This page holds news entries from 2006. Please see our new blog page for news.
Early in the new year we'll be moving Connotea to bigger, better servers. Unfortunately this means that Connotea will be unavailable for two hours on the 2nd of January, 2007, from around 6pm to 8pm EST, while we physically relocate some of the hardware that runs the site.
Please accept our apologies for any inconvenience this may cause you. We'll be trying very hard to keep the amount of actual downtime to a minimum.
If you've recently upgraded to Firefox 2 you may have noticed an issue with the Connotea bookmarklet window: it now appears minimized (or underneath your other browser windows, if you use a Mac) by default.
This is due to a new security setting in Firefox. To fix the problem, open the Firefox options (select "Tools" > "Options" on Windows; select "Preferences.." from the Firefox menu bar on Mac; select "Edit" > "Preferences" on Linux) and then select the "Content" tab. Next to "Enable JavaScript" is a button labeled "Advanced" - click on it and make sure that the box next to "Raise or lower windows" is checked.
You only need to do this once - apologies for the inconvenience.
Today sees the introduction of Google Ads on some Connotea pages. Our aim is to make them unintrusive and, more than that, actually useful to you.
This is quite a big step for Connotea, but should be beneficial to the service in the long term. If we can keep the ads relevant, there will be a source of income that will allow us to continue investing in, developing and improving Connotea. With that aim in mind, we've initially set things up so that you don't see ads when you're using and browsing your own library — only when you're looking at aggregated tag pages or other collections. In other words, you'll see ads when you're exploring the site, which is probably the time when you'll find them most useful. We've done some experiments with Google ads, and while the relevance is a bit wayward to start with, they seem to rapidly improve.
This is, as always, experimental. We'll be watching closely to see how useful and relevant the ads shown are, so if you have any feedback, please do let us know.
One of Connotea's main features is to recognise articles from a variety of scientific sites and automatically save bibliographic information for them. However, we don't (yet) support every single site in the known universe, so one of the most requested features for Connotea has been the ability to manually add citation information for articles from sites which are not supported. Today we have released the first version of this new feature. Now, when you add an article to your library, you will see a new 'Edit Citation' button on the form.
If Connotea has not recognised your article and found the bibliographic information, or you would like to add more details to the information it has imported, click this button. A form will appear for you to enter title, publication details, author names, article type and more.
When you have finished, you can add your tags and save the article as normal. You can, of course, edit this information at any time - just find the article in your library, click 'edit', and then click the 'Edit Citation' button.
We hope this will make Connotea even more useful for those using it to create reference lists and bibliographies. And, of course, all the information you add is searchable, so any extra information you include will help you navigate your collection. Please do contact us with any comments, suggestions or questions you have. This is a fairly big change, so as always, please also let us know if you come across any bugs.
We've just posted an entry on NPG's Web Publishing blog Nascent about some innovative ways that people are using Connotea. We'd love to hear from more of you about what you're doing with Connotea, so if you've got a story to tell, post something in the comments on Nascent or contact us directly.
Connotea is part of a suite of projects that we work on here in the Web Publishing division of Nature, including the podcasts, databases, and lots of other cool things.
We're looking for a Product Development Manager to work on Connotea and other upcoming web publishing projects. If you're web-savvy and into science, we're very interested in hearing from you. Have a look at the job description and then apply, either through Naturejobs or by contacting us.
We've got a new introductory video to help explain what Connotea is to new users. Send it to your friends to get them started!
Hot on the heels of yesterday's support for BibTeX upload, we've greatly expanded the number of ways you can get things into and out of Connotea.
You've always been able to export your library (and indeed any public collection of links) from Connotea using RIS, a format understood by a large number of desktop reference managers. But not all, so we've now expanded that to include the EndNote format, BibTeX, and the Library of Congress' MODS XML format. Just click on 'export my library' in your toolbox, or 'export this list' at the top of any list page, and you'll be presented with these options.
It made sense to mirror this developement with more import options too, so we've also released support for uploading a batch of references in any of these formats. If you do upload a batch of references, it's important to note that each entry should have a URL, DOI, PubMed ID or ASIN associated with it, otherwise Connotea can't add it to your collection.
