Martin says:

This is a curiosity caused by the user’s own login cookie from
connotea.org still being active and being passed to connotea.org during
the loading of the web page when it requests the Javascript file that
contains the posts.

In other words, you see your private posts, but others visiting the
same web page do not.

Well, that’s not really obvious, so we decided to change the behavior of the widget. Updated info here.
The bottom line is that the url to call is now http://www.connotea.org/pub/jsw/user/username which will ignore the cookie, and if you want to see your own private bookmarks you can use
http://www.connotea.org/auth/jsw/user/username for HTTP authentication to see your private bookmarks.

http://www.connotea.org/blog

Connotea Blog

Social Software for Libraries by Meredith Farkas.

From the reviews it looks like a good nuts and bolts introduction to Web 2.0 tools that have a current place in Libraries. I believe Connotea is given a mention.

Of course being in a book format has advantages and disadvantages, and one of the people providing a review on Amazon sums it up nicely:

“If I had a criticism, it would only be “book versus web”, as the web is a river and a book is an island. Printing it ‘fixes’ it in time, and the highly dynamic web will outrun the content of this book in a few years, maybe sooner. Meantime, its succint, direct and practical nature recommend it as a map out of the bewildering tangle of what’s out there. Now is the time to buy it”

Connotea Blog

Connotea Blog

This is a bit experimental at the moment, so we might change things around over the next few weeks. As ever if you have any feedback let us know here or you can mail me at i.mluvany@nature.com

Connotea Blog

We have now fixed this, but the fix is somewhat non-trivial.

The main reason for the problem is that we were usin the same tag compreshension code that is used in the “Add To Connotea” pop-up. This assumes that “mutliple words in quotes” are one tag, and lots, of, tag, separated, words, are individual tags. In addition, since you access tags in conntoea through the url we have to throw away forward slashes since a tag with a forward slash in it is going to confuse the url resover in Connotea.

Now when it comes to pub med records it looks like all of these rules are specifically chosen to break the way Pubmed records describe tags :/

Ben describes the problem very well:

In Pubmed records, and in the Endnote records, /’s are used to separate descriptors such as “Transcription Factors” from qualifiers such as “antagonists & inhibitors” and “metabolism”. For example, you might see a keyword listed as “Transcription Factors/antagonists & inhibitors/metabolism”. When imported, Connotea strips the slashes from the tag and thus adds the tag “Transcription Factorsantagonists & inhibitors metabolism” to the post.

So now we deal correctly with these tags, yay!

MeSH terms sometimes contain commas like “Models, Genetic”. When imported, these compound terms get split into multiple separate tags (Models and Genetic).

That’s because our comma separation parsing used to take precendence over our parsing of collecvie terms, but we have fixed that now.

In addition, it appears that quite a few people have managed to import the “Research Support” aspect of Pubmed Records as well. This is why you see more than a thousand bookmarks with the rather misleading tag “Non-U.S. Gov’t”, often also tagged with the seemingly contradictor “U.S. Gov’t”. (This happens when the research in the paper had both U.S. and non-U.S. funding).

We decided to leave this alone, as solving this problem requires understanding what the tags mean, and the context in which they appear. OK, so you can’t win every time. I guess we are just going to have to wait for the semantic web!

p.s. You will often see a ‘star’ appended to the beginning of tags imported in this manner such as ”’star’Genes”. This indicates that the stared’d term is a major topic (as opposed to minor topic) in the manuscript according to MEDLINE indexing.

OK, so now we strip leading stars from tag names, so that ’’star’gene’ imported becomes the tag ‘gene’ and can connect to all of the other items that have been tagged with ‘gene’ by users.

In a way so far all of the above is pretty straigt forward, now things get a little itneresting,

Martin our developer points out the following behaviour:

“One of the annoying parts of import is that if the keywords are separated by newlines but a tag with commas was collapsed into two, it would likely merge with other tags on the first or second term and then be tedious for the user to pick out later no matter what the UI.

In the RIS importer I’ve added a heuristic test which allows splitting on commas, except where it sort of looks like newlines are being used to demarcate the tags.

Here are some examples:

(1)
KW - aaa, bbb, ccc, ddd, eee, fff, ggg, hhh,

iii, jjj, kkk, lll, mmm, nnn, ooo, ppp

(2)
KW - aaa

bbb

ccc

ddd

Transcription, Genetic

eee

fff

ggg

hhh

iii

jjj

kkk

lll

mmm

nnn

ooo

ppp

(3)
KW - aaa, bbb

ccc, ddd

eee, fff

(Describing this in this blog is a bit hard, you have to ignore the extra lines between text lines as the blog parser treats whitespace in this system in a funny way, but I hope you see what we mean)

So in (1), sixteen tags are evident. In (2), the same tags appear, and I’ve added a comma-containing tag to show how they appear in dang.txt from our friend Ben. Clearly in (2) the newline is supposed to be the separator, not the comma. However, if you eat commas as part of tag names then (1) will fail.

