YOKOFAKUN: wikipedia

In "Building a biomedical semantic network in Wikipedia with Semantic Wiki Links" (Database . 2012 Mar 20;2012) Benjamin Good & al. introduced the Semantic Wiki Link (SWL):

An SWL is a hyperlink on Wikipedia that allows the editor to explicitly specify the type of relationship between the concept described on the page being edited and the concept that is being linked to (http://en.wikipedia.org/wiki/Template:SWL). These SWLs are implemented using MediaWiki templates.
(...)
any programmer can now write computer programs to parse Wikipedia content for SWLs and import them into third-party tools (e.g. triplestores, etc.)

Example: Phospholamban:

The protein encoded by this gene is found as a pentamer and is a major substrate for the cAMP-dependent protein kinase ({{SWL|type=substrate_for|target=protein kinase A|label=PKA}}) in cardiac muscle.

Using Entrez-Ajax (Loman & al.) and the Wikipedia API, I wrote a HTML+JS interface to accelerate the creation of a semantic SWL wiki-text from a PUBMED-id:

http://lindenb.github.io/pages/pubmedwp/index.html

and.. well, that's it,

Pierre

I wrote a tool that use the opensearch API for mediawiki to display the results of a query in wikipedia:

$ opensearch Charles Darw
Charles_Darwin   Charles Robert Darwin FRS (12 February 1809 – 19 April 1882) was an English...
Charles_Darwin_University   Charles Darwin University (CDU) is an Australian public university wi...
Charles_Darwin%27s_health   For much of his adult life, Charles Darwin's health was repeatedly co...
Charles_Darwin_Foundation   The Charles Darwin Foundation was founded in 1959, under the auspices...
Charles_Darwin_National_Park   Charles Darwin National Park is in the Northern Territory of Austr...
Charles_Darwin_Research_Station   The Charles Darwin Research Station (CDRS) is a biological rese...
Charles_Darwin%27s_education   Charles Darwin's education gave him a foundation in the doctrine o...
Charles_Darwin_%281758%E2%80%931778%29   Charles Darwin (3 September 1758–15 May 1778) was the ...
Charles_Darwin%27s_religious_views   Charles Darwin's views on religion have been the subject of ...
Charles_Darwin_and_the_Tree_of_Life   Charles Darwin and the Tree of Life is a 2009 television do...
Charles_Darwin_School   Charles Darwin School is the only secondary school in the Biggin Hill area. 
Charles_Darwin_%28aviator%29   Major Charles John Wharton Darwin was a First World War flying ace...
Charles_Darwin_Reserve   Charles Darwin Reserve is a 686 km2 nature reserve in Western Australia.
Charles_Darwin_bibliography   This is a partial list of the writings of Charles Darwin, including...
Darwin   Darwin may refer to:

This tool is available on github at:

https://github.com/lindenb/ccsandbox/blob/master/src/opensearch.cpp

Bash completion

Now I want to use this tool for bash completion. Say, I wrote a tool named 'foo' that expects the title of a wikipedia article as an argument. In ~/.bash_completion.d/, I wrote a file named opensearch:

_opensearch()

    	{

        local cur choice reply

        COMPREPLY=()

        cur="${COMP_WORDS[COMP_CWORD]}"

        choice=$(opensearch -d -c ${cur})

        reply=$(compgen -W "${choice}" -- ${cur})

        COMPREPLY=( $reply )

        return 0

    	} &&



complete -F _opensearch foo

This script is activated when a new terminal is loaded in ${HOME}/.bashrc:

(...)
if [ -f ${HOME}/.bash_completion.d/opensearch ]; then
    . ${HOME}/.bash_completion.d/opensearch
fi

Now, typing 'foo', a keyword and <TAB> activates this new completion:

$ foo Charles_D <TAB> <TAB>

Charles_Dance              Charles_Darwin_University  Charles_Doolittle_Walcott  Charles_Dutoit
Charles_Darwin             Charles_Dickens            Charles_Durning
$ foo Charles_D

That's it,

Pierre