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View Ubiquity command open-doi
//to install this command, visit
//code is part of
name: "open-doi",
takes: {"selected text": noun_arb_text},
preview: function(pblock, directObject){
if (directObject.text){
var m = directObject.text.match(/(doi:)?.*?\b(10\.\d{4}\/\S+)/i);
if (!m){pblock.innerHTML="The selection <pre>"+directObject.text+"</pre> does not include a recognized doi !";}
else {pblock.innerHTML="press Return to go to the document associated with <i>"+m[2]+"</i>.";}
source-data / more-like-this
Created Oct 8, 2008
Ubiquity command more-like-this
View more-like-this
//to subscribe to the command, go to
//code maintained at
author: {name: "thomas lemberger", email: ""},
license: "GPL",
name: "more-like-this",
takes: {"selected text": noun_arb_text},
help: "The command is based on Jane (, Schuemie & Kors (2008) Bioinformatics.24:727). It lists PubMed records related to the selected text (typically an abstract).",
execute: function(directObj) {
var selectedText=directObj.text;
View whatizit
function HTMLescape(string) {
var LT = new RegExp("<", "g");
var GT = new RegExp(">", "g");
var AMP = new RegExp("&", "g");
var TAB = new RegExp("\t", "g");
return string.replace(AMP,"&amp;").replace(LT, "&lt;").replace(GT, "&gt;").replace(TAB, "...");
name: "whatizit",
View rewrap.js
names: ["rewrap"],
arguments: [{role: "object",
nountype: noun_arb_text,
label: "input"}],
help: "removes unnecessary carriage returns and strings of spaces",
execute: function(arguments) {
var selectedText=arguments.text;
selectedText=selectedText.replace(/[\r\n]+/g," ");
source-data / search-pubmed
Created Sep 29, 2008
Ubiquity pubmed search command
View search-pubmed
//to subscribe to the command ,go to: <>
//project: <>
author: {name: "Thomas Lemberger", email: ""},
license: "GPL",
name: "pubmed",
help: "Search selected terms or directly typed in the input line. The number of records to be displayed can be specified by adding '#number' somewhere in the query (eg. #3 will show only 3 records, default is 5, maximum is 15).",
url: "{QUERY}",
icon: "",
description: "Searches <a href=''>PubMed</a>.",
source-data / word-cloud
Created Sep 29, 2008
generates a word cloud on the fly
View word-cloud
*WordCloud methods below are modifications of wordcloud by and
*wordcloud is part of the following project:
*The visapi-gadgets project is licensed under Apache License 2.0 (
*Modifications include:
* inclusion of a some sort of a log scale
* exclusion of single letter words
* exclusion of excludedTerms
* exclusion of numbers
* attempt to merge plural and singular
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