Indexing and Searching NCBI Genes with Apache Lucene

2009-07-17T21:03:00.005+02:00

In this post I'll show how Apache Lucene can be grammatically used to index the content of a set of NCBI Genes entries and how to query and retrieve those data.(via wikipedia:)Apache Lucene is a free/open source information retrieval java library, It is supported by the Apache Software Foundation. While suitable for any application which requires full text indexing and searching capability,

XSLT+XSL-FO + FOP = PDF

2009-07-01T21:59:00.003+02:00

In a recent short discussion on FriendFeed, Benjamin Good asked me what are the reporting tool I've used. On my potential list there was:Jasper ReportsApache PDFBoxthe recent Eclipse BRIT.But the only tool have used so far to produce a PDF document is a XSL-FO document converted with Apache FOP. XSL-FO is an XML vocabulary for specifying formatting semantics and FOP is a print formatter driven

Back to basics: Postscript

2009-06-23T20:57:00.003+02:00

(Wikipedia): The Postscript language is a vectorial drawing format used to describe a page. It is an interpreted, stack-based language. The language syntax uses reverse Polish notation, which makes the order of operations unambiguous, but reading a program requires some practice, because one has to keep the layout of the stack in mind.For example, the following postscript program draws a line

Event-driven XML parsing (SAX) with Java+JavaScript

2009-06-22T21:19:00.004+02:00

I just wrote SAXScript, an event-driven SAX parser java program invoking some javascript callbacks. It can be used to quickly write a piece of code to parse a huge XML file.DownloadDownload saxscript.jar from http://code.google.com/p/lindenb/downloads/listInvokejava -jar saxscript.jar (options) [file|url]sOptions-h (help) this screen-f read javascript script from file-e 'script' read javascript

RDF storage with a Key/Value Engine

2009-06-12T23:15:00.000+02:00

Just curious, can I store some RDF statements in a Key/Value engine like BerkeleyDB (java Edition) ?Yes, it's like re-inventing the wheel but, again, I like re-inventing the wheel :-)A berkeleyDB Database contains a set of Key/Value. e.g.KeyValueSecurityNumber:9877FirstName:John LastName:DoeSecurityNumber:9899FirstName:Peter LastName:ParkerSecurityNumber:9988FirstName:Edith LastName:ParkerData

RDF : javascript, xsl stylesheets

2009-06-12T20:24:00.004+02:00

A few notes:I've implemented a javascript library to parse RDF (I love re-inventing the wheel, it's always interesting to learn how softwares and algorithms are working ). A demo was uploaded here (XUL/Firefox). The RDF syntax is still not fully implemented (e.g. it don't support xml:lang, parseType=Literal, etc...).I've also created 3 XSLT stylesheets transforming RDF to ....N3:xsltproc rdf2n3.

A RDF Editor for Media wiki (draft)

2009-06-11T23:25:00.004+02:00

(This page was copied from the article I started on mediawiki.org)I've created an applet that can be used as a RDF editor for mediawiki, the wiki engine for Wikipedia. (This is mainly a proof-of-concept, I don't know if I'm going to use this system myself) The XML/RDF syntax of the document is checked and it is validated against a ~RDFS schema. This method was inspired from the one described in

Learning OWL: a simple Ontology for contributions

2009-06-11T20:35:00.005+02:00

This post is a simple reminder for creating a simple OWL ontology, I know RDFS (RDF schema) but I'm not at all an expert with the OWL language, so feel free to make any comment about the following ontology.OK...at the beginning there is an empty RDF document:]>

Exploring JavaFX: creating charts for pubmed

2009-06-09T20:41:00.005+02:00

The JavaFX SDK, a scripting language for Java, is now available for Linux. The API is said to be a new and simplier way to write a graphical interface and it have some nice data bindings to create an immediate and direct relationship between two variables. But it comes after Flash, Air, SVG , Processing, so isn't it already too late for this new language ?However, JavaFX contains a chart API and

Fun with SVG: NCBI/pubchem+XSLT= SVG

2009-06-04T21:31:00.002+02:00

Just for fun. I've played with the compounds stored in NCBI/Pubchem and I've created a XSLT stylesheet transforming the pubchem/xml format into a SVG figure.The XSLT stylesheet is available here:http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/pubchem2svg.xsl This xml format was new to me, so feel free to tell me if I've missed something...Here are two examples: AspirinChol-SdC10The

XML Pipelines/ XProc for bioinformatics: my notebook

2009-05-21T23:06:00.002+02:00

In this post I describe how I used XProc, the XML "pipeline language" to create a workflow of XML data calling the NCBI for some SNP and building a HTML table describing those markers.W3C:XProc: (the) XML Pipeline Language, (is) a language for describing operations to be performed on XML documents.An XML Pipeline specifies a sequence of operations to be performed on zero or more XML documents.

XForms for Bioinformatics : my notebook.

2009-05-20T21:52:00.004+02:00

Here, I describe my experience with XFORMS:(W3C) XForms is an XML application that represents the next generation of forms for the Web. By splitting traditional XHTML forms into three parts—XForms model, instance data, and user interface, it separates presentation from content, allows reuse, gives strong typing—reducing the number of round-trips to the server, as well as offering device

Rare Disease: How-to ?

