guide

Video Tutorials On Getting Started With Connotea

Connotea
A Beginner's Guide
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Building Your
Library
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Managing Your
Library
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If you're looking for something and you don't find it here, and your question isn't answered in the FAQ, or if you just have some comments you want to share, join the Connotea discussion mailing list.

Features

If you're looking for something and you don't find it here, and your question isn't answered in the FAQ, or if you just have some comments you want to share, join the Connotea discussion mailing list.



Adding Articles and Web Pages to Your Library

There are two ways to add an article to your library: direct from the article using the broswer button, or manually, using the Connotea add form. The browser button method is much easier, and you should only use the manual add form for a special task like saving a DOI.

Adding Articles Using the Browser Button

The easiest way to add an article or web page to your library is to use the Connotea browser button.

You should have created the browser button when you signed up for Connotea. But if not, have a look at Getting Started and follow the instructions there.

Whenever you are viewing an article or web page that you want to save to your library, click the 'Add to Connotea' browser button. Note: Some pop-up blockers may block the new window. You should be able to get around this by holding down the CTRL key as you click.

This will bring up a new browser window with the details of the page that you are saving already filled in. Enter some tags to label the page with. If you like, you can also add a short description or a personal comment at this stage.

Click the Add to my library button, and you're finished.

Adding Articles Using the Add Form

The simplest way to add an article to your Connotea library is by using the broswer button. If you prefer to add something to your library without using the button, you can do so manually using the Add form. This is the same form as above %mdash; simply enter the URL of the article you wish to save, add tags and a description and then click Add to my library to save the article.

Adding Articles Directly Using DOIs

As well as saving the URLs for articles, Connotea can recognise and store Digital Object Identifiers (DOIs), so you can 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.

One application of this is that for many journals you can 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, 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.

The bookmarklets can also be used to save an article directly using its DOI. To save a DOI using the bookmarklet, 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 (see below) — 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.

Automatic Collection of Bibliographic Information

You can save any page on the web to your library, but Connotea will automatically fetch additional bibliographic information for pages saved from the following sources:

In addition, any DOI will be recognised, and Connotea can often automatically discover bibliographic information from sites' RSS feeds.

We are adding more sources all the time, and if you have any specific requests please contact us.

Using Tags

A tag is just a label that you assign to an article in order to help you classify and organise your collection. You must assign at least one tag to everything you post.

Tags can be words or phrases, but if you want to use a phrase you must mark it out using either single or double quotes. This is because the tag box allows you to enter multiple tags — each tag being separated by either a space or a comma. As an illustration, entering "U.S. Constitution", history, 1788 would give you three tags, whereas U.S. Constitution, history, 1788 would give you four tags.

Technically, a tag may contain any Unicode character except a comma, forward slash, plus sign, double quote mark or question mark. Additionally, a single quote mark cannot be the first or last character in a tag.

The Toolbox

The Toolbox provides quick links to various administrative tasks you might want to perform on your library. Read on for instructions on how to do each task.

Changing Tags

You can rename any of your existing tags at any time. For example, if you decide that the articles you tagged as Paranthropus would be better tagged as "Robust Australopithecines", you can do this using the rename tags page, in the toolbox on the right hand side of your library.

You can also change one tag into multiple tags. To do this, enter a list of tags into the 'New Tags' box, making sure that multi-word tags are marked out appropriately. All of your articles that matched the old tag will then have that tag removed and the new ones added.

Deleting and Editing Articles

Once you're logged in, you can delete an article from your library by clicking on the 'delete' link above the article's title.

Similarly, you can edit the title, description, tags and your last comment on an article by clicking on the 'edit' link that you will see above your articles.

Copying into Your Library

Another way of adding to your library is to click on the 'copy' link above articles saved by other people. These links are only visible when you're logged in.

Searching Your Library

You can search your Connotea library using the search bar that runs along the top of every page. You can also search everyone else's libraries, and, in fact, any individual listing on Connotea. This 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.

Using the search box, you can find bookmarks that contain your chosen keywords — it allows you to search either your own library, all public bookmarks, or just the collection you are currently viewing. There are also options for quickly going to tag and user listings, and for searching Connotea via Google.

