Documentation


Index

  1. Bioqueries: The objective of our portal
  2. Homepage of Bioqueries portal for registered users
    1. The top-left menu of Bioqueries website: User Login
    2. The central-left menu of Bioqueries website: Main menu
    3. The low-left menu of Bioqueries website: Navigation menu
    4. The low-right menu of Bioqueries website
    5. The high-right menu of Bioqueries website
  3. Homepage of Bioqueries portal for unregistered users


Figure index

  • Figure 1. This image shows the interface of the Bioqueries portal
  • Figure 2. This image shows the interface of the Bioqueries portal
  • Figure 3. The log section presents the username space box and the password space box to fill in by users
  • Figure 4.The request new password allows users to recover the original password previously introduced in the proceeding of registration in the system
  • Figure 5. This page shows all academic information about members our team
  • Figure 6. This image shows three section of Create Query entry section of Add content
  • Figure 7. Create query enter page to enter page. Query to enter SPARQL code, statement, tags, database, revision log languages are shown in the figure
  • Figure 8. Queries explorer shows queries ordered by database, title, ascendant and descendant based on data of entry and number of page per pages
  • Figure 9. Interface to add a comment about a specific query introduced by user. A SPARQL query about a disease, symptoms and category of the disease
  • Figure 10. This interface shows the way to add a new comment in each query accessing at a link from the link in the section about Explore Queries
  • Figure 11. The View section about a simple query. The view section is divided into database, the documentation, the statement, the query box space, tag and an area to introduce opinions of query
  • Figure 12. This image shows the proceeding for editing a specific query
  • Figure 13. All the results are displayed in the web site. In this case all chemicals reactions related to glycolysis pathway
  • Figure 14. This image shows a table of all revisions of the query introduced by users
  • Figure 15.This image shows the unpublish button; an user click on unpublish button, the query is unpublished. When an user click on publish button, the query is published
  • Figure 16.The list of results by using the search engine. User has introduced the term " pathway "
  • Figure 17. Image about advanced research engine
  • Figure 18. A list of recent content introduced in Bioqueries wiki. The list represents the queries and the last updated of the queries
  • Figure 19.Users can access at newest queries and they can view, edit, execute, review and if the query belongs to the group of queries created for themselves, the option publish and unpublish will appear if the query belongs to user
  • Figure 20.Interface image of queries included in the most used query section
  • Figure 21.Image represents the view and execute section in each query introduce in the system


Bioqueries: The objectives of our portal

This portal called Bioqueries is a wiki designed with the objective of registration of biologicals and bioinformatic users to share opinions, publish queries and make use of services provides by this wiki.

This Bioportal uses the technology based on Linked Data. This technology was born in 2007 and it provides a full interconnection between data from different databases in many areas like Life sciences areas. However, this type of technology is far away from biological end-users so this wiki would make closer the relationship between users and Linked data cloud. The URL direction is http://www.bioqueries.uma.es.

This documentation section is divided into two main sections: Bioqueries for registered and unregistered users.


Home page of Bioqueries portal for registered users

The home page of Bioqueries portal is shown in Figure 1. The web interface is divided into four parts: a left part contains three menus, the top-right menu is the user menu to log-in to the system, to access at your account and a log-out option. A central-right menu where user can go at home web site, a documentation link, a link about information of our group and a link to obtain information about the way to make contact with us. The low-right menu called navigation allows users to add content of SPARQL queries, to explore introduced queries to edit or execute, a search option in which user can look up a term and recent content option that allows users to obtain all queries related to this term.

The home page of Bioqueries portal has a central part that provides a short description of the web site about the objectives and information about Linked Data technology. The left menu is composed by two menu: a high-right menu about that refers to new introduced queries by users and a low-right-menu about the most used queries by users.

The top of the Bioqueries web site page provides a search engine to look up information contained in the web site related to term introduced.

This documentation section is divided into five parts based on the usefulness of each menu: the top-left menu, the central-left menu, the low-right menu, the newest introduced queries menu and the most visited queries menu.

Fig.1.This image shows the interface of Bioqueries portal The left side is menu is divided into three menus: a user login menu, a main menu and a navigation menu. The central section is a brief description about the objectives of system. The right side is divided into two menus: new queries menu and the most used queries menu.


The top-left menu of Bioqueries website: User Login

The top-left menu contains My account option and Log out option. My account option is divided into three sections: Create a new account, log in and request new password.The create new account section (see Figure 2) presents several spaces boxes to fill in by users. Newly users have to complete by adding a user name that must be introduced at the home page to access at system Bioqueries wiki, the email address, two boxes to introduce the password and to confirm it and a button to accept these data and to open a new account.