Our support for some of these import formats is still a bit experimental. There's a lot of deviation in real-world files from the specifications, so our import tool may not get everything right first time. If you have a problem importing a collection, please contact us so we can improve the process.
We've just released a number of new features designed to help the growing number of Connotea users who are working in the Physical Sciences.
If you keep your local references in a BibTeX file, you can now upload them in one batch to Connotea. This is still a little experimental, so please contact us if you have any problems importing your file. You should also note that in order for Connotea to add a reference to your library, there will need to be a URL or DOI associated with the entry in the BibTeX file.
We've also added article identification support for arXiv.org, Scitation, and the Smithsonian/NASA Astrophysics Data System. Now, when you save a link to an article in NASA ADS, an abstract in Scitation or a physics abstract in arXiv.org, Connotea will identify it and automatically import extra bibliographic information for the article.
If you'd like to see further sites supported, you can add your request to the community pages. And, as always, you can contact us with any question or problems you have.
As I'm sure you noticed, a few weeks ago the site performance began to slow down. We worked a lot on some changes behind the scenes, and hopefully you'll have noticed that your library is now loading much faster, and that browsing through your tags is nice and responsive again.
If you're interested in the details, we made two major changes. Firstly, we re-wrote all the database queries to make them run much, much faster — up to ten times faster in some cases. Secondly, we made sure that real users get priority over search engines and other programs accessing Connotea. If your request is competing with one from a search engine crawler, or via the Web API, then yours will always be run in preference. You can see the exact rules we apply on the community page.
Connotea now supports all journals published by BioMed Central.
Of course, you could always save a link to a BioMed Central article with Connotea, but now when you do Connotea will automatically identify the article and pull in the bibliographic information for it. It should even work when you bookmark a PDF.
As always, if you find an article or journal where this doesn't work, please contact us. And, of course, you can always add your requests for future supported sites to the Community Pages.
Take the Connotea user survey for a chance to win a free 30GB iPod.
Feedback from users is vital to us in thinking about the future of Connotea. We do regularly receive feedback through our mailing lists, but we would like to know more.
We have therefore created a User Survey to help us get feedback on how you're finding Connotea and what additional features would make it more useful. The survey should only take a few minutes, and we will be using the results to influence the future direction of Connotea development. If that's not enough, there is a free iPod to be won by a respondant drawn at random after the survey closes!
So please take the survey now, and, of course, if you have any feedback you would like to send to us directly or discuss with other Connotea users, please feel free to contact us.
We've made some changes to the look and layout of Connotea.
The changes are mostly aimed at new users and first-time visitors to Connotea, in order to make it easier to get started using the site. In particular there are detailed instructions on creating the 'Add to Connotea' button for your browser. There are also a few small changes to the layout of the rest of the site, but nothing too drastic. Please do let us know if you have any feedback about the new design.
Thanks to the work of Robert Forkel, Connotea now automatically imports bibliographic information when you bookmark articles in Living Reviews.
To enable this, Robert wrote and submitted a Citation Source Plug-in. If you'd like to contribute your own, have a look at Connotea Code or sign up for the connotea-code-devel list.
A lot of you are increasingly bookmarking articles from personal blogs alongside traditional journal-published articles. In response to this, Connotea now has experimental support for treating bookmarked blog posts as citations, and it will automatically import publication data for those articles wherever possible.
For example, here's a screenshot of the bookmark
for this
article from NPG's Web Publishing
blog Nascent:
As you can see, Connotea has recognised the name of
the blog, the publication date of the article, and the name of
its author. It also gives a clean version of the page title.
This feature takes advantage of the fact that most blogs have associated RSS or Atom feeds, and that these feeds often contain a lot of extra data about their posts. Connotea looks for these feeds and imports whatever it can. Those familiar with RSS and Atom will realise that this explains a limitation of this feature — only posts made recently are currently supported in this way.
Today we have released the first version of the Connotea Web API, which will allow programmers to develop applications that read from, and post to, the Connotea database.