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.

Enabling OpenURL Links

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 of your OpenURL resolver (or 'link server') in your advanced account settings. 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.

Enabling OpenID Logins

If you have an OpenID, Connotea allows OpenID login instead of traditional login with your username and password. If you do not yet have a Connotea account, simply login with OpenID to make a new account; some details such as your name and email address will be requested from your OpenID provider as part of the process. If you already have an account, login with your username and password as before and then update your advanced settings to show your preferred OpenID, which will enable future logins from the OpenID login page. We only allow one OpenID to be associated to each account.

OpenID is an open, decentralized, free framework for user-centric digital identity. An OpenID is a URL provided to you by an OpenID provider. At this time, Connotea is an OpenID relaying party (accepts OpenID login) but not an OpenID provider. More information about OpenID.

Importing a Batch of References into Your Library

You can add a batch of references or links directly to your Connotea library by uploading a file from your local system in one of the following formats:

  • RIS
  • BibTeX
  • EndNote
  • MODS
  • ISI Web of knowledge
  • Firefox bookmarks

RIS is probably the choice you should go for first — it is a file format used by many desktop reference managers. RIS files contain citation data about articles, including information such as authors, article title, journal name, publication date and volume number. Connotea can read RIS files and automatically add the articles to your personal library and associate the citation data with them. Note, however, that there must be a URL or recognisable identifier in the RIS data for each article before it can be added to Connotea. The same caveat applies to the other formats supported by Connotea.

Batch import is a very quick way of saving large numbers of references to your library, as entire collections of articles (up to a maximum of 1000 per upload) may be added to Connotea in one batch. Citations can be retrieved as RIS, EndNote or BibTeX files from desktop reference management software, scientific literature databases, and many publishers' websites. For example, a journal article may offer its entire reference list for download as an RIS file. Additionally, Connotea already allows you to download any collection of articles as an RIS, BibTeX, EndNote or MODS file (see Exporting Or Subscribing To Any List), allowing you to quickly copy another user's library, or all articles saved under a particular tag.

In addition to the basic citation data for articles, uploaded files may also list keywords or subject terms. If so, you have the option of using these terms as tags for those articles. Since Connotea saves links to online resources, an uploaded record for an article must have the URL of that article present or it cannot be saved to your library. If some of the references within your file have URLs and some do not, you will be informed of this and only those with URLs will be saved to your library.

In order to import a batch of references, you must have an RIS, BibTeX, EndNote, MODS or ISI file file on your local computer. To obtain this, either export a batch of articles from your desktop reference manager (if you're uploading your local collection) or download an appropriate file from the web (if you're importing from an online archive).

Your Firefox bookmarks can also be uploaded in one batch, and in the same way as keywords can be used as tags, you can choose to use your bookmark folder names as tags. In order to import your 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 (see below).

Uploading local files:

To upload a file, a copy of the file must be saved on your local computer. Once you have the file you wish to upload, navigate to the Connotea import form and click 'Browse'. Select your file, choose your tagging options, and then click 'upload'. You can also specify which type of file you are uploading, but Connotea can automatically detect the file type, so you may wish to just keep that as the default.

Tagging articles and links uploaded from your local computer:

When you import a batch of articles or links, you have a number of options for tagging them. Some RIS files contain keywords which have been used by the creator to describe the subject of the articles — you may use these keywords, your own tags, or a combination of the two to tag your articles. Similarly, Firefox bookmarks files contain the names of your bookmark folders, so you can choose to use them as tag names. If the RIS file does not contain any keywords, or you have no Firefox bookmarks folders, you will need to enter your own tags.

To choose your own tags, enter them into the default tags box on the upload page as you would when normally posting an article. Then select one of the four tagging options:

  • Use the keywords given in the file wherever possible, but use the tag or tags specified by you if there are no keywords.
  • Use the keywords given in the file, supplemented with the tag or tags specified by you.
  • Use the keywords given in the file wherever possible, and skip any records that have no keywords.
  • Tag everything with the tag or tags specified by you, and ignore any keywords in the file.