The log section allows users to introduce their username and password so there are two ways for accessing at Bioqueries wiki once that users have registered on system (see Figure 3). One of the ways is by using the register menu of the front page introducing an username and a password or in the log in section inside of the option create a new account of Bioqueries web site.

The request a new password sections allows users to request a new password that it will be sent to email introduced in data of registration of newly users so this way allows to recover the original password (see Figure 4).


Fig.2.The section of creating new account presents some boxes space to fill in by users.


Fig.3.The log section presents the username space box and the password space box to fill in by users.


Fig.4.The request new password allows users to recover the original password previously introduced in the proceeding of registration in the system.


The log out option of top-left registration menu of the Bioqueries portal interfaces allows users to log out of system deleting all data corresponding to them.


The central-left menu of Bioqueries website: Main menu

The main menu is divided in Home section, a link that directs to the home page of Bioqueries portal, a Documentation section in which user can access at this content as a guide to use the Bioqueries portal. An About us section that shows information about our researching group from University of Malaga that have performed this portal (see Figure 5) and a Contact section that allows users to contact our team to solve any problems, share opinions or suggestions about any thematic.

Fig.5.This page shows all academic information about members our team.


The low-left menu of Bioqueries website: Navigation menu

The low-left menu of Bioqueries website is divided into three sections: the Explore queries section, a search section and Recent content section. If a user is a registered user, the navigation menu presents the Add content section. Figure 6 shows three spaces boxes to be filled in by users: The title, the documentation and the SPARQL query space box.

The Add content section for registered users is divided into the follow sections: Create query enter, a page that allows users to entry a SPARQL query and to transform it in natural language query. This page to introduce a query is divided into the follows parts:

  1. A title: a title about the query to introduce. For example: Chemicals reactions, enzyme, name of enzyme, cofactor and Kegg web direction based on a metabolite.
  2. Documentation: Users should document each query, it would help web site to include information that can be reviewed, used and edited by users.
  3. Query area: This area is reserved to introduce the SPARQL code of the query. It must follows the next structure:
    	select ?Label ?Enzyme ?Synonym ?URL ?Cofactor ?Name_Cofactor ?URL_Cofactor
    	where{
    		?s<http://www.w3.org/1999/02/22-rdf-syntax-ns#type><http://bio2rdf.org/ns/kegg#Reaction> .
    		?s<http://www.w3.org/2000/01/rdf-schema#label>?Label .
    		?Label bif:contains "'Metabolite'" .
    		?s<http://bio2rdf.org/ns/kegg#xEnzyme>?Enzyme .
    		?Enzyme<http://bio2rdf.org/ns/bio2rdf#synonym>?Synonym .
    		?Enzyme<http://bio2rdf.org/ns/bio2rdf#url>?URL .
    		?Enzyme<http://bio2rdf.org/ns/kegg#xCofactor>?Cofactor .
    		?Cofactor<http://purl.org/dc/elements/1.1/title>?Name_Cofactor .
    		?Cofactor<http://bio2rdf.org/ns/bio2rdf#url>?URL_Cofactor .
    	}
    	Limit number
    		

  4. Statement: This area is for filling in by users using the natural language of SPARQL queries. It must be written at the follow way:

    Display chemicals reactions, enzymes, cofactors and the Kegg web direction page based on $metabolite$ introduced. Display a limit $number$ of results.

    The variables that are introduced by users must be between symbol of $. In this example exposed, metabolite and number are between dollar symbols. These words must be written at same way than SPARQL code. In this case, a user cannot enter metabolite with capital letters in SPARQL code and in the statement with non-capital letters.

  5. Fig.6.This image shows three section of Create Query entry section of Add content.
  6. Tags: User can enter a tag by each query.
  7. Database: User can enter a database that is used to obtain information of each query.
  8. Revision log language: This area is for users that want to expose their motivation and it can be read by other users.

    Figure 7 shows the query area, the statement area, tag and database, revision log message. At the bottom of the page users can click on save or preview buttons.
Fig.7.Create query enter page to enter page. Query to enter SPARQL code, statement, tags, database, revision log languages are shown in the figure.

The Queries explorer section is shown in Figure 8. Queries can be organised by databases like Kegg, Chebi, GO etc., title by post and updated date, order by ascendant or descendant and the number of queries per page.

The right menu of Queries Explorer section is divided into Categories and Database menus. For example, diseases or chemical compounds categories and OMIM or Chebi databases. You can access to each query of the list to view, edit, execute, review and to publish or unpublish it. This last option is reserved if the query belongs to user (see Figure 9). Users can add a new comment of each query (see Figure 10)

Fig.8.Queries explorer shows queries ordered by database, title, ascendant and descendant based on data of entry and number of page per pages
Fig.9.Interface to add a comment about a specific query introduced by user. A SPARQL query about a disease, symptoms and category of the disease
Fig.10.This interface shows the way to add a new comment in each query accessing at a link from the link in the section about Explore Queries.

