Help / Tutorial

Link Classification

Each link on the Links Directory is classified into three different types: resources, databases and tools.

Resource
A static resource that conveys bioinformatic information
Database
A collection of biological data than can be queried.
Tool
A bioinformatic webserver or downloadable software that can query, analyze, extract, and/or modify input data

In addition to link type, each link is placed into a category, and within each category, links are further sorted into subcategories.

Searching for Links

To search for links on the Links Directory, enter the desired key words into the search box found on any page.

As noted in the green guide box that appears when a search is conducted, the search terms can be customized to yield more specific results. When regular search terms are entered (without quotations), the search will look for any entry that contains any of the keyword terms within the title, description or tag fields, disregarding the order of the phrase.

When a query or parts of the query are enclosed in quotes, exact matches to the quoted terms are returned.

Narrowing Down Search Results

Once a search is entered into the Links Directory, links matching the search query are returned.

The results page will display:

  • Category matches
  • Search options to refine results
  • Number of links containing requested keywords
  • Link matches

Category Matches

The keywords entered in a search are searched for within the category and subcategory titles. Category Matches returns those category and subcategory fields which contain the keywords, where keywords are highlighted in yellow.

Search Options

The search options allow a user to restrict the link type and number of search results to display on each page. For example, if only “Resources” is checked off, then only the links that are classified as a resource will be returned. Excluded link types may be added back to the search result through the Search Options.

Note: Search results do not include keywords found within the category or subcategory titles.

Displaying Search Results

The default view of search results displays the links one by one with full details of each link. The details include the type, URL, categories of a link, description and options to download a link in XML or JSON format.

In order to view more links at once, “compact view” can be selected from the header. The compact view displays only the link titles, types and URLs in a table.

Additionally, the results can be retrieved as a list in XML or JSON format.

Link Sets

A set of links is a group of links from a specific institution, organization or geographical location. Sets can help find links from a particular institution rather than searching by content similarity. Sets can be accessed via "Sets" on the right hand sidebar. Additionally, sets can be accessed via a single link belonging to a set.

Related Links

Each link entry has several related links associated with it. These links are identified as "Related Links" and they are populated from links provided by the "Related Citations" feature on PubMed based on the publications(s) associated with a link.

Related links for a specific link can be accessed via a link page. In order to access these related links, click the “Related Links” tab located in the header. The related links can be displayed in compact view or by RSS feed, XML and JSON formats.

Links Directory Index

To help determine the strength and popularity of a tool, the Links Directory Index is introduced. The Links Directory Index is a sum of the citations from other papers provided by the Google Scholar Citation Count (if available). The Google Scholar Citation Count is populated from Google Scholar which provides the number of times a publication has been cited by other publications. For links with more than one citation provided, the citation count is shown per PMID and cumulatively. Clicking on the Links Directory Index will display a table showing a breakdown of each publication related to a link and its Google Scholar Citation Count.

Links that have a publication but no citations according to Google Scholar will have a Links Directory Index of 0. Links that have no publication will have a Links Directory Index that is N/A.

Social Media Integration

Links on the Links Directory can be shared via Google Plus and Twitter. In order to access these, click on the "Share This Link" button located beside a link. Beside the Google Plus and Twitter buttons are bubbles with the counts of the number of times that a link has been shared on each social network.

Google Plus
Clicking on the Google Plus button will allow the link to be shared on Google Plus. A comment can be added with the share and the circle to share with can be selected.
Twitter
Clicking on the Twitter button will open a new window that allows the link to be shared on Twitter. The link title is provided with a reference to the Bioinformatics Links Directory twitter account: @biolinksdir.