If you're still reading, you're probably interested in the full details of how this works — see the Web API documentation on the Community Pages. Note that we're calling this version 0.1, in the expectation that things will change as we get feedback from people using it to build applications. Of course, if you dive in and try it now, you'll be able to influence the future direction of the API.
We've also made available wrapper libraries and sample code in Perl and Ruby. Please download the libraries and send us feedback. If you write a wrapper library in another language, you could consider releasing it and listing it on the Web API Libraries Community Page.
Connotea can now automatically import bibliographic information for articles in Public Library of Science journals.
This new feature is thanks to the work of Bartosz Telenczuk (Connotea user btel), who wrote and submitted a citation plug-in for PLoS.
If you're a programmer and would like to contribute a citation plug-in for Connotea, have a look at the Connotea Code. There are some suggestions for sites you might write a plug-in for on the Community Pages.
As always, please contact us if you have any questions or spot any problems. If you have a site you'd like to see Connotea import bibliographic information for, please add it to the request page.
Today we've released the first version of the Connotea Community Pages, a section of the site where you can write and edit articles about all aspects of Connotea.
The idea behind the Community Pages is that you can create pages about tips and tricks, discuss possible future developments, or anything you like to do with Connotea. You can even write a profile of yourself, and there are also special pages for tags and groups.
Because the Community Pages are a wiki, any Connotea user can start new pages or edit existing ones (with the exception of user profile pages). For more information and to read or contribute to the Community Pages, see the Community Pages home.
This is something of an experiment, so we hope you'll contribute and help make the Community Pages a valuable resource for Connotea users. As always, if you have any questions or comments, please contact us.
We've added a Tag Suggestions section to the form for adding a bookmark, and now tags that you've used before will be presented to you as you type.
Here's an example of how it looks:
You can see the suggestions underneath the tags
box — note that they're just based on the second tag
being typed, so everything works as you'd expect when you're
assigning more than one tag to a bookmark.
Connotea will present tags from your own collection that match what you're currently typing. For example, if you can't remember whether you used astronomy or astrophysics, just start typing and Connotea will show you.
A lot of you have asked for some way of managing your increasing number of tags, and help remembering what tags you've used before. Hopefully this will do that and save you from duplicating tags. It should also save you some typing too.
If you have any comments, please contact us.
We're developing new features for Connotea all the time, and inevitably there are sometimes bugs in things that we release. Now, if you see a problem on any Connotea page, you can quickly report it directly to us so that we can fix and improve things.
There's a report a problem link on the right-hand side of every page. If you see something we need to fix — inaccurate bibliographic information or a broken link, for example — click on report a problem and fill in the details. Hopefully this will help us to make Connotea better, although for once it's a new feature that we hope you won't need to use.
We've released a small code collection that enables institutional repositories running on EPrints to easily add tagging, bookmarking, and related article linking to their sites.
The TaggingTool works by connecting the repository content to either Connotea, del.icio.us, or any service based on Connotea Code. It shows tags that have been used on repository items, allows users to save the item in their own Connotea or del.icio.us accounts, and shows links to related articles.
The tool is quick and easy to install, and requires only minimal changes to an existing EPrints repository. If you're a user of a repository and would like to experiment with the TaggingTool, point your administrator at the summary of its features.
As you may have noticed, we changed the Connotea homepage last week. As part of that re-design we created a tag cloud, and now we've made a new introductory video that gives visitors a quick tour of various features of Connotea.
The tag cloud is an attempt to give an at-a-glance view of what Connotea users are currently reading about. It's an alphabetically organised list of the most recently used and popular tags in Connotea, with tags that have been used more recently being redder, and tags used more often being larger.
The new video, A Quick Tour, is a short explanation of tags, bookmarking, automatic bibliographic information import, related tags and users, and sharing. Our hope is that this will help new visitors quickly understand the benefits of the Connotea approach to information management.
If you have any feedback on any of this, please feel free to contact us, either on the Connotea discussion mailing list, or privately via connotea@nature.com.
An updated version of Connotea Code, the open source release of the software that runs Connotea, is out.
Here are the major new features that have been added in version 1.7.1:
Yes, that's right, we have the beginnings of a Web API. Expect to see more details about this soon.