As we have previously described, if an user click on a link of a query, some options are shown:

  1. The View section allows users to obtain a view of a query. Figure 11 shows how view section is structured. Figure 11 shows a simple query about chemical reactions related to a pathway introduced by user. Figure 11 shows the database of query, the documentation of the query, the statement, SPARQL query in query area with styles applied to the code, a tag and a section to add a new comment.
  2. Fig.11.The View section about a simple query. The view section is divided into database, the documentation, the statement, the query box space, tag and an area to introduce opinions of query
  3. The Edit section: The edit section is composed by the title in this case use "Chemicals reactions included in a pathway", a documentation area, the query code area, the statement, tags, database and a revision log message. At the bottom of page, we can find save, preview and delete buttons. Figure 12 shows the Edit section.
  4. Fig.12.This image shows the proceeding for editing a specific query
  5. The Execute section: This section presents the statement with spaces boxes to fill in by users. Figure 13 represents the statement: Display chemicals reactions of a pathway whose name includes the term (e g. glycolysis or citrate clycle). Display a maximum of (e g. 20) results per page and the results obtained of executing the query.
  6. Fig.13.All the results are displayed in the web site. In this case all chemicals reactions related to glycolysis pathway
  7. The Revisions section: This section presents all revisions about the query "Biochemicals reactions included in a pathway" that users have previously edited. The table shows the current revision for this query. Figure 14 represents the table of revisions.
  8. Fig.14.This image shows a table of all revisions of the query introduced by users.
  9. Publish and unpublish: A user can publish a query that has been created or edited previously by himself. Figure 15 shows the publish and unpublish option.
  10. Fig.15.This image shows the unpublish button; an user can click on unpublish button and the query will be unpublished. When an user can click on publish button and the query will be published

In the navigation menu, there is an option of searching, this services provides a searching engine to look up all information about an introduced term like "pathway". Figure 16 shows a list of all information based on the pathway term. The list of results includes some queries like "image of a metabolic pathway", "chemicals reaction included in a pathway"etc.

Fig.16.This image shows the unpublish button; an user can click on unpublish button and the query will be unpublished. When an user can click on publish button and the query will be published.

On the other hand, the search engine contains an advanced search option. Figure 17 shows the spaces box for filling in by users: containing any of the words, containing the phrase and containing none of the words. Users can tick the types: Article, Basic Page or Query entry.

Fig.17.Image about advanced research engine

In the navigation menu, there is section called Recent content. Figure 17 shows the subsection all recent content that refers to the query enter, the title, the author of the query, the number of replies of the query and the last updates of these queries.

Fig.18.A list of recent content introduced in Bioqueries wiki. The list represents the queries and the last updated of the queries.

The Recent content section of navigation menu presents a subsection about My recent content. This subsection shows all queries updated by users; as published and unpublished queries. The table shows the author (the user), title, query entry, replies and last updates of the query

At the bottom of left-side of the Bioqueries interface, users can see the number of online users at the moment


The high-right menu of Bioqueries website

The section New Queries allows users to see the newest queries. If an user click on a query of the newest queries introduced, he can view, edit, execute and review the query. If the query belongs to him, he has the option of publish and unpublish. Figure 18 shows the view, edit, execute, revisions and unpublish or publish (if query belongs to user) section of each query.

Fig.19.Users can access at newest queries and they can view, edit, execute, review and if the query belongs to the group of queries created for themselves, the option publish and unpublish will appear if the query belongs to user.


The low-right menu of Bioqueries website

The low-right menu of Bioqueries portal refers to the most used queries of the wiki. When an user click on queries shown in this menu, the interface that the follows:

Fig.20.Interface image of queries included in the most used query section.


Home page of Bioqueries portal for unregistered users

Unregistered users can access to the follows options by using the main menu: the Home, the Documentation, the About us and the Contact options.

Unregistered users can explore queries by using the option Explore queries of Navigation menu. When an unregistered user access at link of the queries of the list and unregistered user can order queries by database, title, ascendant and descendant order and the number pages per page. The user can access at each query organised by categories or databases; user can click on each link (see Figure 21) and access at view and execute section. These options allow users to test the Bioqueries wiki before their registration process.

Fig.21.Image represents view and execute section in each query intruduce in the system.

Unregistered users can access at recent content stored in Bioqueries system. The information that an user can find is the follows: the type of information (query entry), the title, the author, the replies of each query and the last updates.