Part 1: Using Semantic Notation on TOPSAN

Introduction to TOPSAN Protein Syntax

All calls embedded in the text of TOPSAN documents begin and end with the double brackets

{{

and

}}

. You then make a call to ‘note.link’. There are two ways to call the function, via sequential argument or by named arguments. For sequential arguments, wrap the arguments with ‘(‘ and ‘)’, and type in the values. This is usually only used for the two argument call, when passing the predicate and the object values. Alternatively, if you want to manipulate additional arguments the named argument format is preferred. In this method, the arguments are wrapped with ‘{‘ and ‘}’, and the name of each of argument is given followed by a ‘:’ and then the value. When using the named argument format you don’t have to remember a specific order of arguments.

note.link Arguments:

• rel : Type of relationship
• value : The database to link to, if it is not an identifiable link it is assigned as a literal value
• visible : If false the call does not produce text that is visible on the page
• about : Defaults to the current page
• rev: If the relationship is reversed, so that the destination is the subject and the current page is the object.

Relationships can go in both directions. By default the subject is the current page and the passed value is the object. To reverse this relationship, so that the relationship statement is about the external database pointing to the current page, set ‘rev:true’.

Examples:

Embed a link to PFAM:

{{ note.link( ‘memberOf’, ‘PFAM:PF07980′ ) }}

{{ note.link( ‘citation’, ‘PMID:19191477′ ) }}

Reverse a relationship:

{{ note.link{ rel:’similar’, value:’UNIPROT:Q8A1G2′, rev:true } }}

{{ note.link{ about:’TOPSAN:2aam’, rel:’similar’, value:’UNIPROT:Q8A1G2′ } }}

Predicates

Available Databases

When describing a link to another database, you can use prefix codes that will recognized by TOPSAN and translated accordingly. We have a set of 10 linked databases currently, but this will grow as needed. To use the prefix code, simply name the database by code, followed by a colon and the database identified from the database, ie “PFAM:PF0798″, “UNIPROT:Q8A1G2″, or “PDB:1AAC”.