How to Use the portal?
You
can browse the Metabolite data from various Experiments. You can either browse
the whole database or specify the metabolite name or pathway name in the search
box and browse the data for that particular metabolite. This text will describe
how to browse the whole data. You can look for the details for searching for a
metabolite by using the 
button
near the search text box.
Steps:
- Home Page: First open the home page. It looks like this
- Browse Data and Metadata: Click on the “Datasets” in the main menu. (Green colored band at the top of the page). Press “Browse” on the sub menu that pops up.
- You will get to this screen
Experiment names
- Click on any experiment on the left side to see the data from all the platforms for that experiment. You will see something like this.
- Metadata of the Experiment: Experiment metadata can be viewed by clicking at the various buttons at the green menu bar on the right side of the page from step 4. The following screen shots show the results of these actions.
- Browse Data: Click on the Expand Data button in step 4 to browse the data from a platform. The resulting page shows the metabolite concentration data from that platform. The replicate quality can be checked by clicking on the “Scatterplot of replicates” button (Step 7). The details of the metabolites can be seen by clicking at the metabolite name (Step 8). Platform metadata can be seen by clicking the “Platform Metadata” button (Step 9)
- Replicate Quality Check: Clicking at the “Scatterplot of Replicates”
button shows the following screen. Here the scatter plot and the
correlation number give an idea about the reliability of the replicates.
One can download the R scripts that are used to generate these plots from
this page.
- Metabolite Details: By clicking
at the metabolite name at step 6, one can see the details about a
metabolite as shown in the following screen shot. Various external
database links are also assessable from this page. A bar chart showing the
concentration of a metabolite under different conditions is also shown at
this page.
- Platform Metadata: One can see
the platform metadata (Extraction procedure, Chromatography and MS
metadata) by clicking at the “platform Metadata” button at step 6. The
resulting page is shown in the following screen shot. One can click on
various options at the left side to view and download metadata of a
platform.
- Data Visualization: One can use “Tools” button at step 4 to apply data analysis and visualization tools to the data from an experiment. One can also use the “Tools” option from the main menu in step 1 to choose some other experiment to apply the tool. Press the “Draw” button in the following page. This results in a form where one can choose various options. The resulting page is shown in the following screen shot. The Ratio Plot is clickable and the details of a metabolite can be viewed by clicking at a point in the graph or clicking at the metabolite name in the right side of the screen. This will result in a similar page as shown in step 8.
- Search For a metabolite or a pathway: From the home page in Step 1, click on the “Search” menu option to see the following page.
- Down Load Data: From the home page in step 1 or experiment data page from Step 4, click on the “Download” button to download all the metabolite data. The resulting page is as shown below.
