# About the Animal Metabolite Database (AMDB) <table width="1024"> <tbody> <tr> <td> Table of Contents: <br> <ul> <li>AMDB overview</li> <li>How to use the database</li> <ul> <li>Browsing and searching</li> <li>Generating new Experiments with Cart and Sandbox</li> </ul> <li>How to upload own data and compare it with existing</li> <ul> <li>Create User</li> <li>Upload simplified template-based table</li> <li>Upload extended template-based table</li> </ul> </ul> </td> <td align="right"> <a href="/"> <img src="/media/content_files/1/AMDB_logo_blue_2.png" alt="AMDB logo" width="200px"> </a> </td> </tr> </tbody> </table> --- ## AMDB overview Animal metabolite database (AMDB) is an open database and web-server with built-in statistical analysis tools, which contains information on concentration of metabolites in tissues and fluids of various animal species. Metabolite absolute quantitative content is provided in nanomoles per gram of wet tissue weight (nmol/g). To date, it primarily covers the metabolite content in the eye lens of vertebrates, although a list of species and tissues is constantly growing. A list of investigated species and species loose taxonomy is provided on the [Species](../amdb/taxonomy/tree/) page. A [Sample](../amdb/samples/list/) describes information obtained from a certain tissue of a certain individual animal. Each sample contains data on the metabolite concentrations, the raw data from the instrument (NMR or LC-MS), and the metadata (species, age, weight, location, etc.) describing the sample. Samples that are rather uniform i.e. from one species, one tissue, and one disease/factor are combined into [Groups](../amdb/groups/list/) of samples. Sample groups are further compared in completed [Experiments](../amdb/experiments/list/). [Metabolites](../amdb/metabolites/list/) page contains information about the detected and quantified metabolites in the tissues of species, including those identified de-novo in our laboratory. Metabolites also contain links to other databases (PubChem, HMDB, KEGG, ChEBI) if such entry exist in a database. [Currently](../statistics/), AMDB contains 46 species, 13 tissues, 741 samples, 146 quantified metabolites, and more that 40 000 measured concentration values. --- ## How to use the database ### Browsing and searching ##### [Species](../amdb/taxonomy/tree/) Browse or search for taxa or species of interest on the [Species](../amdb/taxonomy/tree/) page. Search can be done by typing part of its name into the search bar and pressing enter or clicking search button. Clicking on a taxon name (including species) gives the taxon card displaying its description, taxon dependencies, and a list of experiments containing this taxon. Clicking on a species name additionally generates statistical charts, based on the information collected throughout the AMDB. Each species card, in addition to the description of a species, contains statistical charts that are generated from all groups containing this species. Links to experiments with this species are also provided on the card. All the information for a single tissue of the species of interest can be gathered on the [Species comparison](../amdb/taxonomy/compare/) page. Moreover, the metabolite content in a single tissue can be gathered for several species and can be [compared](../amdb/taxonomy/compare/) directly in AMDB based on the information available in the database. ##### [Experiments](../amdb/experiments/list/), [Groups](../amdb/groups/list/), and [Samples](../amdb/samples/list/) [Browse](../amdb/experiments/list/) or [search](../amdb/experiments/search/) over completed experiments available in the database on the Experiments page. A completed experiment usually compares two or more groups of samples in order to determine difference in metabolomes due to difference in some factor (species, disease, ecological factor, etc.). Each experiment card contains description, which groups are compared, which factors are investigated. Below the description statistical charts are provided. These charts are: * *Principal Component Analysis (PCA) 2D score*. Standard overview of the data in metabolomics. Scaling, grouping and excluding samples are available via "Options" button * *PCA 3D score*. Adds third dimension. Same options available. * *PCA 2D loadings*. Scaling and excluding samples are available via "Options" button. * *PIE chart*. Reflects averaged value of most abundant metabolites throughout all samples. Samples can be excluded in "Options". * *Box plot*. Provides box-and-whiskers plot for a metabolite. The metabolite for boxplot, grouping and excluding samples are available via "Options" button. * *Volcano plot*. Allows revealing difference in two groups by combination of Fold change, and the statistical validity of this change. Options allow to change grouping