For a full list of changes, see the Connotea Code documentation.
We've added automatic bibliographic information collection for articles hosted in institutional repositories that are based on EPrints.
Connotea can't automatically support all EPrints-based sites — we need to register custom information for each one individually. However, we have added support for 49 repositories that we were able to initially find and verify.
Please have a look at the list, and if your local EPrints repository isn't listed, contact us with the details and we'll get it supported.
You can, of course, still bookmark pages from other repositories — we'll associate bibliographic information with those bookmarks as and when we can in the future.
As always, let us know if you find any articles that don't work with this new feature.
Connotea now supports automatic bibliographic information collection for journal articles hosted on Wiley Interscience.
This adds a large number of new journals to Connotea's supported sources, but we're always looking for more. So, if you have a suggestion for a site that you'd like to see Connotea support, please contact us.
As always, let us know if you find any articles on Wiley Interscience that don't work with this new feature.
Connotea user Pierre Lindenbaum has created two new tools to help Firefox users work with Connotea.
The
first, PubMed2Connotea,
can be used by Firefox users who
have Greasemonkey
installed. Greasemonkey is a Firefox extension that allows
people to write scripts that alter web pages. Pierre's
Greasemonkey script works with PubMed, and inserts Add to
Connotea links next to articles in the search results
page. You can then simply click the Connotea logo to add the
article to your library.
If you would like to use this tool, but haven't
installed Greasemonkey, don't worry, it's very easy: go to
the Greasemonkey
homepage and select the release appropriate for your
version of Firefox. When you have installed it, return to
the PubMed2Connotea
page and follow Pierre's instructions to activate the script.
The second tool allows Firefox users to
To install it, simply follow Pierre's
instructions. Connotea will then appear in the list of options
for the Firefox search box.
Pierre has previously created two other interesting tools, Connotea Client andConnotea Explorer, for using with Connotea. If you have any feedback on any of Pierre's tools, or if you would like to contribute to Connotea by developing your own tools, please feel free to send your comments to the Connotea discussion list.
The Connotea servers are being moved this weekend. Unfortunately the service will therefore be unavailable between 3pm EST on Friday 16th December and approximately 12 noon EST on Saturday 17th. Please accept our apologies for any inconvenience this causes you.
We will make every effort to keep the amount of time that Connotea is unavailable to a minimum. Please contact us if you experience any problems related to this, or have any other questions or concerns about the move.
We've added automatic bibliographic information support for articles hosted on Blackwell Synergy, which increases the number of journals that Connotea covers by more than 800.
Please let us know if you find any articles whose information is not automatically imported. You can also contact us at any time to suggest other journals and sites that you'd like Connotea to support.
We've also updated the Connotea bookmarklets to work with the latest version of Internet Explorer. If you're an IE user, please replace your 'Add to Connotea' bookmarklet with the new one. If you still have problems using the bookmarklet, please contact us.
Connotea was a finalist in the Best STM Information Product category at the International Information Industry Awards held in London last night.
We were shortlisted alongside OVID's Database Link, McGraw Hill's Digital Engineering Library, Elsevier's Scopus, PsycBOOKS from the American Psychological Association, and the OCLC's NetLibrary.
Our hearty congratulations go to Scopus, who were the winners of the award.
We've created some additional video tutorials to help you make the most of Connotea.
In addition to the existing Beginner's Guide, there is a new video called Building Your Library that takes you through DOI bookmarking, privacy, and other advanced options. The second new video, Managing Your Library, demonstrates navigating through your collections, searching Connotea, editing bookmarks, and renaming tags.
The Connotea Coders are pleased to announce that we will migrate the Connotea Computers to a new hosting facility on Friday 4th November 2005 at approximately 16:00 UTC.
Our new hosting platform will more than double our current serverresources and provide easier scalability. The web site may be unavailable for up to two hours around this time as we perform the migration, though we will aim to minimize the downtime. We apologize for any inconvenience this may cause.
Pierre Lindenbaum, a Connotea user, has created two utilities that offer interesting new interfaces to Connotea.