The heuristic I came up with is that if there are at least three lines and no line runs longer than 60 characters then it should be treated as newline-separated and include the commas in the tag names. Otherwise, separate on commas as well.

This makes (3) not do the right thing, so it’s up to you if you think this will help or hurt. (3) IMHO is not likely to be computer generated… a computer would either write one per KW line (avoiding all this), split on newlines, or fill up lines to ~80 chars split on commas and add in newlines to keep going. All of which work with my test.”

And so that’s how we have left it for now.

Connotea Blog

Martin, our developer had a look at their site and came up with some options. He takes up the story:

“Although the DOI appears in the URL, and we could switch off to CrossRef
for citation data, we lose the authors and full publication date, so
that’s not as good.

They embed citation metadata using Dublin Core conventions inside HTML
meta tags, but here we’re missing journal, volume, and issue data.

I noticed that their site allows download in RIS, BibTeX, etc. format,
and in looking for a similar existing citation source module that does
such a download of a secondary RIS file, that Blackwell.pm was actually
a perfect module to do the work. Too perfect – it works with a domain
name change! So then I realized that these two domains, plus more, are
using software from Atypon (www.atypon.com) and that if we recognized
the pages served from this software, we could immediately support all
their current and future customers. Considering that their customer list
includes places like MIT Press that seemed like a good idea.

So I’ve produced Atypon.pm which is reasonably short and can replace
Blackwell.pm as well as supporting many of their other customers.”

Atypon provide publishing software for the following (and so now we support the following too!:

Commercial publishers

• Alexandrine Press
• AOAC International
• Australian Academic Press
• Blackwell Publishing
• eContent Management Pty Ltd.
• Expert Opinion
• FDI World Dental Press Ltd.
• Future Drugs
• Future Medicine
• Guilford Publications, Inc.
• IAHS Press
• IFIS Publishing
• Intellect Ltd.
• Lawrence Erlbaum Associates, Inc.
• Logos
• Lynne Rienner Publishers
• Mary Ann Liebert, Inc., publishers
• Morgan & Claypool Publishers
• Oldenbourg Wissenschaftsverlag, GmbH
• Oxford Business Group
• PNG Publications
• S. Karger AG
• Salem Press
• Scientific Journal Publishers Ltd.
• SCR Publishing Ltd.
• Sheridan Press
• Thomas Telford Publishing
• Uitgeverij Boom
• Vathek Publishing
• VEETECH Ltd.
• Walter de Gruyter

Not-for-profit / society publishers

• AIS Educator Association
• Aluka
• American Academy of Periodontology
• American Accounting Association
• American Anthropological Association
• American Association of Cereal Chemists
• American Chemical Society
• American Economic Association
• American Marketing Association
• American Phytopathological Society
• American Society for Bone and Mineral Research
• American Statistical Association
• American Veterinary Medical Association
• Annual Reviews
• Association for Childhood Education International
• BioOne
• British Institute of Non-Destructive Testing
• CFA Institute
• Chartered Institute of Building
• Commonwealth Forestry Association
• Countertrade & Offset
• CrossRef
• Institute of Electrical and Electronics Engineers
• Journal of Neurosurgery Publishing Group
• JSTOR
• Modern Language Association
• Pharmacotherapy Publishing Inc.
• Production and Operations Management Society
• TASH

University presses

• American School of Classical Studies in Athens
• Cold Spring Harbor Laboratory Press
• Edinburgh University Press
• Govi Verlag
• Indiana University Press
• Johnson Graduate School, Cornell University
• MIT Press
• Monash University ePress
• University of California Press
• University of Chicago Press

Connotea Blog

If you are interested in press clippings about Connotea you can follow a list of them here.

Connotea Blog

Connotea Blog

If you don’t know what OpenID is then head over to the OpenID page to get an introduction. The short version is that it is a system for managing access to sites through a trusted ID provider.

Why are we doing this? We are hoping that the introduction of OpenID on Connotea will help you guy’s with managing your online personas, and in addition we are talking with some other groups about using it as a way of creating bridges between Connotea and some other services.