If the keywords contained within a file are separated by commas, they will be considered as separate tags. Keywords and folder names may occasionally be modified to suit Connotea tag standards, and you will be informed of this before the article is saved. All tags can, of course, be changed or deleted after an article has been saved.

Once you've clicked upload, you will be presented with a confirmation page. This page will inform you of which articles will be posted, and what tags will be used for them. You can then confirm the action, cancel, or choose to just import certain records.

Note that difficulties may arise as real-world files can vary from the various specifications, so please contact us if you have any problems so that we can improve our import tools.

Viewing Comments

There is also a comments bookmarklet. This will allow you to read the comments that other Connotea users have made about any page that you're viewing.

  • Connotea Comments
    Save this to your browser, and then when you are reading an article, click on it to see comments that have been made about that article on Connotea.

Adding Comments

You can add extra comments to any of your saved articles at any time, in one of two ways. Either use the form at the bottom of the Connotea comments page, or use the bookmarklet:

which will show you a 'Connotea comments' form from any page on the web. If you haven't already saved the article, you'll be sent to the add form instead.

Creating A Tag Note

In order to make your collection of links more memorable and useful, you can create notes for your tags. A note is simply some 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.

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.

You could also use a note to clarify your use of a tag for visitors to your library. If you wish to point colleagues who are unfamiliar with Connotea to your reference list on a particular topic, you can add a note which briefly explains what this collection of links is. See below for an example of a note attached to a tag.

You can add a note to any tag you have used in Connotea. Each tag can only have one note, but you may edit that note as often as you like. There is no limit on the length of notes, and you can use HTML for simple formatting and for inserting links to other relevant resources.

To add a note to a tag, click on Create a Tag Note in the toolbox on your library page. Enter the name of the tag you would like to add a note to, and the note itself. This note will then be displayed at the top of pages listing the articles and links you've tagged with that particular keyword. If you wish to edit a note later, you can do this either using the same form, or via the edit link that will be displayed immediately below the note in your library. You can delete a note entirely at any time by simply editing the note and deleting all the text.

Navigating

As you're viewing the various articles listed in Connotea, you can click on tag names to see things that other users have saved under that tag. You can explore further by clicking on other usernames to see what other links they've saved and what other tags they use. Hopefully you'll be able to find new or related content this way.

User Groups

Anyone can set up a new user group in Connotea. Once you're logged in, the Create a new group link in your tool box will take you to a form for creating a group and adding users to it. Groups can be either public or private — if private, only the group's members will be aware of its existence. If public, all users and visitors can see the group, and the name of the group's owner is displayed. A group is owned by the user who created it, and only that user can add or remove members.

Groups are a good way of tracking what your colleagues or collaborators are reading, or for co-operating on the creation of reference collections. They are also a useful way of finding new and related articles. Every user's library page has a box at the top of the left-hand column that lists the groups that they either created or are a member of — click on the group name to navigate the list of articles posted by members of that group.

Note that there is no requirement for you to be a member of any group you create, and that currently there is no way of requesting to become a member of an existing group.

Multiple Users and Tags

Clicking around on user and tag names allows you to view the articles for one user or one tag, but you can actually filter for combinations of users and tags by editing the Connotea URL. For example, to see a list of articles for the users fdr and jfk, construct the URL as:

http://www.connotea.org/user/fdr/jfk

This, in fact, filters for fdr OR jfk — to see a list of bookmarks posted by both fdr AND jfk, construct the URL as:

http://www.connotea.org/user/fdr+jfk

So, a plus signs means AND, whereas a forward slash means OR. This works for tag names too, and you can combine user names, tag names, +'s and /'s in any combination. For example:

http://www.connotea.org/user/fdr+hst/jfk+lbj/tag/topsecret/classified

would give you a list of articles tagged as 'topsecret' or 'classified' by both fdr and hst, or by both jfk and lbj.