Connotea Explorer is a tool that helps you visualise and explore the contents of Connotea. It allows you to navigate through the articles and links in the database using the tags that have been applied to them.
Connotea Client is an an alternative way of bookmarking PubMed articles in Connotea. You can search PubMed from within the application, and can easily use MeSH terms or words from an article abstract as tags.
Pierre is a bioinformatician working at Integragen. He completed a PhD in molecular biology at INRA, studying protein-protein interactions between a rotavirus and its host cell. He then moved into a career in bioinformatics at the National Center of Genotyping before going on to his current position.
Please feel free to send your feedback on Pierre's contributions to the Connotea discussion mailing list.
Connotea now supports articles published in Science . When you add a Science article to your collection, its bibliographic information will be automatically associated with your bookmark.
As with the PubMed Central support launched on Tuesday, any Science articles you already have in your collection will be upgraded to full citations the next time we run the retro-active citation import.
Please contact us if you have any questions, especially if you find an article that is not recognised by Connotea.
Connotea now recognises and imports the bibliographic information for articles bookmarked from PubMed Central.
A number of users already have links to PubMed Central-hosted articles in their libraries — these will automatically be supplemented with bibliographic information when we next run the retro-active citation import.
As always, please contact us if you have any questions, particulary if find a PubMed Central article that is not recognised.
You can now search your Connotea library by keyword. You can also search everyone else's libraries, and, in fact, any individual listing on Connotea. This new feature supplements tagging as an organisational tool for your library, and adds an extra dimension to Connotea's use as a tool for discovering new content.
The
new search box appears in the bar that runs along the top of
every page. It allows you to find bookmarks that contain your
chosen keywords, and allows you to search either your own
library, all public bookmarks, or just the collection you are
currently viewing. The old options of quickly going to tag
and user listings are also available.
For example, you could use this to search for an individual author, or for the name of a particular journal. Exact matches appear at the top of the list, but all fields are searched for every query. So a search for 'James Crickson' would return articles where that name appears in the list of authors, assuming Connotea has the bibliographic information for the articles. In addition, it would also return bookmarks where the user mentions that name in the comments or description.
If you use more than one word in the search box, Connotea looks for bookmarks where all of the words are used. However, they don't all have to be present in the same field — a search for 'human evolution' would, for example, match an entry that had 'human' in the title and 'evolution' in one of its tags. Searching for exact phrases is not supported, so there's no need to use quotes in your searches. You can, however, exclude terms from the results by prefixing them with a minus sign (-). For example, 'evolution -human' would return bookmarks that mention the word 'evolution' but not 'human' — again, this works across different fields. There is no support for other boolean operators.
Note that this feature only searches the information held in the Connotea database (titles, bibliographic information, descriptions, tags and comments), not the full text of the article or web page.
At its annual dinner last night, the Association of Learned and Professional Society Publishers announced that Connotea was the winner of the 2005 ALPSP Award for Publishing Innovation.
From the ALPSP press release:
The judges, chaired by Richard Gedye, commented that the quality of all the finalists was especially good, but in the end they were unanimous in agreeing that Connotea had the edge, and it was duly and enthusiastically declared the winner for 2005.
We're really pleased to receive this award, so thank you to everyone who has taken part in in the creation of Connotea. This includes all the users, whose participation is an integral part of the value of Connotea.
The latest version of Connotea Code, the open source release of the software that runs Connotea, is out. This version contains all the new features developed for Connotea over the past few months.
New features in version 1.5:
You can now add your Firefox bookmarks to your library by uploading them in one batch.
In order to import your Firefox bookmarks, you must create a file on your local computer. To do this, export your links from Firefox by selecting Bookmarks > Manage Bookmarks, and then File > Export. Save the file and then upload it to Connotea. You have the option of using your bookmark folder names as tags, creating new tags or combining the two.
You now have the option of viewing your list of tags based on the way you use them, rather than simply alphabetically.
Until now, the list of tags that appears on the left hand side of your library has been ordered alphabetically. There are now two buttons at the top of the list that allow you to switch between that default view and a new option that sorts the list by your pattern of tag usage. The aim of this feature is to make the process of navigating round your library quicker and easier, so that the tags that you are most likely to want to click on appear at the top of the list.
