I Really need to sleep: inserting the SNPs into MongoDB with C++

In the previous post I showed how to parse dbSNP/XML with libxml. In the current post I'll insert the results into MongoDB using the native Mongo C++ API. Some others have already posted about MongoDB: for example see Jan's, Brad's or Neil's posts The Boost-C++library is required: my code failed to compile with boost 4.* but it compiled fine with boost 3.9.

Starting mongoDB

> mkdir ~/tmp/MONGODB/data
> mongodb-linux-i686-1.2.2/bin/mongod -dbpath ~/tmp/MONGODB/data
Sun Feb 7 19:22:36 Mongo DB : starting : pid = 12123 port = 27017 dbpath = /home/pierre/tmp/MONGODB/data master = 0 slave = 0 32-bit
** NOTE: when using MongoDB 32 bit, you are limited to about 2 gigabytes of data
** see http://blog.mongodb.org/post/137788967/32-bit-limitations for more

Sun Feb 7 19:22:36 db version v1.2.2, pdfile version 4.5
Sun Feb 7 19:22:36 git version: 8a4fb8b1c7cb78648c55368d806ba35054f6be54
Sun Feb 7 19:22:36 sys info: Linux domU-12-31-39-01-70-B4 2.6.21.7-2.fc8xen #1 SMP Fri Feb 15 12:39:36 EST 2008 i686 BOOST_LIB_VERSION=1_37
Sun Feb 7 19:22:36 waiting for connections on port 27017

Refactoring the XML parser for dbSNP

I've added a 'mongo::DBClientConnection connection' to the MondoDB database in the class DBSNPHandler. This connection is simply opened with

state.connection.connect("localhost");

.
Now, in the method "endElement" when a new SNP is found, a new mongo::BSONObjBuilder object is filled with the fields describing a snp. The "rs####" is used as the key of the database.

mongo::BSONObjBuilder b;
b.append("_id", state->rs_id);
b.append("name", state->rs_id);
b.append("seq5", state->seq5);
b.append("observed", state->observed);
b.append("seq3", state->seq3);

This object is then converted to a mongo::BSONObj and inserted into the MondoDB database:

mongo::BSONObj p = b.obj();
state->connection.insert("ncbi.dbsnp", p);

At the end, we can loop over all the items:

std::cout << "count:" << state.connection.count("ncbi.dbsnp") << std::endl;
mongo::BSONObj emptyObj;
std::auto_ptr<mongo::DBClientCursor> cursor = state.connection.query("ncbi.dbsnp", emptyObj);
while( cursor->more() )
{
std::cout << cursor->next().toString() << std::endl;
}

Compilation

Here , the program was compiled using

export LD_LIBRARY_PATH=../boost/boost_1_39_0/stage/lib:../mongodb-linux-i686-1.2.2/lib

g++ `xml2-config --cflags --libs` \
-I ../mongodb-linux-i686-1.2.2/include/mongo\
-I ../boost/boost_1_39_0\
-L ../mongodb-linux-i686-1.2.2/lib \
-L ../boost/boost_1_39_0/stage/lib \
dbsnp.c \
-lmongoclient \
-lboost_thread-gcc43-mt \
-lboost_filesystem-gcc43-mt

Execution

./a.out ds_ch17.xml.gz
count:740
{ _id: "rs69624490", name: "rs69624490", seq5: "CTCCAGCCCGGGCCCACCCTACAGCCGACACCAAGTTGCGTCACCGTGATCTGGACACCCAGACGTACAT...", observed: "C/G", seq3: "GGTACTCCACCAGCAGGAGCAGGAGGCTCTCCCACCTCCACCTGCCACTGGCCGACAGCTCCCAGTGCGT..." }
{ _id: "rs69626771", name: "rs69626771", seq5: "GAAATTCCTACAAAAATCCATCTTTGTGGCATCATCAGGGGTGATCTGTCCTTGCAGGAATATCTCACGT...", observed: "G/T", seq3: "CTGTAGTTAAACTGGTAACGAAGGTTCCACCCTTCCTCCCAGGCCACAGCGCCCCCAGCAGTCTTGCACC..." }
{ _id: "rs69628798", name: "rs69628798", seq5: "ACCTCAGTAAAATGAAGATTATTACTATGTGCCCTATGCAGGACAGGGACTGTGTTCTGATACAGGCCCT...", observed: "A/G", seq3: "TTGAACAGATATCAGAAAAAGGGGGAGAGAGAAATCAGTTGGTTGGGAGGAGAATGAGGGGGGCAGGAGG..." }
{ _id: "rs69633675", name: "rs69633675", seq5: "GTTGTTGGTGAGGGGAGGGAGTGGGGCAAGAGGAACAGTGTGGTCTAGAGGATAGAGCAAGGGAATGGGA...", observed: "A/G", seq3: "TGGCTCAGTGGAAAGAACACGGGCTTTGGAGTCAGAGATCAGGGGTTCGAATCCCGGCTCTGCCACTTGG..." }
{ _id: "rs69638381", name: "rs69638381", seq5: "GGCCACGCTGCTTGTCATAGCGGCTTTCCAGCTCTGCCCTCCGCAGCAAGGGCAGCGCTCACCTAGGCAA...", observed: "G/T", seq3: "GGGCCGTACCGATGAGTTCTCCCGGGGAGAGACCAGGAGCTCTGAGTCAGGAAGGGAATCAAAAGGCGAC..." }
{ _id: "rs69640257", name: "rs69640257", seq5: "TTTCCTCTTCTCCTTGGCCCTGCATTATCCCCACTATTTGACTTGTCCAGGTCAGCCTTTGTAAATAAAA...", observed: "A/G", seq3: "ACTCTTTACCATCACTTATTCTCAAGGCTGGTCAAAACCTTCTCTGTCATTGTCATTTGTTTATTGAGCA..." }
{ _id: "rs69640260", name: "rs69640260", seq5: "CTCAAAAGAGAATGGTTCCTTTAGGTCCCTGAGGACACCCCAGGAAGGTTGGGTATCCCTTGCTTCAATT...", observed: "C/T", seq3: "AGCGTGTCTTAGTGGAAAAAGCACAAGTCTGGGAGTCAGAGTATCTGGGTTCTAATCCCCACCACCCAAT..." }
{ _id: "rs69641743", name: "rs69641743", seq5: "TCTATACATTGTTTAGTTCCTCTCCCCCACTAGACTGTAAACACCTTGAGGGCAAGGAGCATCTCTTCTG...", observed: "A/C", seq3: "CTAGCAAATAGAGCACGGGCCTGGGAATCTGAATAGGTTCTAATCCTGGCTCTGCCACTTGTCTGCTATG..." }
{ _id: "rs69642295", name: "rs69642295", seq5: "AGCATGCACGATATAAAAAATGCCTGAGCACGTTTTCGACCACCTGAGGGAAGCAGAGGAAAGAGTGAAA...", observed: "A/G", seq3: "GGGATAGCTCTTGTGTGGATCAGGAGTGTGGTTCAACAGCACAAATTCATTTACAGAGATCACTAGAAGC..." }
{ _id: "rs69643084", name: "rs69643084", seq5: "AATTCCCTGATACAGTGTTTTGCACAGGGTGCTTTACTGCTGAAAGACTGAATGCTGCCCTATAGCCTGC...", observed: "C/T", seq3: "GTTTTCTTAAGAACCCATGGGGCTCTGGGCTACTTCTTTTCTTTGTGACTCCATAGTAGTTTACAAAAGC..." }
(...)