The search box offers another way of finding articles for multiple tags or multiple users (but not, currently, both). In the search box, you don't need to separate tags that you want to OR with a forward slash (although you can) — a space is enough. You should still use a plus sign to AND tags. For example, entering topsecret classified and selecting 'Find exact tag' would get you a list of bookmarks tagged by anyone as either topsecret or classified, whereas entering fdr+hst jfk+lbj and selecting 'Find exact user' would result in a list of bookmarks posted by both fdr and hst, or by both jfk and lbj.

Active Users and Tags

On the Connotea homepage and the Popular links page, there are lists of active users and tags. These are a list of users who have posted the most articles to their libraries, and the most popular tags used to describe all the articles posted to Connotea. You can use these lists as a starting point to explore the most popular subjects in Connotea, and see changing trends as they emerge.

Exporting Your Library

You can export your references to EndNote and other desktop reference managers by clicking on the 'Export my library' link in the tool box. When you do, you'll be presented with a list of options for downloading your library in different formats. Connotea can export your library in the following formats:

  • RIS
  • BibTeX
  • EndNote
  • MODS
If you're not sure which format to go for, try RIS, since this is most likely to be supported by your desktop software. Once you've chosen your format, click 'Download' and save the file to your local system. You can then import the file using your desktop software.

Exporting Or Subscribing To Any List

At the top of each list of articles in Connotea, you will see a button () that allows you to export that list to your local reference manager. This works in exactly the same way as exporting your personal library.

You will also see a button () that links to an RSS feed.

What is RSS?

RSS feeds are an easy way for users to keep up to date with new content added to websites. An RSS feed is simply a computer readable file which summarises the information published on the site. To more easily monitor updates, enter the address of the appropriate RSS feed into an RSS Reader and the program will regularly check it, immediately alerting you to any new items it finds. This is a more convenient way of staying up to date with the content of a large number of sites than checking each one individually.

How to use RSS

The easiest way to read an RSS file is through a desktop RSS Reader — there are Readers available that are free to download and install. Alternatively, RSS Feeds can be read in the same way through a web-based interface: a list of desktop and web-based readers can be found here.

When your RSS Reader is set up, it will ask you if you wish to add new feeds. New feeds can easily be added at any time. To subscribe to a feed, go to the page you wish to keep up to date with, click the RSS icon on that page, and copy the address (URL) of that RSS feed. Paste this into the appropriate place in your RSS Reader. You are now subscribed to that feed, and the RSS Reader will automatically check each it on a regular basis — commonly once an hour.

RSS in Connotea

Connotea provides RSS feeds for every list of articles (and the news page). These allow you to subscribe to individual user's lists, postings categorised under specific tags, or a combination. For example, if you discover another user who seems to be bookmarking interesting things under the tag readme, you can navigate to the page listing those articles, click the RSS icon at the top of the page, and subscribe to the RSS feed. You will then be notified every time the user adds a new item under the readme tag.

You can access the RSS feed url directly by appending "/rss/" after "http://www.connotea.org", so for instance the RSS feed of the library page of a user 'bob' is "http://www.connotea.org/rss/user/bob". The same trick works for any page that has an rss feed.

Showing Connotea Articles on Other Web Sites

Using our remote JavaScript facilities you can add a widget to your web site that displays the most recent additions to your Connotea library, the last posts under any tag, or other valid Connotea query.

We also offer functions to facilitate "Add to Connotea" links on your web site that open a popup for Connotea users.

Geotagging An Article

Connotea supports 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.

In order to geotag something, you must discover the latitude and longitude of the relevant geographical location. Once you know these, enter geotagged and the appropriate special tags geo:lat=xxx and geo:long=yyy along with the other tags you are using for that article.

For example, if you were geotagging an article about somewhere in London, you might enter geotagged, geo:lat=51.534484, geo:long=-0.121622 into the tags box.

This excellent article discusses geotagging and del.icio.us, including how to find latitude and longitude coordinates, and the information equally applies to Connotea.

Community Pages

The Connotea Community Pages are a section of the site where you can write and edit articles about all aspects of Connotea. Because the Community Pages are a wiki, any Connotea user can start new pages or edit existing ones, so you can talk about anything you like to do with Connotea. You can also create a page about yourself, and there are also special pages for tags and groups. For more information and to read or contribute to the Community Pages, see the Community Pages home.