The By Usage option takes account of both the number of times you have used a particular tag and when you last used it. The list will be re-ordered to reflect changing patterns of usage — for example, if you create a new tag it will initially appear at the top of the list, but will quickly drop down the order if you don't use it again. The formula that calculates the usage score for each tag is experimental, so please contact us if you find it doesn't work well for you, or if you have any suggestions for improvements.
We've put up a Frequently Asked Questions page — thanks to everyone who asked the questions in the first place. We've also tweaked the database queries, so you should notice some speed improvements as you're using the site.
We're experimenting with geotagging, which allows you to use special tags to associate latitude and longitude coordinates with your articles, and then view their geographical distribution using Google Earth.
For example, a number
of Connotea
user Declan's AvianFlu bookmarks have geotags. If you
have Google Earth installed, click on the 
button at the top of that list. You will then see the
locations of the Avian Flu outbreaks discussed in those
articles displayed on a map of the earth, along with links to
the relevant stories.
We've also started a list of geotagged universties — feel free to add your own to the collection. You can geotag any link by simply including the tag geotagged, along with appropriate geo:lat=xxx and geo:long=yyy tags.
For more details on how to use geotags,and the various ways you can use the data in Google Earth, see the site guide.
This is a new and experimental feature, so please do contact us if you have any problems. We'd also be interested to hear about any new applications for geotagging that you come up with.
Connotea now enables you to create and display notes to explain your tags and annotate your library.
A Tag Note is a piece of text, placed at the top of the list of all the bookmarks you have posted with a particular tag, that you can use to explain to visitors and yourself a little about the collection of articles and links under that tag. Adding notes to your tags helps to make your reference collections more useful.
For example, you might be compiling a list of your own publications, tagged under bibliography. You could create a note for this tag, explaining that these links are the papers you have published throughout your career. You could use the note to provide information to other users about your affiliated institutions, a link to your homepage or any other information you choose.
For more information, suggestions on use and details on how to createtag notes, see the site guide.
Connotea can now offer OpenURL links for many of the items in your collection.
If you have access to an OpenURL resolver, perhaps as part of your institution's library services, Connotea can create links that let you look-up your institution's holdings for anything in your collection that Connotea has bibliographic information for. Simply enter the location your OpenURL resolver (or 'link server') in your registration details. In addition, enter some text that Connotea can use when creating the links — for example, 'OpenURL' or 'Library holdings look-up' — and you'll then see that text, linked to your local resolver, beneath the citation details for your articles and books.
An OpenURL is a link, constructed to a standard format, that carries bibliographic information. When a user clicks on an OpenURL link, the bibliographic information it contains is sent to a library's link server. The results of clicking on the OpenURL will vary depending on the library's holdings, but may include showing links to all online versions for which the user has access, or giving information about the location of a print copy of an article. More information about OpenURLs.
We've updated the Connotea bookmarklets to take advantage of the new DOI functionality. Be sure to replace your existing bookmarklets with these latest versions.
To save a DOI, simply highlight the DOI in the page you are
viewing and then click the bookmarklet. For example, here's
the DOI being highlighted for an online Nature article:
Clicking the bookmarklet would send the DOI, rather than the
nature.com URL for the story, to Connotea. This is useful for
sites that Connotea doesn't yet automatically recognise links
for, or that use un-bookmarkable or session-based URLs. It
also means that you can save an article even when you're not
viewing it by, for example, highlighting and saving a DOI in a
table of contents or a reference list.
If there's no text highlighted, the page's URL is sent to Connotea as normal. The same applies to the view and add comments bookmarklets — if you highlight a DOI before using the bookmarklet, the DOI will be looked up in Connotea, if not, the current page will be.
Note that the bookmarklet does a preliminary check on the selected text before sending it to Connotea. If the text doesn't look like a DOI, then the add form won't be opened. Connotea itself also does a further check — if the text is not registered as a DOI in CrossRef, then it won't be added. This can happen if you have not quite highlighted the entire DOI, or if the publisher has not registered the DOI with CrossRef.