Source code

#include <libxml/parser.h>
#include <string>
#include <cstring>
#include <iostream>
#include "client/dbclient.h"
#include "db/jsobj.h"

/**
* Hold the state of the parser
*/
class DBSNPHandler
{
public:
mongo::DBClientConnection connection;
// current rs### id
std::string rs_id;
// current 5' sequence
std::string seq5;
// current observed variation
std::string observed;
// current 3' sequence
std::string seq3;
// current string handler by the SAX handler
std::string* content;
//did we find the sequence ?
bool sequence_found;

DBSNPHandler():content(NULL),sequence_found(false)
{
}

~DBSNPHandler()
{
clear();
}

void clear()
{
if(content!=NULL) delete content;
content=NULL;
sequence_found=false;
rs_id.clear();
seq5.clear();
observed.clear();
seq3.clear();
content=NULL;
}
};

/** called when an TAG is opened */
static void startElement(void * ctx,
const xmlChar * localname,
const xmlChar * prefix,
const xmlChar * URI,
int nb_namespaces,
const xmlChar ** namespaces,
int nb_attributes,
int nb_defaulted,
const xmlChar ** attributes)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(strcmp( (char*) localname,"Rs")==0)
{
state->clear();

for(int i=0;i< nb_attributes;++i)
{
if(strcmp((char*) attributes[i*5],"rsId")!=0) continue;
int len=(char*) attributes[i*5+4]-(char*) attributes[i*5+3];
state->rs_id.assign("rs");
state->rs_id.append(
(char*) attributes[i*5+3],
len
);
break;
}
}
else if((strcmp( (char*) localname,"Seq5")==0 ||
strcmp( (char*) localname,"Observed")==0 ||
strcmp( (char*) localname,"Seq3")==0) &&
state->sequence_found==false
)
{
state->content=new std::string;
}
}


/** called when an TAG is closed */
static void endElement(void * ctx,
const xmlChar * localname,
const xmlChar * prefix,
const xmlChar * URI)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(strcmp( (char*) localname,"Rs")==0)
{
mongo::BSONObjBuilder b;
b.append("_id", state->rs_id);
b.append("name", state->rs_id);
b.append("seq5", state->seq5);
b.append("observed", state->observed);
b.append("seq3", state->seq3);
mongo::BSONObj p = b.obj();

state->connection.insert("ncbi.dbsnp", p);


//we're done with this SNP, clear the state
state->clear();
}
else if(state->content!=NULL && strcmp( (char*) localname,"Seq5")==0)
{
state->seq5.assign(*(state->content));
delete state->content;
state->content=NULL;
}
else if(state->content!=NULL && strcmp( (char*) localname,"Observed")==0)
{
state->observed.assign(*(state->content));
delete state->content;
state->content=NULL;
}
else if(state->content!=NULL && strcmp( (char*) localname,"Seq3")==0)
{
state->seq3.assign(*(state->content));
delete state->content;
state->content=NULL;
state->sequence_found=true;
}
}

static void handleCharacters(void * ctx, const xmlChar * ch, int len)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(state->content!=NULL)
{
state->content->append((char*)ch,len);
}
}


int main(int argc,char **argv)
{
int res;
LIBXML_TEST_VERSION
xmlSAXHandler handler;
DBSNPHandler state;

memset(&handler,0,sizeof(xmlSAXHandler));


handler.startElementNs= startElement;
handler.endElementNs=endElement;
handler.characters=handleCharacters;
handler.initialized = XML_SAX2_MAGIC;

state.connection.connect("localhost");

for(int i=1;i< argc;++i)
{
res=xmlSAXUserParseFile(&handler,&state,argv[i]);

if(res!=0)
{
std::cerr << "Error "<< res << argv[i] << std::endl;
}
}

//dump results
std::cout << "count:" << state.connection.count("ncbi.dbsnp") << std::endl;
mongo::BSONObj emptyObj;
std::auto_ptr<mongo::DBClientCursor> cursor = state.connection.query("ncbi.dbsnp", emptyObj);
while( cursor->more() )
{
std::cout << cursor->next().toString() << std::endl;
}

xmlCleanupParser();
xmlMemoryDump();
return(0);
}

Hey... here come the sandman.. :-)


That's it !
Pierre

Id rather bee sleeping: fast parsing of dbsnp/XML with libxml

Hello world ! I'm now in Japan for Biohackathon 2010 it's 00H30 here and, of course, I cannot sleep. I should be tired : I spent 11H00 in a plane, 1H30 in a train and three hours skating in Tokyo with my kick scooter :-)

I'm killing the time with libxml, the C library for parsing XML. In the current post I'll write a simple SAX parser extracting the flanking sequences from the SNPs of dbSNP/xml.
First we need to include a few files:

#include <libxml/parser.h>
#include <string>
#include <cstring>
#include <iostream>

The the C++ class DBSNPHandler that holds the current state of the parser:

class DBSNPHandler
{
public:

// current rs### id
std::string rs_id;
// current 5' sequence
std::string seq5;
// current observed variation
std::string observed;
// current 3' sequence
std::string seq3;
// current string handler by the SAX handler
std::string* content;
//did we find the sequence ?
bool sequence_found;

DBSNPHandler();
~DBSNPHandler();
void clear();
}

I defined a number of callback methods that will be called when events occur during parsing. 3 callbacks are needed here: when the parser opens an element, when the parse closes an element and when it finds some text. Each callback uses a DBSNPHandler as the value of the user data (ctx);
startElement is called when the parser opens an element. If it is a <Rs> tag then we go threw the attributes to find the rs## id. If it is a component of the sequence then we tell the DBSNPHandler that it should store the text in the 'content' variable.

/** called when an TAG is opened */
void startElement(void * ctx,
const xmlChar * localname,
const xmlChar * prefix,
const xmlChar * URI,
int nb_namespaces,
const xmlChar ** namespaces,
int nb_attributes,
int nb_defaulted,
const xmlChar ** attributes)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(strcmp( (char*) localname,"Rs")==0)
{
state->clear();
//loop over the attributes an find the rs###
for(int i=0;i< nb_attributes;++i)
{
if(strcmp((char*) attributes[i*5],"rsId")!=0) continue;
int len=(char*) attributes[i*5+4]-(char*) attributes[i*5+3];

state->rs_id.assign(
(char*) attributes[i*5+3],
len
);
break;
}
}
else if((strcmp( (char*) localname,"Seq5")==0 ||
strcmp( (char*) localname,"Observed")==0 ||
strcmp( (char*) localname,"Seq3")==0) &&
state->sequence_found==false
)
{
//tells the DBSNPHandler we need to get the next text content
state->content=new std::string;
}
}

handleCharacters is called by the SAX parser it finds some text. This text is appended to the current content if we are parsing the sequence component of the current rs####.

static void handleCharacters(void * ctx, const xmlChar * ch, int len)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(state->content!=NULL)
{
state->content->append((char*)ch,len);
}
}

endElement is called when the parser closes an element. If it is a component of the sequences, the fields (seq5,seq3...) of the current state are updated. It it is a <Rs> element, then its sequence is printed out and the state is re-initialized.

static void endElement(void * ctx,
const xmlChar * localname,
const xmlChar * prefix,
const xmlChar * URI)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(strcmp( (char*) localname,"Rs")==0)
{
std::cout << "rs" << state->rs_id <<
"\t" << state->seq5 <<
"[" << state->observed << "]" <<
state->seq3 << std::endl;

//we're done with this SNP, clear the state
state->clear();
}
else if(state->content!=NULL && strcmp( (char*) localname,"Seq5")==0)
{
state->seq5.assign(*(state->content));
delete state->content;
state->content=NULL;
}
else if(state->content!=NULL && strcmp( (char*) localname,"Observed")==0)
{
state->observed.assign(*(state->content));
delete state->content;
state->content=NULL;
}
else if(state->content!=NULL && strcmp( (char*) localname,"Seq3")==0)
{
state->seq3.assign(*(state->content));
delete state->content;
state->content=NULL;
state->sequence_found=true;
}
}

