Finding Pathways, Compounds, Reactions, Genes and Enzymes in PMN databases

There are several different ways to perform searches or browse for information in PlantCyc, AraCyc, and the other species-specific plant metabolic databases hosted by the PMN.

Searching in PMN databases****

To begin a new search in the PMN, there are four main options:

From any page enter a term in the search bar (on the right side of the header) and select one of the databases from drop-down menu to execute a search across all the categories of information within the chosen database.
From any page to get to the Query page with more search options, select from the menu bar:

Databases -> search and then select the database of interest from the drop-down menu

From any detail page enter a term in the “Quick Search” bar at the bottom of the page to execute a search across all the categories of information within your current database.
From the PMN main page to get to the Query page, click the “search” button for one of the individual databases listed in the “Plant Metabolic Pathway Databases” section

The main Query page provides three options for finding data in the database

The “Query” function allows you to search entries by name / term
The “Browse Ontology” function allows to search by class hierarchies
The “Choose from a list” function allows you to search entries displayed in a list

Each of these options gives a drop down menu of sub-categories the user can choose to to further refine the search. For example the Query function has ‘all’, ‘genes’, ‘proteins’, ‘compounds,’ ‘reactions’ and, ‘pathways’ as sub categories.

Using the Query function

Go to the section marked “Query”.
Specify a subset of data using drop down menu selector (e.g. All).
Enter the search term (e.g. sucrose) into the text entry box.
Click the “submit” button.

Note: the following also applies to text entered in the search bar at the top of every page or in the “Quick Search” bar at the bottom of each detail page.
This example search will find ALL objects in the database containing the term ‘sucrose’ as a substring anywhere in the name.

Shorter strings such as ‘suc’ can also be used. Note that the substring search ‘suc’ would also return phrases like the reaction: “isocitrate = glyoxylate + succinate”.
The search is case insensitive.

One or more terms can be used in a single search. If more than one term is included in the search, you must format the query according to the following rules:

A. If the two terms are separated by a comma, the search is treated as a logical OR. That is, a search for “starch”, “biosynthesis” will return results where either “starch” OR “biosynthesis” is included in the name.
B. If no comma is included, then the search is treated as a logical AND. Therefore, the search will return results where both terms (“starch biosynthesis”) are included in the name.

A query executed using the “All” option returns a list of all possible types of items in the database that contain this term in the name.

In the result page the items are grouped by data types (e.g. compounds, reactions, pathways).
Scroll through the results to find the specific item of interest. For example, if you are interested in the sucrose biosynthetic pathway, locate the section labeled “pathways” and click on the name “sucrose biosynthesis”.
Each item listed in the result is linked to a detail page that contains all of the information about the item in the database. Detail pages in a database are inter-linked; therefore it is possible to find detailed information about related data from any detail page. For example, details about genes, proteins, reactions and compounds involved in sucrose biosynthesis can be obtained by following links from the pathway detail page.(See tutorial on Understanding Detail Pages.)

Browsing by ontology

The ontology browser allows you to browse related categories for each data type (Pathways, Compounds, Genes and EC hierarchy(a.k.a. Reactions)). This option is useful if you want to view specific subsets of data, such as only pathways involved in hormone biosynthesis. The representation of data in hierarchies also is useful for describing the relationships among different data types- such as related pathways, compounds, reactions and genes.

Go to the section marked “Browse Ontology”.
Choose a data type (e.g. Pathways) from the drop down menu
Then click on the “submit” button

In the result page, the top level of superclasses within the ontology will be displayed in a hierarchical tree view.

A plus sign next to the superclass indicates that there are ‘children’ terms for that class. The names of classes with children are in bold. The names of instances are not in bold.
To expand a node, click on the plus sign next to the name. Alternatively, to expand all nodes, click on the “Expand All” button above the tree view.
Multiple levels of classes can be found for most of the classes. To see individual instances, continue to expand a node of interest until no more plus (or minus) signs appear.
Expanded classes can be collapsed by clicking on the minus sign next to the name. Alternatively, all expanded classes can be collapsed by clicking on the “Collapse All” button at the top of the hierarchy.

Clicking directly on the name of a class will bring you to a page about that class.

There you will get a list all of the children of the class. Each of these has a number in parentheses next to it which indicates the number of instances contained in that class.
Each “child” class can be expanded from this page by clicking on its name.
Any instances of the class that do not fall into a specific child class will be listed separately under the “instances” heading. The parent class is listed as well.

To view a specific instance in the ontology, click on the item name (e.g. sucrose biosynthesis). This will open a new window showing the detail page. (See tutorial on Understanding Detail Pages.)

Browsing by list

The browse by list option can be used to scan through a list of all entries for a given data type (Pathways, Reactions, Proteins and Genes).

Go to the section marked “Choose from the list of all”.
Select a data type from the drop down list such as “Pathways.”
Click “submit” button.

A list of all the pathways in the database will be displayed in alphabetical order. Browse through the list and click on the name of the pathway to view detailed information about the pathway

****Searching the text of PMN webpages

To search for a term in the text of the PMN webpages, please enter a term in the search bar (on the right side of the header) and choose “Google PMN” from the drop-down menu.
To find a particular term within a page, please use the “Find” option in your browser.

Please contact us if you have any questions or check our FAQs page for answers to common questions.

Searching and Browsing

Finding Pathways, Compounds, Reactions, Genes and Enzymes in PMN databases