The updated bookmarklets should work in Internet Explorer, Firefox and Safari. If you experience any problems, please contact us.
Connotea can now recognise and store Digital Object Identifiers (DOIs). As well as bookmarking general web URLs, you can now bookmark a DOI directly. Connotea will convert the DOI to a web link and retrieve the citation information for that DOI from CrossRef.
DOIs are used to provide persistent identifiers and stable links for electronic resources. CrossRef is the DOI registration agency for scholarly publishers. For more information about DOIs and CrossRef, see the CrossRef information page for researchers.
To save a DOI, simply type doi: followed (with no space) by the DOI into the URL box on the add form.
This development means that for many journals you can now save an article to your Connotea library whilst reading the printed version of the article. There's no need to for you to find the article online before you can add it to your collection — any journal that prints the DOI for an article is supported in this way.
For example, here's what a
Nature
article looks like on paper:
As the figure shows, the DOI for this article is printed
in the strap at the top left hand side of the page. To add
this article to your collection, you can go directly to
the add form and
type the identifier (including doi:) into the Bookmark
URL box:
You
can then simply add your tags and other information as normal,
and click 'Add to my library'. The article is then added to
your library, along with its citation information, and the DOI
is converted into a functioning link. In the example above,
the link would
become http://dx.doi.org/10.1038/nature03660
You can also enter the dx.doi.org link directly into the form, and the citation information will be imported in the same way.
As well as being able to share a link with all Connotea users and visitors, or keep it private, you can now choose to share individual links with other members of one of your groups.
User groups allow you to collect together individual Connotea users in order to be able to view, browse and subscribe to their combined collections in one location. Now you can choose one of your groups as a privacy option when adding something to your library — if you select this option, only members of your chosen group will be able to see that you have added that resource. Note that this privacy is independent of group privacy — even if the group itself is public, your link will remain private to members of that group.
Embargo dates now apply to both privacy options, too. You can enter a date and time to release a link to all, irrespective of whether you kept it totally private or shared it within a group.
Today's update to Connotea brings some general performance improvements. You should notice that pages load much faster, and that your library feels more responsive as you're browsing through it.
In order to accomplish this we have made extensive changes behind the scenes, so please contact us if you have any comments or questions, or notice any features that have changed in their behaviour.
Following on from Tuesday's expansion of automatic bibliographic information collection, we have started retro-actively applying new journal recognition to links that have already been posted.
What does this mean? Say that you post a link to an article on the website of Journal X, but Connotea doesn't recognise the link and so can't automatically import the Journal name, list of authors, and so on. In that case, a standard bookmark will be created, just as when you save a link to an ordinary web page. However, say that a couple of weeks later we add the ability to recognise links for Journal X. We will then apply that knowledge not only to new postings, but also to all the links that had previously been added to Connotea. Your old ordinary link will become a full citation automatically.
Today sees two major upgrades to Connotea. Users now have the ability to import a batch of references from an RIS file, and citation information is automatically collected for 773 more journals.
You can now add a batch of references directly to your Connotea library by uploading an RIS file. RIS is a file format for holding citation information that is supported by many desktop reference managers, so now you can upload your local reference collection to Connotea. For more details, see the site guide.
In addition, Connotea can now directly import the citation data for 773 of the journals hosted by Highwire Press. These include the Proceedings of the National Academy of Sciences, the Journal of Neuroscience and Bioinformatics — three of the most popular journals in Connotea to date. There is a full list of all the journals supported available.
Connotea will be unavailable for two hours on Tuesday 31st May 2005 while we perform a site-wide upgrade. Access to your library will be suspended at 4pm BST (11am EDT) and will resume at 6pm BST (1pm EDT).
Version 1.0.1 of the code behind Connotea has been released.
Download the code from SourceForge.
This is a minor bug fix release that includes a couple of template files that were missing from v1.0.
Connotea users now have the ability to create user groups. This allows you to collect together, browse and monitor the libraries of a defined set of users.
For example, a research group could now use Connotea to share references and other online resources among themselves. Or a group of lecturers could use the groups feature to collaborate on the reading list for a lecture series — feel free to contact us with suggestions for new features that would facilitate these and other uses.