In the main part, the SAX handler is initialized with the previous callbacks and the xml files are parsed:

xmlSAXHandler handler;
DBSNPHandler state;
(...)
handler.startElementNs= startElement;
handler.endElementNs=endElement;
handler.characters=handleCharacters;

for(int i=1;i< argc;++i)
{
xmlSAXUserParseFile(&handler,&state,argv[i]);
}

Compiling

g++ `xml2-config --cflags --libs` dbsnp.c

Running

a.out ds_ch17.xml.gz
rs69624490 CTCCAGCCCGGGCCCACCCTACAGCCGACACCAAGTTGCGTCACCGTGATCTGGACACCCAGACGTACATTAGAGCTGCTTTCCTTGATGAGCTCAGAACC[C/G]GGTACTCCACCAGCAGGAGCAGGAGGCTCTCCCACCTCCACCTGCCACTGGCCGACAGCTCCCAGTGCGTTCTTCAGGCGCCACTTTCTCGCTGGAGAAAA
rs69626771 GAAATTCCTACAAAAATCCATCTTTGTGGCATCATCAGGGGTGATCTGTCCTTGCAGGAATATCTCACGTCCTCTGTTTGTACCTTGACACGCTTGGCTGA[G/T]CTGTAGTTAAACTGGTAACGAAGGTTCCACCCTTCCTCCCAGGCCACAGCGCCCCCAGCAGTCTTGCACCAGATTCGAATTTATGAACCCACAGCACTTGC
rs69628798 ACCTCAGTAAAATGAAGATTATTACTATGTGCCCTATGCAGGACAGGGACTGTGTTCTGATACAGGCCCTGATTAGGTTAGTACAGTGCCTGGCACATAGT[A/G]TTGAACAGATATCAGAAAAAGGGGGAGAGAGAAATCAGTTGGTTGGGAGGAGAATGAGGGGGGCAGGAGGGTCCTGCAGGGTGTTGCAGGTGAGAAATGAC
rs69633675 GTTGTTGGTGAGGGGAGGGAGTGGGGCAAGAGGAACAGTGTGGTCTAGAGGATAGAGCAAGGGAATGGGAGTCAGAAGGACCTGTGTTCTGGAGAAGCAGC[A/G]TGGCTCAGTGGAAAGAACACGGGCTTTGGAGTCAGAGATCAGGGGTTCGAATCCCGGCTCTGCCACTTGGCAGCTGTGTGACTGTGGGCAAGTCACTTCAC
rs69638381 GGCCACGCTGCTTGTCATAGCGGCTTTCCAGCTCTGCCCTCCGCAGCAAGGGCAGCGCTCACCTAGGCAAGCCCAGAGGGCTTAGGAGGGAGGGGCGGGGC[G/T]GGGCCGTACCGATGAGTTCTCCCGGGGAGAGACCAGGAGCTCTGAGTCAGGAAGGGAATCAAAAGGCGACAGGCTCTCATCATCAGTGTTGCCCAGGATCT
rs69640257 TTTCCTCTTCTCCTTGGCCCTGCATTATCCCCACTATTTGACTTGTCCAGGTCAGCCTTTGTAAATAAAAACAACAGGCTTACCAGCCTACCTTTCTCCCA[A/G]ACTCTTTACCATCACTTATTCTCAAGGCTGGTCAAAACCTTCTCTGTCATTGTCATTTGTTTATTGAGCATCCATCTTCTACAGAGCCCTGGAGTAAGCGT
rs69640260 CTCAAAAGAGAATGGTTCCTTTAGGTCCCTGAGGACACCCCAGGAAGGTTGGGTATCCCTTGCTTCAATTATCAGAGGTAAAAACTCTCTCTCTAAAGGAG[C/T]AGCGTGTCTTAGTGGAAAAAGCACAAGTCTGGGAGTCAGAGTATCTGGGTTCTAATCCCCACCACCCAATGCTTGCTGTGTGACCTTGGGCCTCAGTTACC
rs69641743 TCTATACATTGTTTAGTTCCTCTCCCCCACTAGACTGTAAACACCTTGAGGGCAAGGAGCATCTCTTCTGAATCTGTTATATTCTCACAGGAGCAGCATGG[A/C]CTAGCAAATAGAGCACGGGCCTGGGAATCTGAATAGGTTCTAATCCTGGCTCTGCCACTTGTCTGCTATGGGACCTTGGGCAAATGATTTAACTTCTCTGT
(...)

The code

#include <libxml/parser.h>
#include <string>
#include <cstring>
#include <iostream>
/**
* Holds the state of the parser
*/
class DBSNPHandler
{
public:
// current rs### id
std::string rs_id;
// current 5' sequence
std::string seq5;
// current observed variation
std::string observed;
// current 3' sequence
std::string seq3;
// current string handler by the SAX handler
std::string* content;
//did we find the sequence ?
bool sequence_found;

DBSNPHandler():content(NULL),sequence_found(false)
{
}

~DBSNPHandler()
{
clear();
}

void clear()
{
if(content!=NULL) delete content;
content=NULL;
sequence_found=false;
rs_id.clear();
seq5.clear();
observed.clear();
seq3.clear();
content=NULL;
}
};

/** called when an TAG is opened */
static void startElement(void * ctx,
const xmlChar * localname,
const xmlChar * prefix,
const xmlChar * URI,
int nb_namespaces,
const xmlChar ** namespaces,
int nb_attributes,
int nb_defaulted,
const xmlChar ** attributes)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(strcmp( (char*) localname,"Rs")==0)
{
state->clear();

for(int i=0;i< nb_attributes;++i)
{
if(strcmp((char*) attributes[i*5],"rsId")!=0) continue;
int len=(char*) attributes[i*5+4]-(char*) attributes[i*5+3];

state->rs_id.assign(
(char*) attributes[i*5+3],
len
);
break;
}
}
else if((strcmp( (char*) localname,"Seq5")==0 ||
strcmp( (char*) localname,"Observed")==0 ||
strcmp( (char*) localname,"Seq3")==0) &&
state->sequence_found==false
)
{
state->content=new std::string;
}
}


/** called when an TAG is closed */
static void endElement(void * ctx,
const xmlChar * localname,
const xmlChar * prefix,
const xmlChar * URI)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(strcmp( (char*) localname,"Rs")==0)
{
std::cout << "rs" << state->rs_id <<
"\t" << state->seq5 <<
"[" << state->observed << "]" <<
state->seq3 << std::endl;