If you know what OpenID is already then just have a go and log in at http://www.connotea.org/openid. At the moment we are a relying party. This means that we don’t host or generate OpenID’s but if you have one you can use it to log in to Connotea.

Each Connotea account can have one OpenID associated with it. You can set this in the Advanced settings section of your account, now available in the Toolbox on the right hand side of the page.

If you don’t already have an account, one will be generated automatically for you when you log in with an OpenID.

http://www.connotea.org/blog

Connotea Blog.

A normal API call on a group will look like:
http://www.connotea.org/data/group/Human%20Mitochondrial%20Phylogeny

But if you want to get the tags used by the group directly then you can use the following call:

http://www.connotea.org/data/tags/group/Human%20Mitochondrial%20Phylogeny

Which will also tell you how many times each tag has been used, and by how many people!

Connotea Blog

“Are Connotea accounts ever pruned for inactivity? I tried to register
with the username sciurus but found that it was taken. Visiting
http://www.connotea.org/user/sciurus suggests that this account is
unused and perhaps was intended as a joke (sciurus is the latin for
squirrel).?”

We hadn’t thought about this before, but looking at this library, although it only contains only one bookmarks, and it is about squirrels, it does have tags and in some sense it enriches the doi namespace, so even though this is not an active account it adds in some way to the wharf weave of meta-data surrounding academic content. I guess the implication is that although this person is not making an active contribution, the trail that they have already left has some value as an atom of the whole. It also indicates that pruning accounts can’t just be based on activity or volume, and is probably beyond our curatorial capacity to do.

Connotea blog

Here’s a Zotero thread on the subject of embedded metadata.

link to blog on connotea site
We have created a HTMLMetaTags module and have tested it successfully from these web sites:

oxfordjournals.org
content.nejm.org
content.onlinejacc.org

link to blog on connotea

• display Pubmed results in XML format
• send to tmp.txt file
• execute bibutils tools
  • med2xml.exe tmp.txt > xml.txt
  • xml2ris.exe xml.txt > ris.txt
• import of ris.txt into Connotea

Does anyone have a better way of doing this?
Is this something that people would like to see more support for?

user
bookmark
user_bookmark
user_bookmark_comment
user_bookmark_details
user_bookmark_tag

and the unique key in the bookmark table was the hash of the url. This is where the entire problem with buggotea stems from. All of the functionality of connotea was built on top of this structure. You could say that philosophically the structure was set up for people to share web pages that represented articles rather than articles represented by web pages.

We have changed the tables to the following structure:

user
article
bookmark
user_article (with preferred bookmark and citation pointers)
user_article_comment
user_article_details
user_article_tag

Where the article is an abstract entity more representative of the fact that people want to reference an abstract piece of work that can exist in many different locations. We now normalise bookmark entries via PMID and DOI into a single article object. It seems to be working so far for entries in connotea that have PMID and or DOI information.

This is a first step and for sure there are things that can be improved, support for normalisation based on other meta data, how the information about an article with multiple instances is displayed, concatenation of the best metadata from multiple authoritative sources. Its not rocket science but this is a good step towards making connotea more useful in the academic realm. I won’t be surprised if there are some hiccups at first, so if you spot any odd behavior please let us know.

- You are doing a search in Pubmed and find an article familiar to you. Have you bookmarked this paper before? Currently, the best option is to have a Connotea page open and search for the Pubmed record in your bookmarks (e.g. by using paper’s PMID), or press the ‘add to Connotea’ button to see if you have already bookmarked that paper. Using Pubconn, your bookmarked records in Pubmed are highlighted and the tags and descriptions you have provided for the bookmarked are displayed next to the Pubmed record.

- You are doing a literature review in a collaborative project with several other people, you have created a user group in Connotea and are bookmarking relevant papers in that group. When you start searching, you are interested in knowing whether a particular paper has already been reviewed by one of your teammates. Using Pubconn, all the bookmarks highlighted by your colleagues are highlighted.

- When you are doing a Pubmed search, you are interested to see if other people have bookmarked any of the papers you have in your search results. Currently, you should query Connotea for each and every record returned by Pubmed. Using Pubconn, any of the Pubmed records that have been bookmarked are highlighted within your search results.

It also works offline and online.

This is a Fire fox extension file and you can get the xpi file here.

The basic database unit in connotea is a bookmark and each individual url bookmarked in connotea creates a bookmark. We are going to introduce an abstract article element and join bookmarks with similar pmid or doi to an article entity. This will go someway to cleaning up the connotea database. I’ll post more details later this week.

The description pretty much describes how to use Connotea as well, except of course with Connotea you get extra citation meta-data when you bookmark an academic paper, and you can import and export in many different formats too.