To set up a new group, simply click on the Create a new group link in your tool box. In the open spirit of Connotea, any user can create a group containing any other user.
Nature Biotechnology, Nature Immunology, Nature Cell Biology, Nature Genetics, Nature Medicine, Nature Methods, Nature Neuroscience and Nature Structural & Molecular Biology articles now have direct links for adding the article to your Connotea library. Look for 'Save this link' on the right-hand side of abstract and full text pages.
You can now set an embargo date on private links.
For example, if you're using Connotea to store the reference list for a paper, you could use the embargo date to automatically release the list after the paper has been published. Please contact us if you have any comments, questions, or suggestions about this.
One of the great advantages of storing and managing your reference list online is the ability to easily share it with other people. But do you sometimes need to keep something private? If so, you can now mark a link or article as private when you save it to Connotea.
You can go back and make it public at any time (or make things that are currently public private) by clicking on the edit link above your article. A private article is visible only by you — it will not appear in the recent activity list, and other users viewing your library will not see it. In addition, a private article is disregarded when compiling the related tags and related users lists for other people. For example, if you and another user both save http://www.example.org/, but you mark it as private, you will see the other user in your related users list, but he will not see you.
On the 29th March, EPS published an Insight discussing Connotea and CiteULike. They have kindly given us permission to share it with you here.
This EPS Insight is taken from the EPS Market Intelligence Service, asubscription offering combining written comment and analysis with access to consultants and analysts for research and briefing purposes. More details can be found at http://www.epsltd.com or by contacting Nicola Foster (020 7837 3345; nicola@epsltd.com).
Steve Sieck, EPS's US Managing Partner, has 20 years' experience inconsulting and research for content and enabling-technology providers.
Connotea and CiteULike:
"folksonomies" emerge within scholarly communities
Nature articles now have a direct link to Connotea. Each article has 'Save this link' functionality — these links lead directly to a pre-populated 'add to Connotea' form.
For example, see this article and look for 'Save this link' in the box over on the right-hand side.
As well as being able to export your personal library to EndNote and other desktop reference management tools, you can now export any list of articles or bookmarks in Connotea.
Importing behaviour varies slightly between desktop reference managers, so if you experience any problems please contact us.
We have published two articles about social bookmarking tools in D-Lib Magazine.
The first is a general overview of social bookmarking and tagging systems:
The second is a more detailed case study of our own Connotea as a social bookmarking tool geared towards online reference management:
There's also an interesting editorial in the same issue.
We have released the source code to Connotea.
Connotea Code is released as open source software under the GNU General Public License. We are making the code available in the hope that it will be useful for people who want to see how Connotea handles their data, to write plug-ins to expand the number of sources that Connotea can import bibliographic information from, or to set up their own social bookmarking service.
We have also set up two mailing lists for public use. Connotea-discuss is a general list for discussion, comment and questions about Connotea the service. Connotea-code-devel is a list intended for discussion of the core code base and the development of new citation plug-ins.
Today sees a major redesign of the look and feel of Connotea, and a new feature to enable the export of your library to desktop reference management tools.
You can now export your collection of links, articles and books to an RIS file, which can be then imported into EndNote or other desktop reference management tools. This feature is accessible from the tool box on your personal library page, part of the new Connotea design.
The new design also features a clearer separation between your own and other users' tags, simpler navigation and more easily accessible RSS links.
If you have any comments or questions about the new design, please contact us.
Today's update involves a number of system improvements including changes to the commenting system and to the search facility.
We've made a short film that shows you how to get up and running with saving article links to Connotea.
Watch the film — Flash | QuickTime | Windows Media.
When you bookmark books from amazon.com, amazon.co.uk, amazon.ca, amazon.de, amazon.fr or amazon.co.jp, Connotea will recognise the URL and automatically add the book's title and authors as bibliographic information for that bookmark.
Articles from D-Lib Magazine now have their citation information automatically added to Connotea.
Make sure you use the Connotea bookmarklet, or hit the 'update' button when manually adding an article.
A few more improvements to Connotea
Today we have the first major upgrade to Connotea.
As always, please contact us with any questions or requests.