//we're done with this SNP, clear the state
state->clear();
}
else if(state->content!=NULL && strcmp( (char*) localname,"Seq5")==0)
{
state->seq5.assign(*(state->content));
delete state->content;
state->content=NULL;
}
else if(state->content!=NULL && strcmp( (char*) localname,"Observed")==0)
{
state->observed.assign(*(state->content));
delete state->content;
state->content=NULL;
}
else if(state->content!=NULL && strcmp( (char*) localname,"Seq3")==0)
{
state->seq3.assign(*(state->content));
delete state->content;
state->content=NULL;
state->sequence_found=true;
}
}

static void handleCharacters(void * ctx, const xmlChar * ch, int len)
{
DBSNPHandler* state=(DBSNPHandler*)ctx;
if(state->content!=NULL)
{
state->content->append((char*)ch,len);
}
}


int main(int argc,char **argv)
{
int res;
LIBXML_TEST_VERSION
xmlSAXHandler handler;
DBSNPHandler state;

memset(&handler,0,sizeof(xmlSAXHandler));


handler.startElementNs= startElement;
handler.endElementNs=endElement;
handler.characters=handleCharacters;
handler.initialized = XML_SAX2_MAGIC;

for(int i=1;i< argc;++i)
{
res=xmlSAXUserParseFile(&handler,&state,argv[i]);

if(res!=0)
{
std::cerr << "Error "<< res << argv[i] << std::endl;
}
}
xmlCleanupParser();
xmlMemoryDump();

return(0);
}

That's it !
Pierre

LinkedIn+XSLT = FOAF / People from Biohackathon 2010

I've created a XSLT stylesheet transforming the public HTML pages on LinkedIn about the people going to Biohackathon 2010 to FOAF. The stylesheet worked fine (of course it won't work anymore if LinkedIn change the layout of the HTML pages) and it is available here:

http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/linkedin2foaf.xsl

Note: if possible, the XSLT stylesheet uses geonames.org to find the foaf:based_near. At the end, here is the FOAF file of the people attending Biohackathon 2010:

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:doac="http://ramonantonio.net/doac/0.1/">
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=11054862">
<foaf:name>Alberto Labarga</foaf:name>
<foaf:givenname>Alberto</foaf:givenname>
<foaf:family_name>Labarga</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/1/000/002/120/050aad5.jpg">
<dc:title>Alberto Labarga</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>CEO at Experimental Serendipity</doac:summary>
<doac:skill>building</doac:skill>
<doac:skill>team</doac:skill>
<doac:skill>management</doac:skill>
<doac:skill>project</doac:skill>
<doac:skill>design</doac:skill>
<doac:skill>visual</doac:skill>
<doac:skill>architecture</doac:skill>
<doac:skill>information</doac:skill>
<doac:skill>SOA</doac:skill>
<doac:skill>analysis</doac:skill>
<doac:skill>data</doac:skill>
<doac:skill>mining</doac:skill>
<doac:skill>data</doac:skill>
<doac:skill>ELN)</doac:skill>
<doac:skill>HIS</doac:skill>
<doac:skill>LIS</doac:skill>
<doac:skill>(LIMS</doac:skill>
<doac:skill>management</doac:skill>
<doac:skill>data</doac:skill>
<doac:skill>scientific</doac:skill>
<doac:skill>bioinformatics</doac:skill>
<doac:experience>
<doac:Experience>
<doac:title>LIMS Consultant</doac:title>
<doac:location>LabWare</doac:location>
<doac:date-starts>2009-10-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Information Architect and Data analysis consultant</doac:title>
<doac:location>Experimental Serendipity</doac:location>
<doac:date-starts>2008-10-01</doac:date-starts>
<doac:activity>We work with companies who want to get more value from their information. We help them develop new ways to manage, analyze and visualize their information. We are currently working in different web 2.0 related projects, including the Elsevier Grand Challenge (http://www.elseviergrandchallenge.com) and the Webservices BioHackaton (http://hackathon2.dbcls.jp/)</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>PhD student</doac:title>
<doac:location>Universidad de Granada</doac:location>
<doac:date-starts>2008-10-01</doac:date-starts>
<doac:activity>I am currently finishing my PhD studies in the genome Alhambra group (http://genome.ugr.es/), within the Computer Science and Artificial Intelligence Department. My thesis is focused in developing new data mining techniques for analysis and visualization in biomedicine..</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Coordinador Grupo de Voluntarios de Granada</doac:title>
<doac:location>Fundación Ayuda en Acción</doac:location>
<doac:date-starts>2007-12-01</doac:date-starts>
<doac:activity>Coordinador Grupo de Voluntarios de Granada</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Chief Technology Officer</doac:title>
<doac:location>Integromics S.L.</doac:location>
<doac:date-starts>2007-11-01</doac:date-starts>
<doac:date-ends>2008-10-01</doac:date-ends>
<doac:activity>I have led the development, from inception to implementation, of a microarray data analytics product based on the TIBCO Spotfire platform (http://www.integromics.com/IBD.php) and a laboratory and clinical data management system based on the Apache Cocoon framework and other Java technologies such as Xindice or JMaki.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Software Engineer</doac:title>
<doac:location>EBI</doac:location>
<doac:date-starts>2005-06-01</doac:date-starts>
<doac:date-ends>2007-11-01</doac:date-ends>
<doac:activity>I worked in the External Services Group, which is part of the IT Services Department, where I lead the migration of the EBI databases and applications infrastructure to a Services Oriented Architecture (SOA). I was involved in the development of the new unified website and the new search engine EB-Eye. My daily work included modelling, design and software development. Also I was responsible for the web infrastructure (Apache and Tomcat servers). This position also involved training and dissemination tasks related to EBI services in courses, workshops, conferences, etc.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Chief Technology Officer</doac:title>
<doac:location>IMAGINA BIOTEK</doac:location>
<doac:date-starts>2002-10-01</doac:date-starts>
<doac:date-ends>2005-12-01</doac:date-ends>
<doac:activity>I was in charge of the technical direction and research project coordination at this bioinformatics start-up company. Between our contracts we had the management of the bioinformatics infrastructure of the Applied Medicine Research Center (www.cima.es) in Pamplona (Spain) and the bioinformatics support of the main Affymetrix service provider in Spain (www.progenika.com). We took part in different joint research projects at national and european levels, with cancer being one of our main collaboration topics with the Universitary Hospital and the University of Navarra.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Associate Professor</doac:title>
<doac:location>Universidad Pública de Navarra</doac:location>
<doac:date-starts>1997-10-01</doac:date-starts>
<doac:date-ends>2005-06-01</doac:date-ends>
<doac:activity>I taught different subjects related to Digital Signal Processing for Telecommunication Engineering students and Computer Science and Programming for Civil Engineers. I was also the coordinator of the research line in bioinformatics in the Health Sciences School.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Researcher</doac:title>
<doac:location>CEIT</doac:location>
<doac:date-starts>2000</doac:date-starts>
<doac:date-ends>2002</doac:date-ends>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Universidad de Granada</foaf:organization>
<doac:title>PhD. in Computer Science and Artificial Intelligence</doac:title>
<doac:date-starts>2008-01-01</doac:date-starts>
<doac:date-ends>2009-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Universidad Complutense de Madrid</foaf:organization>
<doac:title>Experto en habilidades Directivas y Gestión de Equipos</doac:title>
<doac:date-starts>1998-01-01</doac:date-starts>
<doac:date-ends>1999-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Universidad Pública de Navarra</foaf:organization>
<doac:title>MSc. in Telecomunication Engineer</doac:title>
<doac:date-starts>1991-01-01</doac:date-starts>
<doac:date-ends>1997-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>University of Surrey</foaf:organization>
<doac:title>MSc. in Information Systems</doac:title>
<doac:date-starts>1994-01-01</doac:date-starts>
<doac:date-ends>1995-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=11054862">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=3144981">
<foaf:name>Andrea Splendiani</foaf:name>
<foaf:givenname>Andrea</foaf:givenname>
<foaf:family_name>Splendiani</foaf:family_name>
<doac:summary>Senior Bioinformatics Scientist - Data Integration at Rothamsted Research</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>London, GB</dc:title>
<geo:long>-0.125532746315002</geo:long>
<geo:lat>51.5084152563931</geo:lat>
</geo:Point>
</foaf:based_near>
<foaf:homepage rdf:resource="http://www.sgtp.net/AndreaSplendiani/"/>
<foaf:homepage rdf:resource="http://www.leafbioscience.com"/>
<foaf:homepage rdf:resource="http://sergentpenguin.blogspot.com"/>
<doac:skill>Databases</doac:skill>
<doac:skill>Microarrays</doac:skill>
<doac:skill>Pathways</doac:skill>
<doac:skill>Biology</doac:skill>
<doac:skill>Systems</doac:skill>
<doac:skill>Web</doac:skill>
<doac:skill>Semantic</doac:skill>
<doac:skill>Ontologies</doac:skill>
<foaf:homepage rdf:resource="http://www.sgtp.net/AndreaSplendiani/"/>
<foaf:homepage rdf:resource="http://www.leafbioscience.com"/>
<foaf:homepage rdf:resource="http://sergentpenguin.blogspot.com"/>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=3144981">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=34738971">
<foaf:name>Atsuko Yamaguchi</foaf:name>
<foaf:givenname>Atsuko</foaf:givenname>
<foaf:family_name>Yamaguchi</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/1/000/047/16f/1b494b3.jpg">
<dc:title>Atsuko Yamaguchi</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>Project Associate Professor at Database Center for Life Science</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>Japan, JP</dc:title>
<geo:long>139.753088951111</geo:long>
<geo:lat>35.6853569043379</geo:lat>
</geo:Point>
</foaf:based_near>
<foaf:homepage rdf:resource="http://dbcls.rois.ac.jp/"/>
<foaf:homepage rdf:resource="http://lifesciencedb.jp/"/>
<doac:experience>
<doac:Experience>
<doac:title>Project Associate Professor</doac:title>
<doac:location>Database Center for Life Science</doac:location>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Assistant Professor</doac:title>
<doac:location>Kyoto University</doac:location>
<doac:date-starts>2002-04-01</doac:date-starts>
<doac:date-ends>2005-03-01</doac:date-ends>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Kyoto University</foaf:organization>
<doac:title>Ph.D</doac:title>
<doac:subject/>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Kyushu University</foaf:organization>
<doac:title>MS</doac:title>
<doac:subject/>
</doac:Education>
</doac:education>
<foaf:homepage rdf:resource="http://dbcls.rois.ac.jp/"/>
<foaf:homepage rdf:resource="http://lifesciencedb.jp/"/>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=34738971">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=18346806">
<foaf:name>Bruno Aranda</foaf:name>
<foaf:givenname>Bruno</foaf:givenname>
<foaf:family_name>Aranda</foaf:family_name>
<doac:summary>Software Engineer at European Bioinformatics Institute</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>Cambridge, GB</dc:title>
<geo:long>0.1166667</geo:long>
<geo:lat>52.2</geo:lat>