2009-05-18T20:29:00.005+02:00

I had a conversation with a colleague about how to study a gene involved in a rare human lethal disease. A set of mutations in this gene favors the apparition of the symptoms and only a tiny number of samples is available . How can we learn more about this gene ? I've just got a one or two ideas (hey ! I've not been working at the bench for 10 years :-)...)using the product of this gene as a

WebServices/JAXWS for SNP, Glassfish, Taverna: my notebook

2009-05-14T23:41:00.004+02:00

In this post I describe how to deploy a WebService in the GlassFish web server and to to use it via the Taverna workflow engine.Server sideClassesThe JAX-WS API (the java API for Web Services) was used here. Our Web Service will be designed to find the position of the SNP from his namefind the SNPs in a given regionFirst of all, a simple POJO (Plain Old Java Object) for a SNP (name, chromosome,

Beautiful Data : The Stories Behind Elegant Data Solutions

2009-05-01T23:45:00.005+02:00

My contribution to this book was minor, so I really want to thank Jean Claude Bradley, Rajarshi Guha, Andrew Lang, Cameron Neylon, Antony Williams and Egon Willighagen for keeping my name in the list of authors. They wrote a great chapter for this book.Pierre

CouchDB for Bioinformatics: Storing SNPs - My Notebook

2009-04-29T21:19:00.003+02:00

In a previous post, I've been playing with Apache Hadoop.I've encountered some technical difficulties with Hadoop (such as the simple question: "How should can I read my data from a file stored on the Hadoop File System (HDFS) ?? ") , so I now have a look at Apache CouchDB(Via http://couchdb.apache.org/:) Apache CouchDB is aA document database server, accessible via a RESTful JSON APIAd-hoc and

A Tag Cloud for my Resume.

2009-04-23T21:57:00.002+02:00

I'm revising my CV as I'll move to Nantes and I wanted to create a Tag Cloud to illustrate my resume. Paul and Richard suggested to use wordle to generate the cloud but I wanted to generate it on the fly, for any language, whenever I want, etc...so I stored my skills in a RDF file which looks like this:

Hadoop, my notebook: HDFS

2009-04-21T22:24:00.002+02:00

This post is about the Apache Hadoop, an open-source algorithm implementing the MapReduce algorithm. This first notebook focuses on HDFS, the Hadoop file system, and follows the great Yahoo! Hadoop Tutorial Home. Forget the clusters, I'm running this hadoop engine on my one and only laptop.Downloading & Installing~/tmp/HADOOP> wget "http://apache.multidist.com/hadoop/core/hadoop-0.19.1/hadoop-

Resolving LSID: my notebook

2009-04-10T19:09:00.004+02:00

This post is about LSID (The Life Science Identifier) and was inspired by the recent activity of Roderic Page on Twitter and by Roderic's paper "LSID Tester, a tool for testing Life Science Identifier resolution services".OK.At the beginning, there is a LSIDurn:lsid:ubio.org:namebank:11815ubio.org is the authority.It is followed by a database and an id.We need to resolve this authority to find

XML to DOM using XSLT

2009-04-10T18:45:00.003+02:00

A short post. I was fed up with writing javascript/java code for creating dynamic web interfaces ( You know all those document.createElementNS, document.createTextNode node.appendChild etc... statements for building the DOM), so I wrote a XSL stylesheet taking as input a XML file and echoing the code that should be used to build the document. The stylesheet is available at:http://code.google.com/

Go West !

2009-04-06T21:33:00.003+02:00

After one year at the Center for the Study of Human Polymorphisms I will follow my wife in Nantes (France) on September 1st 2009. Hum... that is not the right period to find a new occupation, so I hope I'll find a new job there (related to science or to the semantic web). Wanna hire me? Here is my profile on LinkedIn.Nantes Image via wikipedia.

Consequences : SNP, cDNA, proteins, etc....

2009-04-03T21:41:00.003+02:00

This post is about Consequences, a tool finding the consequences of a set of mutations mapped on the human genome. It was motivated by a recent post of FriendFeed, Daniel MacArthur asked:“Given a list of human b36 coordinates for a list of genic SNPs (most not in dbSNP), what would be the quickest way to get a list of the genes they're found in and, if possible, the amino acid position they would

A few nightmares before biohackathon 2009.

2009-03-12T22:36:00.002+01:00

OK, after Scifoo 2007 (http://plindenbaum.blogspot.com/2007/07/scifoo-07-anxiety-from-homebody.html). Here are my apprehensions for BioHackathon 2009, you know, I'm lost and anxious when I cannot see the Peripherique ;-)

My notebook for a Stupid RDF Server

2009-03-12T21:33:00.006+01:00

In this post, I'm writing my notes about the java package com.sun.net.httpserver.*. This package contains a lightweight HTTP server and I've tested it to create a simple-and-stupid RDF server.The source code is available at:StupidRDFServer.javaOK. First we need a 'Statement' class holding a RDF triple:private static class Statement { /** subject of this statement */ private

A lightweight java parser for RDF

2009-03-07T21:47:00.002+01:00

About one year ago, I wrote a lightweight java parser for RDF based on the Stream API for XML (Stax). It is far from being perfect as , for example, it does not handle the reified statements, xml:base, ... but it is small (24K) and works fine with most RDF files. Inspired by the XML SAX parsers, this RDF parser doesn't keep the statements in memory but calls a method "found" each time a triple is

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