IRbase Tutorial

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A tutorial on the use of the insecticide resistance database interface for end users

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IRbase Tutorial

  1. 1. IRbase Tutorial Introduction IRbase aims to become a global repository for insecticide resistance data. It is a relational database based on the Mosquito Insecticide Resistance Ontology (MIRO) and it is accessible though the Internet at http://anobase.vectorbase.org/ir. Most browsers (Firefox, Safari, Opera, Internet Explorer) will work but please note that Mozilla Firefox is the only heavily tested. All work needed to develop and maintain IRbase was done using free and open source software (FOSS) and was funded by a NIH grant to VectorBase. Data can be submitted to IRbase on-line by using a web interface or off-line by filling in a spreadsheet. Users may use the website to search and retrieve data using a single or a combination of search criteria (ontology terms & dates) can be used. Matching results can be displayed on screen, exported to a tab separated file for further analysis, or visualized using color coded Google maps. Entering data is a restricted process. Users wanting to do so should contact VectorBase in order to obtain a user name and password. The address of the web interface for entering data is http://anobase.vectorbase.org/ir/login.php. For more inforation and help please send an email to help@vectorbase.org. Searching and Viewing Data On the main page of IRbase users can find the search form as well as links to browse the data. Screen shot 1. The main page of IRbase.
  2. 2. Searching and Viewing Data (cont.) There are two ways for entering the search parameters into the form. The first one is to use the drop down menus and find the requested term by following the correct path. This method implies that the user is familiar with MIRO, or has a good knowledge for some of the properties of the requested term. For example, to find the insecticide “deltamethrin” the user must know that this insecticide belongs to the pyrethroid family and that this family of insecticides modulates sodium channels. Screen shot 2. Specifying search criteria using drop down menus. Depending on the quality and speed of your network connection the response time of the drop down menus may vary. In order to decrease the amount of data downloaded when the page is first viewed only the top ontology terms are loaded. As the user clicks on the menu the relative set of data is fetched from the server.
  3. 3. Searching and Viewing Data (cont.) Alternatively, auto-complete input boxes can be used. In these boxes the user needs to type in two letters from the requested term and a list of all possible matching terms will appear. As more letters are typed the search is narrowed down the number of options in the list decreases. When the requested term appears on the list click on it and the term will now appear in the input. All terms are listed alphabetically. The drop down menu and the input box cannot be used in conjunction. If both elements are populated then an error message will appear. Screen shot 3. Specifying search criteria using drop down menus. After filling the desired search criteria, click on the “Search” button at the bottom right end of the form. Shortly thereafter a new page will appear on your browser with all matching results – if any. This table contains the very basic information about an insecticide resistance assay. These include collection site, insecticide, species, year, and resistance mechanism. To view all the available data for a particular assay click on the “View report” icon of the respective row and a page similar to the one below will appear on your screen.
  4. 4. Searching and Viewing Data (cont.) Screen shot 4. Search results. Screen shot 5. Viewing method details and results of an assay.
  5. 5. Searching and Viewing Data (cont.) If you wish to view more date on the insect sample that was used to run this assay then click on the number next to “Collection ID” and the following page will come up. Screen shot 6. Insect collection details and assays performed using this collection. On the top portion of this page you may view all the details available regarding the particular insect collection such as the collection site, species, collection date, etc. Listed at the bottom of the page are all the assays that were performed using this particular collection. More information about the people behind the study and where it is archived can be seen by clicking on the number next to “Study ID”.
  6. 6. Searching and Viewing Data (cont.) Screen shot 7. Viewing author/data owner and archive information. Mapping Data Along providing the user a text based interface to view data, IRbase also provides a map based interface to access the same data. This interface utilizes Google Maps to visualize the data and is very rich in features such as grouping by color, zooming in and out, adding layers of related data, etc. By clicking at the collection sites marked on the map users can access all the relevant insecticide resistance data. It should be noted though that not all the data currently in the database appear on the map since the submitters did not provide the precise location or coordinates of the collection site. When the page is first loaded a world map with all the collection sites spotted with small markers will appear (Screen shot 8). After leaving the mouse pointer on one of these markers one line of text will appear displaying some of the information regarding the particular collection site such as species name, collection dates and insecticide used. By clicking on the marker a pop up balloon will appear with the same data but also with a link to a detailed report. To zoom in or out use the “plus” and “minus” button respectively, or click and drag the lever
  7. 7. Mapping Data (cont.) between the two. Double left click on the map will simultaneously center the map and zoom in at the position clicked. A double click on the right mouse button will center the map and zoom out at the position clicked. To move the map you may click and drag at any point on the map or use the arrows on the top left corner. Screen shot 10. A world map with the locations of all the collection sites currently in the database. Screen shot 11. Brief information displayed after leaving the mouse pointer on a marker.
  8. 8. Mapping Data (cont). Screen shot 12. Pop up display of brief information and a link to a full report.

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