</geo:Point>
</foaf:based_near>
<foaf:homepage rdf:resource="http://www.ebi.ac.uk"/>
<foaf:homepage rdf:resource="http://myfaces.apache.org"/>
<doac:skill>JSF.</doac:skill>
<doac:skill>and</doac:skill>
<doac:skill>Java</doac:skill>
<doac:skill>in</doac:skill>
<doac:skill>Specialist</doac:skill>
<doac:experience>
<doac:Experience>
<doac:title>Software Engineer</doac:title>
<doac:location>European Bioinformatics Institute</doac:location>
<doac:date-starts>2006-03-01</doac:date-starts>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>PMC Member</doac:title>
<doac:location>Apache Software Foundation</doac:location>
<doac:date-starts>2006-02-01</doac:date-starts>
<doac:activity>PMC Member of the Apache MyFaces project (http://myfaces.apache.org)</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Committer</doac:title>
<doac:location>Apache Software Foundation</doac:location>
<doac:date-starts>2005-06-01</doac:date-starts>
<doac:activity>Committer for Apache MyFaces (http://myfaces.apache.org)</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Software Engineer</doac:title>
<doac:location>Ebiointel</doac:location>
<doac:date-starts>2002-09-01</doac:date-starts>
<doac:date-ends>2006-02-01</doac:date-ends>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Software Developer</doac:title>
<doac:location>e-ntra</doac:location>
<doac:date-starts>2000-04-01</doac:date-starts>
<doac:date-ends>2002-08-01</doac:date-ends>
<doac:activity>Part-time</doac:activity>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Universitat Autònoma de Barcelona</foaf:organization>
<doac:title/>
<doac:date-starts>1998-01-01</doac:date-starts>
<doac:date-ends>2002-12-31</doac:date-ends>
</doac:Education>
</doac:education>
<foaf:homepage rdf:resource="http://www.ebi.ac.uk"/>
<foaf:homepage rdf:resource="http://myfaces.apache.org"/>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=18346806">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=17090435">
<foaf:name>Christian Zmasek</foaf:name>
<foaf:givenname>Christian</foaf:givenname>
<foaf:family_name>Zmasek</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/1/000/048/104/1280869.jpg">
<dc:title>Christian Zmasek</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>Postdoctoral Associate at Burnham Institute for Medical Research</doac:summary>
<foaf:homepage rdf:resource="http://monochrome-effect.net/publications.html"/>
<foaf:homepage rdf:resource="http://monochrome-effect.net/"/>
<foaf:homepage rdf:resource="http://bioinformatics.burnham.org/pages/index.html"/>
<doac:skill>SQL.</doac:skill>
<doac:skill>Perl</doac:skill>
<doac:skill>C++</doac:skill>
<doac:skill>Ruby</doac:skill>
<doac:skill>Java</doac:skill>
<doac:skill>languages:</doac:skill>
<doac:skill>Programming</doac:skill>
<doac:skill>+</doac:skill>
<doac:skill>culture.</doac:skill>
<doac:skill>cell</doac:skill>
<doac:skill>(ES)</doac:skill>
<doac:skill>stem</doac:skill>
<doac:skill>embryonic</doac:skill>
<doac:skill>and</doac:skill>
<doac:skill>techniques;</doac:skill>
<doac:skill>microscopy</doac:skill>
<doac:skill>analysis;</doac:skill>
<doac:skill>and</doac:skill>
<doac:skill>purification</doac:skill>
<doac:skill>expression</doac:skill>
<doac:skill>protein</doac:skill>
<doac:skill>analysis;</doac:skill>
<doac:skill>and</doac:skill>
<doac:skill>manipulation</doac:skill>
<doac:skill>isolation</doac:skill>
<doac:skill>DNA</doac:skill>
<doac:skill>in</doac:skill>
<doac:skill>Experienced</doac:skill>
<doac:skill>Biology:</doac:skill>
<doac:skill>Molecular</doac:skill>
<doac:skill>+</doac:skill>
<doac:skill>development.</doac:skill>
<doac:skill>algorithm</doac:skill>
<doac:skill>analysis</doac:skill>
<doac:skill>sequence</doac:skill>
<doac:skill>protein</doac:skill>
<doac:skill>and</doac:skill>
<doac:skill>DNA</doac:skill>
<doac:skill>Biology:</doac:skill>
<doac:skill>Computational</doac:skill>
<doac:skill>Genomics</doac:skill>
<doac:skill>+</doac:skill>
<doac:skill>analysis.</doac:skill>
<doac:skill>functional</doac:skill>
<doac:skill>wide</doac:skill>
<doac:skill>genome</doac:skill>
<doac:skill>and</doac:skill>
<doac:skill>inference</doac:skill>
<doac:skill>duplication</doac:skill>
<doac:skill>gene</doac:skill>
<doac:skill>analysis</doac:skill>
<doac:skill>phylogenetic</doac:skill>
<doac:skill>in</doac:skill>
<doac:skill>experience</doac:skill>
<doac:skill>Extensive</doac:skill>
<doac:skill>Evolution:</doac:skill>
<doac:skill>Molecular</doac:skill>
<doac:skill>+</doac:skill>
<doac:experience>
<doac:Experience>
<doac:title>Postdoctoral Associate</doac:title>
<doac:location>Burnham Institute for Medical Research</doac:location>
<doac:date-starts>2006-06-01</doac:date-starts>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Principal Investigator</doac:title>
<doac:location>Genomics Institute of the Novartis Research Foundation (GNF)</doac:location>
<doac:date-starts>2002-03-01</doac:date-starts>
<doac:date-ends>2006-06-01</doac:date-ends>
<doac:activity>Research projects I worked on: + Large scale phylogenetic analyses of multiple ion channel gene families from species ranging from Ciona intestinalis to mammals + Phylogenetic analysis of non-protein kinases + Text and data mining + Statistical analyses of high throughput functional cell based cDNA and siRNA screening experiments + mRNA expression analyses Furthermore, I spent significant time developing software (J2EE, Oracle, Perl).</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Intern</doac:title>
<doac:location>Monsanto Company</doac:location>
<doac:date-starts>1998-06-01</doac:date-starts>
<doac:date-ends>1998-08-01</doac:date-ends>
<doac:activity>I performed research on the reconstruction of signaling pathways by mining the knowledge present in scientific literature and databases.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Washington University in St. Louis School of Medicine</foaf:organization>
<doac:title>PhD</doac:title>
<doac:date-starts>1994-01-01</doac:date-starts>
<doac:date-ends>2002-12-31</doac:date-ends>
<doac:subject>Graduate work in molecular genetics and computational biology under thesis advisor Sean Eddy.</doac:subject>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Eidgenössische Technische Hochschule Zürich</foaf:organization>
<doac:title>Diploma</doac:title>
<doac:date-starts>1989-01-01</doac:date-starts>
<doac:date-ends>1994-12-31</doac:date-ends>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Kantonsschule im Lee, Winterthur</foaf:organization>
<doac:title>Matura Type C</doac:title>
<doac:date-starts>1985-01-01</doac:date-starts>
<doac:date-ends>1989-12-31</doac:date-ends>
</doac:Education>
</doac:education>
<foaf:homepage rdf:resource="http://monochrome-effect.net/publications.html"/>
<foaf:homepage rdf:resource="http://monochrome-effect.net/"/>
<foaf:homepage rdf:resource="http://bioinformatics.burnham.org/pages/index.html"/>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=17090435">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=65214809">
<foaf:name>Luke McCarthy</foaf:name>
<foaf:givenname>Luke</foaf:givenname>
<foaf:family_name>McCarthy</foaf:family_name>
<doac:summary>Programmer at The University of British Columbia</doac:summary>
<doac:experience>
<doac:Experience>
<doac:title>Programmer</doac:title>
<doac:location>The University of British Columbia</doac:location>
<doac:date-starts>2007-07-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Queen's University</foaf:organization>
<doac:title>BSCH</doac:title>
<doac:date-starts>1997-01-01</doac:date-starts>
<doac:date-ends>2001-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=65214809">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=14919228">
<foaf:name>François Belleau</foaf:name>
<foaf:givenname>François</foaf:givenname>
<foaf:family_name>Belleau</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/1/000/048/18b/316de1e.jpg">
<dc:title>François Belleau</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>Bioinformatician at bio2rdf.org</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>Quebec City, CA</dc:title>
<geo:long>-71.2145376205444</geo:long>
<geo:lat>46.8122791164294</geo:lat>
</geo:Point>
</foaf:based_near>
<foaf:homepage rdf:resource="http://bio2rdf.org"/>
<foaf:homepage rdf:resource="http://bio2rdf.blogspot.com/"/>
<doac:skill>applications</doac:skill>
<doac:skill>oriented</doac:skill>
<doac:skill>Service</doac:skill>
<doac:skill>databases</doac:skill>
<doac:skill>Bioinformatics</doac:skill>
<doac:skill>web</doac:skill>
<doac:skill>Semantic</doac:skill>
<doac:experience>
<doac:Experience>
<doac:title>Bioinformatician</doac:title>
<doac:location>bio2rdf.org</doac:location>
<doac:date-starts>2005</doac:date-starts>
<doac:activity>I am the main designer of the Bio2RDF project.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Master Student in Bioinformatics</doac:title>
<doac:location>Centre de recherche du CHUL/CHUQ</doac:location>
<doac:date-starts>2005</doac:date-starts>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Architecte technologique</doac:title>
<doac:location>Ministère du Développement économique, de l'Innovation et de l'Exportation (MDEIE)</doac:location>
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<doac:Experience>
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<foaf:organization>Universität Wien</foaf:organization>
<doac:title>MSc</doac:title>
<doac:date-starts>2000-01-01</doac:date-starts>
<doac:date-ends>2005-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<foaf:homepage rdf:resource="http://samwald.info"/>
<foaf:homepage rdf:resource="http://deri.ie"/>
<foaf:homepage rdf:resource="http://kli.ac.at"/>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=41305706">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
