As a brief introduction, the three formats we have provided contain semantic web related data, which better enables data organization and easier machine parsing. The three formats include:

• RDFa: The text extract of a page, with semantic web microtags embedded in the XHTML. Use this download if you want the full text of the articles.
• RDF: A pure XML description of relationship triples that can be used to create a searchable database. Use this download if you want to build an semantic database with graph context.
• N3: A simpler format to describe semantic web triples. Use this download if you want the easiest to read version of TOPSAN triples.

Every article on TOPSAN is identified with a unique alias. For example, the record on the PDB protein 2ASH, found at http://topsan.org/Proteins/JCSG/2ash, is identified as TPS1300. The alias ID for topsan records begins with the prefix TPS and is followed by a unique number. You can find this ID in the ‘Alias Ids’ field of the page header. This identifier can be used to download the ‘light’ versions of TOPSAN pages. So for the TPS1300 example, the RDFa record can be found at http://topsan.org/rdfa/TPS1300, while the RDF record can be found at http://topsan.org/rdf/TPS1300.

The bulk download of all RDFa files in a single XML file can be found at http://files.topsan.org/topsan.xml.gz. The full RDF extract of TOPSAN be found at http://files.topsan.org/topsan_rdf.tar.gz.  This tarball contains every TOPSAN page entry as a seperate RDF file, as well as a file called ‘graphMap’ that can be used to map the context of the graphs on a quad store server.

We hope that by providing TOPSAN articles and knowledge in these formats we will enable better collaboration with other protein annotation efforts.

SPARQL

The main reason to embed semantic information into TOPSAN pages is to allow for easy extraction of information from the site.  Every day, all of the embedded semantic information on the site is scrapped and compiled into a single file, which you can find at http://files.topsan.org/topsan.n3.gz This ‘N3′ format file is a collection of all the semantic triples found on the TOPSAN site.  Once you’ve downloaded and unzipped it, it is very easy to import it into a large number of different styles of semantic web ‘triple store’ systems. These systems will have the ability to parse database queries written in the ‘SPARQL’ syntax. One such system is RDFLib, found at http://www.rdflib.net/.  Once you installed this library, you can use it to open and query the topsan.n3 file.

Example 1: Retrieve Molecular weights

PREFIX core:<http://purl.uniprot.org/core/>
SELECT ?pfam ?go WHERE {
?pfam a core:Pfam_Family ;
core:memberOf ?go
}

Example 3: Finding Domains of Unknown Function with PDB structures.

This query finds all of PFAM families that start with ‘DUF’ with PDB structures on TOPSAN that are associated with them. The associations are found with the ‘seeAlso’ type link to a common tag, whose title is filtered with the regular expression “^PF”.

At this point, the query will take several minutes and over a GB of memory. In the next article we’ll demonstrate how to set up a Joseki based server to query Semantic Topsan data.

What is the semantic web:

• Semantic Web
• Semantic Bioinformatics

• Day 1
• Day 2 — Python SPARQL query builder
• Day 3 — Fish, interoperating and data retrieval
• Day 4 — Improved python SPARQL query interface
• Day 5 — the final day

How the data is being stored:

• RDFa Basics

• Rules and Semantic Web

• SPARQL: Some Hands-On examples using Twinkle and Uniprot
• Generating and Querying Semantic Metadata and Ontologies

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”.

Data Mining on TOPSAN

1. Select the pubmed icon in the WYSIWYG tool bar while in edit-mode:

Pubmed Icon

2. A dialog box will appear that allows you to enter a Pubmed Id, ISBN number, or keyword (author, title, etc.). Click on the selected reference to insert it into the text.

Reference Dialog

3. Once you are finished editing the section, save your changes.  The references within the text  will appear in numerical order (i.e [1], [2]), with the full reference in the ‘Reference’ tab at the bottom of the protein page with links to the full article,  Pubmed, and Hubmed:

Reference Tab

4. By clicking on the reference in the text (i.e [1]) or from the ‘Discuss this page’ link in the References tab you will link to an Article page which is automatically generated on TOPSAN. From this article page, users can discuss the article and can view all pages on TOPSAN that also refer to an article.

Article Page

You may also use this feature to easily add your own publications to your User profile page (i.e User:<username>).

Error propagation in the automatic annotation of proteins has been previously described (Valencia 2005). I have notified the PDB of the problem. It will be interesting to see the time it takes to correct the error and whether or not the correction back-propagates.

Ok, so we all have some misgivings about how scientific discourse has been traditionally structured. TOPSAN represents what we hope is a tractable approach to a more modern scientific procedure. Apparently, however, some people are thinking in creative ways that may prove a bit beyond practical. Economist Robin Hanson wrote a paper almost two decades ago outlining how the scientific process could be enhanced by using gambling. The idea is strange, but he argues convincingly that just as in insurance underwriting and market speculating, science could be enhanced by using the same techniques that are essentially used with bookmaking.

The nice thing about this approach is that it is basically a money-where-mouth-is approach which would pretty quickly rule out insincere scientific propositions. He has obviously thought seriously about possible corruption and rightly points out that, “Fortunately nature has no insiders…”

He makes an interesting point that:

“Influence in academia, as measured for example by number of papers published, is far more concentrated than in most walks of life. It seems unlikely that markets would make things worse…”

The author contemplates the difficulty involved in changing the status quo to this kind of approach. In the “Strategy” section the author wonders if some kind of reputation based game could be enough. I think so because it sounds a lot like MarketGuru.com which does exactly this and is quite successful at letting people show off how smart they are (or are not). It would be nice to see some non-traditional scientific reputation system demonstrate that peer reviewed publications aren’t necessarily the last word in scientific efficiency.

Hanson also says:

“We could do much worse than having intellectual institutions as open, flexible, diverse, and egalitarian as the stock market, with incentives as well-grounded and with estimates on important issues as unbiased and predictive.”

To which I say, let’s try to do better than the stock market!

TOPSAN is built on MindTouch’s Deki platform and we are very impressed with it. TOPSAN requires performance, flexibility, nonrestrictive licensing, and customer support, all of which MindTouch does an excellent job of providing.

TOPSAN endorses MindTouch Deki and if you’d like to also, go to the mashable.com voting widget on TOPSAN and cast a vote for them.

“So far WikiCafe is exceeding the company’s expectations. The system is currently logging 14,000 user Edit Actions per day, up from 4000 in September. In my book Metacafe deserves kudos in this respect as well because forming a collaborative community is in many respects far more difficult than delivering the collaborative technology.”

It’s nice that TechCrunch feels the same about this kind of venture as we do at TOPSAN:

“Time will tell whether Metacafe’s gamble on WikiCafe will pay off, but you have to admire the company’s vision and courage. Instead of sitting still it’s pushing the envelope in delivering its audience the most accurate video results.”

More information about TOPSAN’s integration with the StarCAVE is provided in this interview with TOPSAN’s Krishna on the MindTouch blog.