As Mirko points out on his page, waiting for calls from the Connotea API can take a while. The speed issue with Connotea is definitely a concern. There are a few things that cause this problem. The main issue is that we allow privacy and each time someone calls up a page we need to calculate what they can and can’t view. This added to what at the moment is a somewhat naive way of dealing with caching are mainly responsible for our lag times. We do have an extra machine that we can throw at the problem and we are trying to fit it into our server room right now. We may make this just serve API requests, which should help, but in the long term a bit of back-end redesign is going to be required.

Anyway, have a look at Mirko’s page and give him some feedback if you have any. The issue of visualizing complex data sets is going to be a huge challenge for many areas of science. Yesterday we met Tom Carden from Stamen Design for lunch yesterday and the discussion ranged over many of these issues. I don’t know what the solution is going to be, but I do hope that we can create some nice ways of interrogating Connotea that can help in understanding the information that is contained in there.

I should also mention that if you are working on any interesting projects that might benefit from a data set like connotea’s then I am always happy to discuss the project. There are some strict limitations, such as us not giving personal user details or private data, but in principle I am open to discussion.

The format he us using seems to have settled down to the following form:
http://rdf.openmolecules.net/?info:inchi/InChI=1/CH4/h1H

Your account was deleted by us during a crackdown on people using Connotea for marketing and other commercial purposes. Connotea is a service designed for scientists and clinicians to manage their academic references, and while we do not expect every link to be academic, we do take exception to people using Connotea solely to market products or to drive traffic to their own websites. I’m afraid your usage fell into this category, which is why we have deactivated you. I’m sure you will understand that the pollution of Connotea with these commercial links has a significant impact on the other users of the service.

If you would like to use Connotea for academic purposes, then you are, of course, very welcome to open a new account. However, if you wish to use it to drive traffic to other websites, then I’m afraid we can’t help you, and I suggest you look for another social bookmarking website where this kind of use is acceptable. In a nutshell, it is fine if you are using Connotea to organise your own links so that you can find then again. What is not fine is using Connotea so that others can find links.

I hope this is clearer to you now: please let me know if you have any further questions or comments.

Well, now we have taken a different approach. Instead of removing accounts we are just making them invisible, or quarantining them. The person owning the account can still log in, see their bookmarks, and post to the account, but no one else can see them. Their contributions don’t get included in searches or listed in lists by tags. There are a number of reasons for this. It means that if we make a mistake in identifying an account that that is bad, then fixing it is really really easy, we just life the quarantine. Instead of alerting spammers to the fact that they have been nobbled some just continue to post into a location that does not help with increasing google rank or attracting attention to specific sites or products.

We have not documented this feature before but I wanted to mention it here in the context of another topic, terms and conditions. We don’t currently have any for Connotea, but it came up recently when I was contacted by an organization that is interested in investigating using Connotea to help index it’s scientific collection. They need to have a terms and conditions in place, so that they have some degree of confidence in what they are doing with the system. We have always taken an open approach to people’s data, with the API you can extract everything you put into Connotea, but now it is time to formulate a TOC that codifies the feeling that we have been working on up to now. I’ve started looking at some being used by similar sites, and I’ll post a preview here of what I am thinking about soon.

As ever any comments from the community are welcome.

- Ian

While I was away Ben Good posted a paper about his Entity Describer
on Nature Precedings.

You can pop over and have a look at the paper here.

You can download the code from the sourceforge connotea page.

This is a bets release because we have not tested the install on a clean system yet, and when we do we may make a few changes, so you can possibly expect an updated release in two weeks.

What’s changed? I’ve listed info from the release notes below, but one main change is that we have re-arranged things so that the full 1.8 release will be available via a darcs repository into which we envision people can directly submit patches.

And on that note I’m off bouldering in France for a week.

• Web API in regular use.
  • Template Toolkit based templates in regular use.
  • More optimized SQL queries for common requests.
  • Greater use of transactions in MySQL.
  • Greater flexbility for citation source modules.
  • New citation source modules, plus improvements to existing modules.
  • Blog component to create news page from external blog.
  • Wiki component to create custom wiki.
  • Admin component with user search.
  • Integration with Bibutils library for BibTeX and MODS output.
  • Antispam system with captcha and quarantine responses.
  • Click tracker for all posts.
  • Alpha-version proxy module system to handle known proxied post URL’s.
  • Alpha-version stand-alone citation server capability.
  • Additional tools such as command-line post by API, user recovery, and test suite launch.
  • Automated deployment scripts, now supporting Darcs instead of CVS.
  • Updated code to support newer versions of CPAN modules.
  • More test suite scripts.