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</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=13686406">
<foaf:name>Mitsuteru Nakao</foaf:name>
<foaf:givenname>Mitsuteru</foaf:givenname>
<foaf:family_name>Nakao</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/3/000/012/09b/360cf38.jpg">
<dc:title>Mitsuteru Nakao</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>Project Researcher at DBCLS</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>Japan, JP</dc:title>
<geo:long>139.753088951111</geo:long>
<geo:lat>35.6853569043379</geo:lat>
</geo:Point>
</foaf:based_near>
<doac:experience>
<doac:Experience>
<doac:title>Project Researcher</doac:title>
<doac:location>DBCLS</doac:location>
<doac:date-starts>2009-04-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Affiliated Researcher</doac:title>
<doac:location>Kazusa DNA Research Institute</doac:location>
<doac:date-starts>2009-04-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Staff</doac:title>
<doac:location>Creative Commons Japan</doac:location>
<doac:date-starts>2008-11-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Affiliated Researcher</doac:title>
<doac:location>National Institute of Advanced Industrial Science and Technology (AIST)</doac:location>
<doac:date-starts>2006-04-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>BioRuby project developer</doac:title>
<doac:location>Open Bioinformatics Foundation</doac:location>
<doac:date-starts>2001</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Postdoc researcher</doac:title>
<doac:location>Kazusa DNA Research Institute</doac:location>
<doac:date-starts>2006-04-01</doac:date-starts>
<doac:date-ends>2009-03-01</doac:date-ends>
<doac:activity>Plant and microbe genomics. Developing web services (CyanoBase, RhizoBase, KazusaAnnotation, KazusaNavigation, KazusaWiki and NandemoGFF) to distribute and analyze genome and gene annotations.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Postdoc</doac:title>
<doac:location>National Institute of Advanced Industrial Science and Technology (AIST)</doac:location>
<doac:date-starts>2004-04-01</doac:date-starts>
<doac:date-ends>2006-03-01</doac:date-ends>
<doac:activity>Developed a source code search server for bioinformatics, b-src.cbrc.jp. Investigated a classification of a human alternative spliced protein variants.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Researcher</doac:title>
<doac:location>The Institute of Medical Science, The University of Tokyo</doac:location>
<doac:date-starts>2002-04-01</doac:date-starts>
<doac:date-ends>2004-03-01</doac:date-ends>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Kyoto University</foaf:organization>
<doac:title>Ph.D</doac:title>
<doac:date-starts>1996-01-01</doac:date-starts>
<doac:date-ends>2000-12-31</doac:date-ends>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Hokkaido University</foaf:organization>
<doac:title>BS</doac:title>
<doac:date-starts>1992-01-01</doac:date-starts>
<doac:date-ends>1996-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=13686406">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
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</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=34770184">
<foaf:name>Paul Gordon</foaf:name>
<foaf:givenname>Paul</foaf:givenname>
<foaf:family_name>Gordon</foaf:family_name>
<doac:summary>Research Associate/PhD Candidate at University of Calgary</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>South Calgary, CA</dc:title>
<geo:long>-114.103375459</geo:long>
<geo:lat>51.04177898</geo:lat>
</geo:Point>
</foaf:based_near>
<doac:skill>discovery</doac:skill>
<doac:skill>Motif</doac:skill>
<doac:skill>analysis</doac:skill>
<doac:skill>Microarray</doac:skill>
<doac:skill>Semantics/Ontologies</doac:skill>
<doac:skill>Design</doac:skill>
<doac:skill>Interface</doac:skill>
<doac:skill>User</doac:skill>
<doac:skill>Services</doac:skill>
<doac:skill>Web</doac:skill>
<doac:skill>development</doac:skill>
<doac:skill>Algorithm</doac:skill>
<doac:skill>analysis</doac:skill>
<doac:skill>Genome</doac:skill>
<doac:skill>Bioinformatics</doac:skill>
<doac:experience>
<doac:Experience>
<doac:title>Research Associate/PhD candidate</doac:title>
<doac:location>University of Calgary</doac:location>
</doac:Experience>
</doac:experience>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=34770184">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
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</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=16314219">
<foaf:name>Raoul Bonnal</foaf:name>
<foaf:givenname>Raoul</foaf:givenname>
<foaf:family_name>Bonnal</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/3/000/017/08b/094f8d0.jpg">
<dc:title>Raoul Bonnal</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>at Fondazione INGM, Integrative Biology Program</doac:summary>
<doac:skill>PostgreSQL.</doac:skill>
<doac:skill>)</doac:skill>
<doac:skill>X</doac:skill>
<doac:skill>OS</doac:skill>
<doac:skill>(Linux</doac:skill>
<doac:skill>Amin</doac:skill>
<doac:skill>Java.</doac:skill>
<doac:skill>C</doac:skill>
<doac:skill>Rails)</doac:skill>
<doac:skill>(BioRuby</doac:skill>
<doac:skill>Ruby</doac:skill>
<doac:skill>Devel:</doac:skill>
<doac:skill>Solving.</doac:skill>
<doac:skill>Problem</doac:skill>
<doac:skill>(454)</doac:skill>
<doac:skill>data</doac:skill>
<doac:skill>Sequencing</doac:skill>
<doac:skill>DNA</doac:skill>
<doac:skill>High-throughput</doac:skill>
<doac:skill>Analysis</doac:skill>
<doac:experience>
<doac:Experience>
<doac:title>Bioinformatics Research Scientist</doac:title>
<doac:location>Fondazione Istituto Nazionale Genetica Molecolare -INGM-</doac:location>
<doac:date-starts>2009-02-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Bioinfo</doac:title>
<doac:location>BioHackathon</doac:location>
<doac:date-starts>2009</doac:date-starts>
<doac:date-ends>2009</doac:date-ends>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Bioinformatician</doac:title>
<doac:location>Institute for Biomedical Technologies, Italian National Research Council</doac:location>
<doac:date-starts>2003-03-01</doac:date-starts>
<doac:date-ends>2009-01-01</doac:date-ends>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>ITB CNR collaboration with</doac:title>
<doac:location>454 Life Sciences</doac:location>
<doac:date-starts>2005</doac:date-starts>
<doac:date-ends>2005</doac:date-ends>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Università degli Studi di Milano-Bicocca</foaf:organization>
<doac:title>Bachelor</doac:title>
<doac:date-starts>1998-01-01</doac:date-starts>
<doac:date-ends>2002-12-31</doac:date-ends>
</doac:Education>
</doac:education>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=16314219">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=13051716">
<foaf:name>Rutger Vos</foaf:name>
<foaf:givenname>Rutger</foaf:givenname>
<foaf:family_name>Vos</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/1/000/015/1b4/25a8ae4.jpg">
<dc:title>Rutger Vos</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>Marie Curie fellow at the University of Reading and bioinformatics consultant</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>Reading, GB</dc:title>
<geo:long>-1.0</geo:long>
<geo:lat>51.4333333</geo:lat>
</geo:Point>
</foaf:based_near>
<foaf:homepage rdf:resource="http://www.ohloh.net/accounts/6958"/>
<foaf:homepage rdf:resource="http://www.nexml.org"/>
<foaf:homepage rdf:resource="http://rutgervos.blogspot.com"/>
<doac:skill>German</doac:skill>
<doac:skill>Dutch</doac:skill>
<doac:skill>English</doac:skill>
<doac:skill>development</doac:skill>
<doac:skill>web</doac:skill>
<doac:skill>sql</doac:skill>
<doac:skill>c</doac:skill>
<doac:skill>xml</doac:skill>
<doac:skill>java</doac:skill>
<doac:skill>corba</doac:skill>
<doac:skill>perl</doac:skill>
<doac:skill>patterns</doac:skill>
<doac:skill>design</doac:skill>
<doac:skill>middleware</doac:skill>
<doac:skill>engineering</doac:skill>
<doac:skill>software</doac:skill>
<doac:skill>bioinformatics</doac:skill>
<doac:skill>phyloinformatics</doac:skill>
<doac:skill>phylogenetics</doac:skill>
<doac:experience>
<doac:Experience>
<doac:title>Marie Curie Fellow</doac:title>
<doac:location>University of Reading</doac:location>
<doac:date-starts>2009-11-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Bioinformatics consultant</doac:title>
<doac:location>University of Pennsylvania</doac:location>
<doac:date-starts>2008-09-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Software Engineer</doac:title>
<doac:location>BioPerl Project</doac:location>
<doac:date-starts>2007</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Computational biologist</doac:title>
<doac:location>the international scientific community</doac:location>
<doac:date-starts>2001-01-01</doac:date-starts>
<doac:activity>This position is a "catch all" position to describe contacts through conferences, work-meetings, public lectures and various collaborations. LinkedIn is too focused on business-to-business contacts to be entirely applicable to scientists in academia, in my opinion.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Postdoctoral research fellow</doac:title>
<doac:location>University of British Columbia</doac:location>
<doac:date-starts>2006-05-01</doac:date-starts>
<doac:date-ends>2009-09-01</doac:date-ends>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Software Engineer</doac:title>
<doac:location>CyberInfrastructure for Phylogenetic Research</doac:location>
<doac:date-starts>2003</doac:date-starts>
<doac:date-ends>2009-09-01</doac:date-ends>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Developer</doac:title>
