.uic.edu/arrowsmith_uic/index.html
- The Arrowsmith Project represents a targeted effort to provide sorted/filtered information relevant to scientific references. There are in fact tools on the site that allow researchers to go far “beneath the skin” of ordinary reference information, permitting the extraction of new information by data mining. How, you might wonder, does Arrowsmith accomplish this? A fair question. It starts with a tool called Arrowsmith that attempts to identify links between two different articles using words/phrases common in their titles. A second tool called Author-ity aims to identify Medline articles written by a single author (under construction at press time). Other interesting features of the site include WetLab, an open-source electronic lab notebook (surprisingly, for Windows only); ADAM (Another Database of Abbreviations in MEDLINE); and links to other biomining text tools. Though it is aimed mainly at nerds, Arrowsmith appears to have a stranglehold on the field of scientific reference analysis/retrieval.
- Intriguing idea
- Nothing significant
- Rating
- The Company of Biologists Limited
- www.biologists.com/web/index.html
- I like the tagline on this one—A charity run by biologists for biologists. The title is a bit misleading, inasmuch as the site provides online scientific research journals via the Open Access Initiative. As the site notes, authors can publish their work free of charge in a traditional publication format or by paying for a subscription-free format that provides visitors completely free access to the material. The site, from the descriptions, appears to be a bit of an experiment, and it sounds like a worthwhile one. Three journals are offered by the publisher: Development, Journal of Cell Science, and The Journal of Experimental Biology. The company also provides travel grants and fellowships of up to $4,000 to postdocs interested in collaborations with other laboratories.
- Interesting collection of links
- Could cover genomics more thoroughly
- Rating
- The Genomics Web Page
- www.genomics.co.uk
- Speaking of Horizon Press-related sites, this one appears to have some connection, as witnessed by its appearance and its links back to the Horizon Press site. In some ways this site is better—less of a focus on commercial sites—and in some ways it is worse—not quite as broad of a scope. Everything is a trade-off, I suppose, and it was that compromise that convinced me this site was worthy of mention. Link topic areas include Analysis of DNA/Protein Sequences, Genomic Institutes, Companies, Books, and Other. In contrast to the previous site, this one seemed to have a much higher percentage of links to places that had nothing to do with trying to sell you something. Curiously, many of the listed books appeared to have no link at all, so I’m not sure what to make of that. A useful, if somewhat puzzling, site.
- A few useful links
- VERY uninspired
- Rating
- The Microbe Project
- www.microbeproject.gov
- Hmmmm. This site turned out to be quite different from what I thought it would be when I first picked it for inclusion here. It has an attractive front end with techie looking images on the front page and a panel on the left that appears to link to a wide variety of related information. The site bills itself as a portal, which basically means it provides links to a variety of places. Yawn. The panel of links on the left turn out to be links to simple pages about the support of various federal agencies for the project. Yawn. Some of the links that the site does lead to that are useful include connections to genomic sequencing efforts, federal reports on the project, and several funding opportunities. Overall, a disappointing site.
- Excellent resource
- None
- Rating
- The Stem Cell Community
- www.stemcellcommunity.org/metadot/index.pl
- Here’s a site you’ll probably be interested in from the name alone. As almost everyone knows, stem cell research in the U.S. is considerably restricted due to limitations on federally funded research imposed by President Bush. Research outside the U.S. is not so restricted, so having a site for stem cell researchers to stay in touch with cell lines and happenings in this enormously potential field is essential. Welcome, therefore, The Stem Cell Community with descriptions of more than 200 human embryonic cell lines from 13 countries. Visitors can search the cell database, look up publications on the subject, view U.S. patents 18 months after filing, and examine gene-expression data in spreadsheet formats. There is community-related info (meetings, news archives, opinions, training courses) and a useful collection of relevant links that round out this well-designed site. A great resource for its target audience.
- Specific organization of links
- Limited by current index of sites
- Rating
- Vadlo
- vadlo.com
It’s one of the pitfalls of the Internet—search for PCR in your favorite search engine, and you might just as well find information on purple-colored rockets as on polymerase chain reaction. Enter Vadlo (named for a fig tree), a biology-oriented search engine created by two biologists. Website owners can submit their sites for inclusion to the index, which contains only sites that fall within one of five categories: protocols, online tools, powerpoints, databases, and software. You can spend hours surfing through sites you didn’t know you were interested in finding, thanks to the random search feature—whenever you click to one of the categories, a search term is automatically entered and the results displayed. Yet, this site is also the home to a more whimsical scientific gem—its Life in Research cartoon series. (Yes, we all need some humor to combat negative results and failed experiments.)
*The opinions expressed are solely those of the author(s) and should not be construed as reflecting the viewpoints of the publisher, Genetic Engineering News, the Mary Ann Liebert, Inc., publishing house, or employees or affiliates thereof.
Suggestions of websites for review are welcome and should be addressed to .
INTERVIEW:
(BIO) BANKING IN LUXEMBOURG - Interview with Robert Hewitt, Ph.D., CEO, Integrated Biobank of Luxembourg, and European Editor, Biopreservation and Biobanking (published by Mary Ann Liebert, Inc.)
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