I talked about conntoea, and I have uploaded the slides to Slideshare

I’m mainly posting here so that there is a link out to these slides from the connotea blog page.

Now Benjamin Good from the
The Wilkinson Lab at the University of British Columbia has released a greasemonkey add on for connotea which allows you to plug in to an ontology that you might which to use for categorizing the references in your library.

He has names is the EntityDescriber
and there is plenty of info on it’s connotea page.

I think this is a major addition to connotea, and I would be glad to hear about people’s experiences with this. I must admit that I’m not working in an ontologically driven field myself, so I’m not using the tool in a formal way, which is why I would really like to hear back from people who do work with ontologies.

The issue of ontologies vs tags is one that is interesting and in my opinion there is great scope for both in a service like connotea.

Thanks Ben.

Ben’s Nature Network Page

Other wrappers are available in the following languages:

www-connotea-perl (Perl)

www-connotea-ruby (Ruby)

PyConnotea (Python)

And just a reminder, the lists are connotea-discuss for general discussion and connotea-code-devel list for discussing the open source code.

‘txt’ provides a unicode formatted list of references with a line separating each entry. ‘plain’ gives the uri for each resource, one per line.

Have a look at these samples:
http://www.connotea.org/txt/tag/immunity
http://www.connotea.org/plain/tag/immunity

You can of course also get the tags of a user, the users of a tag, the simple URL’s of a tag, etc:

http://www.connotea.org/txt/tags/user/IanMulvany

http://www.connotea.org/txt/users/tag/biology

http://www.connotea.org/txt/bookmarks/tag/biology

Enjoy,

We have been in discussion with a Munich based company called Proximic about providing an alternative solution to google. (By way of disclosure MacMillan, the company that owns Nature, is owned in turn by Holtzbrinck, and Holtzbrinck is a shareholder in Proximic).

The Proximic guy’s are good, and I’ve rolled out a demo of their technology on a dev version of connotea. You can have a look at it here.

Next to each bookmark you will see a small “Prox it” link. This is a piece of javascript that when you click on it indexes that link and pulls related content from a number of sources indexed by Proximix. These can include related information, along with related advertisements.

When we roll this out we hope to be able to include chanels with information such as nature news, perhaps links to nature articles, as well as related ad links, that I hope will be of value.

The “Prox it” link text is going to be changed on the live site to give a better indication of what the link provides, and after we roll it out we will start indexing what we hope will be sources of information of interest to you.

I am a firm believer that the value of such efforts will be measured by how much you use a system like this. We are going to roll it out, and over the next few months work on making the content indexed as relevant to you as we can. I think the proof will be in the pudding, and I hope that we can serve up a reasonably sweet dessert.

Let me know what you think!

If you bookmarks an author’s version of the article and you come back to connotea are you more interested in the article itself or do you also expect to be returned to the specific location that you bookmarked that article at?

This is related to how we go about engineering the connotea database to to resolve this issue, at a first pass.

I’d love to hear your thoughts.

After rolling out the new site design last week one of the people here in the office amended the connotea css to give a super-clean feel to the site. If you are browsing on Firefox and you have the mozilla greasemonkey extension then you can have a go with the following script: ConnoteaClean.user.js

It pulls in a modified set of css elements and overwrites some of the default css elements.

Alternatively if you have the Stylish firefox extension you can use that instead. You can find the modified css fragment here.

In the meantime I hope you enjoy the slightly new layout.

If you browse to one of their publications you can see the link for bookmarking the item in connotea, thanks Vittorio!

You can see other user contributed tools for connote a here.

One of the prominent tensions that exists between traditional library methods and the rise of web2.0 technologies seems to be the status of fixed taxonomies vs. emergent folksonomies.

Having finally gotten around to reading this article by Golder and Huberman on the structure of collaborative tagging systems last week while I was on holiday, I was intrigued to see that they have a proof that tag clouds that are used by many people draw down to a semi-stable state according to dynamics that follows the urn model that Eggenberger and Polya developed to describe stochastic disease contamination.

One of the processes that makes this happen is by displaying a list of tags that other people have used for a resource. In this way certain tags become infectious, if you will.

I noticed that Connotea does not at the moment support one of the mechanisms thst lesd to this behaviour, as we only give a list of tags that a person has used, however this should not totally stop the effect from happening in connotea, if we have a population of people who have a shared information background. Still we could do better, and this is one of this areas that we are looking at at the moment.