type, select statistical test (Student's *t*-test, Mann-Whitney *U*-test), apply the false discovery rate correction, and adjust the cut-off values. Samples are as well can be excluded from the analysis. * *Metadata analysis*. If samples contain continuous attribute/factor such as animal weight or age, the chart based on these values can be plotted for metabolites. The attribute and the metabolite for chart can be selected with Options. Grouping and excluding samples are also available. Below statistical charts there are four tables (collapsed by default). Clicking the **Concentration table** will expand table that provides average concentrations of metabolites in groups. Values represent average ± standard deviation, in nmoles per gram of wet tissue (nmol/g). **Concentration table** reflects concentration of metabolites in each sample, in nmol per gram of wet tissue (nmol/g). These two tables can be sorted in descending/ascending oder by values in columns (metabolite name, avg. concentration in a group, concentration in a sample). **Metadata** table describes properties each sample - (Group, Species, tissue, gender, origin, sample weight, sampling place, attributes/factors, etc.) Clicking on the property name will display its card. Clicking on the group name or sample name will display its card. **Raw files** table allows select samples raw data for downloading. Experiment details (data and metadata) are also available for downloading with the "Download *.csv file" button. [Browse](/amdb/groups/list/) or [search](../amdb/groups/search/) over groups on the Groups page. Group consist of samples that are rather uniform i.e. from one species, one tissue, and one disease/factor. A Group card as well contains standard description similar to Experiment card- statistical charts, data tables, metadata tables, and raw data. The list of individual [Samples](../amdb/samples/list/) is provided in the sample page. Search over samples can also be done on the [Search samples](/amdb/samples/search/) page. ##### [Metabolites](/amdb/metabolites/list/) [Browse](/amdb/metabolites/list/) or [search](/amdb/metabolites/search/) over metabolites identified and quantified in AMDB. The table can be sorted by name, AMDB ID and external databases IDs. Each metabolite card provides short metabolite description, metabolite parameters, links to external resources, and possibility to search for Samples, Groups, and Experiments containing this metabolite. Alternatively, search for a specific metabolite or for a combination of several metabolites in samples, sample groups, or experiments on a [dedicated page](/amdb/metabolites/searchby/). Nuclear Magnetic Resonance parameters for metabolites (Functional group, Multiplicity, Chemical shift, and Number of protons) are provided on the [NMR metabolite table](/amdb/metabolites/nmr/) page. The table can be sorted by name and NMR chemical shift. ### Generating new Experiments with Cart and Sandbox Groups and completed Experiments can be combined into larger experiments, or into newly generated experiments. There are several ways to do it. Search for a Group of interest and add it to the Cart with the "Add group to comparison" button on the very bottom of Group card. Now the icon in the top-right corner has "(1)" Group in a Cart. Continue searching for Groups of interest and picking up Groups for comparison. The number in the top-right corner will reflect the number of added groups in a Cart. Click the Cart icon, and the list of selected Groups will be shown. Revise the list, remove unnecessary groups, and click "Compare" button. Groups are transferred into the [Sandbox](/amdb/experiments/sandbox/). Alternatively, available groups can be added for comparison directly in the [Sandbox](../amdb/experiments/sandbox/). Search for groups via their names or IDs on the right part of the Sandbox, then grab and move groups of interest to the left part, displaying the list of selected groups. Click "Generate" button, this procedure will generate new experiment that collects all the information about selected groups with a standard experiment description - statistical charts, data tables, metadata tables, and raw data. Generated experiment and corresponding raw data can be downloaded. All groups from completed Experiments can be added to card simply by clicking "Add experiment to comparison" button on the bottom of the experiment Card. Similarly, [Species comparison](../amdb/taxonomy/compare/) page gathers all the information for a single tissue in one or several species of interest, and generates new experiment. --- ## How to upload own data and compare it with existing #### Create User AMDB allows registered users to upload own quantitative metabolomic data and compare it with existing in AMDB data. To do this, first create a User by clicking the "Sign up" right button in the AMDB top menu. Enter e-mail address, desired username, password and repeat password, press "Sign up". Once registered, log in using username and password. If you forget the password, use the [Forgot password?](/accounts/password/reset/) link in the [Login](/accounts/login/) page. Tick the checkbox "Remember me" if you want to log in automatically. For registered users [Data manager](/amdb/profile/manager/) page will appear. Here User can [create own](/amdb/profile/manager/#ownExperiments) experiment automatically by uploading *.csv file (from template) or create empty experiment to enter values manually. #### Upload simplified template-based table To quickly compare own data with existing in AMDB data, the User can perform the following simplified procedure: Download simplified [template for experiment](/amdb/experiments/template/) from the Data manager page. This Excel template contains only required fields that need to be filled (Groups, Samples, Metabolites). Follow the instructions in the template. Cells with a red upper-right corner contain tooltips that pop up upon pointing over them. Fill the experiment name in the first row (in B1 cell), the name should not match with existing ones in AMDB. Fill the text of experiment description in the second row (in B2 cell). Populate the Groups row, number of cells should match the number of samples. Fill the text description of groups in 5,6 rows if experiment contains two groups. Add 7, 8, etc. rows, if experiment contains more than two groups. Fill the Sample names in corresponding row. Fill rows with metabolite names and their corresponding concentration in samples (in nmol/g) under "Metabolites" row. Empty and N/A values indicate difficulties in quantitation (overlapping peaks, etc.). Zero values indicate that the value is below LOQ (or LOD) of the instrument. Metabolite names are provided in the second Excel sheet. Save table as *.csv or *.xslx. Navigate to [Data manager → Experiments → Create experiment → Create from *.csv file](/amdb/experiments/import/), select filled template file and click "Proceed" button. The next step is template validation, including validation of metabolite names. Check that the names of the metabolites match correctly with existing in AMDB, correct if needed, and press "Confirm". Several warnings will be displayed "species is not specified, tissue is not specified", as the template used is the simplified one. The standard experiment card (description, statistics, tables) will be shown below warning messages. The created experiment is private, i.e. visible only for user, and can be found in the [Data manager](/amdb/profile/manager/#ownExperiments) page. User can view or delete the created experiment, if something is incorrect. Now the Groups created by User is available for comparison with existing in AMDB Groups, although the created experiment will not be available publicly (will not be shown in the [Experiments](/amdb/experiments/list/) list). If everything correct, User can publish the experiment in AMDB by sending it on validation on the [Data manager](/amdb/profile/manager/#ownExperiments) page. This will also create discussion, where User can describe additional information for the experiment and discuss it in chat; the chat is visible only for AMDB staff. Once the submitted experiment has been validated, it will appear in the database publicly. #### Upload extended template-based table Extended template allows to design a more appropriate structure for the submitted Experiment to conform the AMDB. Download [extended template for experiment](/amdb/experiments/template/?extended) from the Data manager page. This Excel template contains additional fields that User can fill, besides the required ones (Groups, Samples, Metabolites). The second Excel sheet of the template contains database entries that can be selected to describe the metadata (species, tissue, diseases, gender, origin, additional factors/attributes). If metadata entry (eg. Species or metabolite) is absent in the AMDB, [contact us](/contact/) first. Our team will add the information to the database. Follow the instructions in the template. Additionally to the simplified procedure, fill the metadata for samples (species, tissue, diseases, gender, origin, additional factors/attributes). Most metadata fields are selected from the drop-down lists (species, tissue, etc.) indicated with red upper-right corner of a cell. Values of neighboring cells in a row can be filled in a usual way, by pointing over a cell and dragging the fill handle. Leave blank cells if no information available or not applicable. Navigate to [Data manager → Experiments → Create experiment → Create from *.csv file](/amdb/experiments/import/), select filled extended template file and click "Proceed" button. ---