<doac:location>BioMedia</doac:location>
<doac:date-starts>2000</doac:date-starts>
<doac:date-ends>2000</doac:date-ends>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Simon Fraser University</foaf:organization>
<doac:title>PhD.</doac:title>
<doac:date-starts>2001-01-01</doac:date-starts>
<doac:date-ends>2006-12-31</doac:date-ends>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Universiteit van Amsterdam</foaf:organization>
<doac:title>MSc.</doac:title>
<doac:date-starts>1994-01-01</doac:date-starts>
<doac:date-ends>2000-12-31</doac:date-ends>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Het Wageningsch Lyceum</foaf:organization>
<doac:title/>
<doac:date-starts>1988-01-01</doac:date-starts>
<doac:date-ends>1994-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<foaf:homepage rdf:resource="http://www.ohloh.net/accounts/6958"/>
<foaf:homepage rdf:resource="http://www.nexml.org"/>
<foaf:homepage rdf:resource="http://rutgervos.blogspot.com"/>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=13051716">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=40227171">
<foaf:name>Shuichi Kawashima</foaf:name>
<foaf:givenname>Shuichi</foaf:givenname>
<foaf:family_name>Kawashima</foaf:family_name>
<foaf:depiction>
<foaf:Image rdf:about="http://media.linkedin.com/mpr/mpr/shrink_80_80/p/2/000/036/2c7/2512d10.jpg">
<dc:title>Shuichi Kawashima</dc:title>
</foaf:Image>
</foaf:depiction>
<doac:summary>Research associate at University of Tokyo</doac:summary>
<foaf:based_near>
<geo:Point>
<dc:title>Japan, JP</dc:title>
<geo:long>139.753088951111</geo:long>
<geo:lat>35.6853569043379</geo:lat>
</geo:Point>
</foaf:based_near>
<foaf:homepage rdf:resource="http://www.genome.jp/kegg/soap/"/>
<foaf:homepage rdf:resource="http://www.genome.jp/aaindex/"/>
<foaf:homepage rdf:resource="http://kanehisa.hgc.jp/"/>
<doac:experience>
<doac:Experience>
<doac:title>Research associate</doac:title>
<doac:location>Institute of Medical Science, University of Tokyo</doac:location>
<doac:date-starts>2004-09-01</doac:date-starts>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Instructor</doac:title>
<doac:location>Institute for Chemical Research, Kyoto University</doac:location>
<doac:date-starts>1999-08-01</doac:date-starts>
<doac:date-ends>2004-08-01</doac:date-ends>
<doac:activity/>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Kyoto University</foaf:organization>
<doac:title/>
<doac:date-starts>1995-01-01</doac:date-starts>
<doac:date-ends>1999-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Kansai University</foaf:organization>
<doac:title/>
<doac:date-starts>1990-01-01</doac:date-starts>
<doac:date-ends>1995-12-31</doac:date-ends>
<doac:subject/>
</doac:Education>
</doac:education>
<foaf:homepage rdf:resource="http://www.genome.jp/kegg/soap/"/>
<foaf:homepage rdf:resource="http://www.genome.jp/aaindex/"/>
<foaf:homepage rdf:resource="http://kanehisa.hgc.jp/"/>
<foaf:holdsAccount>
<foaf:OnlineAccount rdf:about="http://www.linkedin.com/ppl/webprofile?id=40227171">
<foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com"/>
</foaf:OnlineAccount>
</foaf:holdsAccount>
</foaf:Person>
<foaf:Person rdf:about="http://www.linkedin.com/ppl/webprofile?id=12409171">
<foaf:name>Thomas Kappler</foaf:name>
<foaf:givenname>Thomas</foaf:givenname>
<foaf:family_name>Kappler</foaf:family_name>
<doac:summary>Bioinformatics Software Developer at Swiss Institute of Bioinformatics</doac:summary>
<foaf:homepage rdf:resource="http://jugglingbits.wordpress.com/"/>
<foaf:homepage rdf:resource="http://jugglingbits.wordpress.com/about"/>
<doac:experience>
<doac:Experience>
<doac:title>Bioinformatics Software Developer</doac:title>
<doac:location>Swiss Institute of Bioinformatics</doac:location>
<doac:date-starts>2008-05-01</doac:date-starts>
<doac:activity>I develop and maintain several web-based applications, some of them in-house database curation tools. Along with the applications, I'm involved in maintaining and further developing the data models, including relational schemas as well as an XML and an RDF/OWL distribution. I'm in constant exchange with biologists and bioinformaticians at other sites.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Software Architect and Developer</doac:title>
<doac:location>University of Heidelberg</doac:location>
<doac:date-starts>2007-10-01</doac:date-starts>
<doac:date-ends>2008-04-01</doac:date-ends>
<doac:activity>Working as independent developer, I created a web-based application for the creation and publishing of a dictionary/thesaurus, for the DEAF group at University of Heidelberg, who create a dictionary of medieval French and are one of the most renowned groups in this field internationally. After extensive requirements engineering, I took over the lead as sole full-time developer. The task included designing the domain model and storage architecture as Java POJOs with Hibernate ORM, and developing a web application using Apache Wicket. The implementation includes different user roles and authentication, versioning of data, and a complex UI with AJAX. I worked with two student assistant programmers, assigning tasks and supervising them. The application will accelerate the process of dictionary creation, which involves a large number of sources and is currently done on paper, and will allow electronic publishing of completed articles.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Assistant developer and researcher</doac:title>
<doac:location>University of Karlsruhe</doac:location>
<doac:date-starts>2005-07-01</doac:date-starts>
<doac:date-ends>2006-07-01</doac:date-ends>
<doac:activity>Developer in two text mining projects with Dr. Rene Witte. For an architecture project (“Durm”), I designed an XML schema for given historical documents and developed a conversion from a non-standard textual format to XML and an automatic upload to a wiki, in Python. For a project about text mining biomedical publications (“Mutation Miner”), I implemented several components for the GATE text analysis framework in Java. I developed a tool in Python for inserting large plain text data sets from public databases into SQL databases and populating an OWL ontology from the data. The GATE components use this ontology for entity and relation discovery, including the grounding of discovered entities in reference databases. The system enables protein engineers to annotate 3D protein models with data extracted from biomedical literature, whose review would be impossible due to the amount of publications. These projects resulted in three publications I co-authored.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:experience>
<doac:Experience>
<doac:title>Software and database developer</doac:title>
<doac:location>Zentrum für Kunst und Medientechnologie (ZKM)</doac:location>
<doac:date-starts>2004-02-01</doac:date-starts>
<doac:date-ends>2004-08-01</doac:date-ends>
<doac:activity>Developed and modified web-based software in PHP. Designed an SQL database and implemented it including final deployment. Implemented a conversion tool from Filemaker to the new database.</doac:activity>
</doac:Experience>
</doac:experience>
<doac:education>
<doac:Education>
<foaf:organization>Indian Institute of Technology, Delhi</foaf:organization>
<doac:title/>
<doac:date-starts>2007-01-01</doac:date-starts>
<doac:date-ends>2007-12-31</doac:date-ends>
<doac:subject>I wrote my Master's thesis at IIT under guidance of Prof. P. Jalote, in an exchange program by the German Academic Exchange Service (DAAD), from February to July 2007.</doac:subject>
</doac:Education>
</doac:education>
<doac:education>
<doac:Education>
<foaf:organization>Universität Karlsruhe (TH)</foaf:organization>
<doac:title>Diplom</doac:title>
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<doac:skill>Rails.</doac:skill>
<doac:skill>and</doac:skill>
<doac:skill>Ruby</doac:skill>
<doac:skill>AJAX</doac:skill>
<doac:skill>CSS</doac:skill>
<doac:skill>HTML</doac:skill>
<doac:skill>XML</doac:skill>
<doac:skill>REST</doac:skill>
<doac:skill>SOAP/WSDL</doac:skill>
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<doac:Experience>
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<doac:Experience>
<doac:title>Senior Programmer / Analyst</doac:title>
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<doac:title>Software Engineer</doac:title>
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<doac:Experience>
<doac:title>Research Associate</doac:title>
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<doac:Education>
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<doac:Experience>
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<doac:Experience>
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<doac:Experience>
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<doac:Experience>
<doac:title>visitor</doac:title>
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<doac:Experience>
<doac:title>attendee</doac:title>
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<doac:Experience>
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<doac:Education>
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<doac:Experience>
<doac:title>PhD Student</doac:title>
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<doac:title>Visiting fellow</doac:title>
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<doac:Experience>
<doac:title>Scientific programmer</doac:title>
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<doac:title>Researcher</doac:title>
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<doac:subject>Developed following ontologies:　Ontology of Genetic Susceptibility Factors(OGSF);Ontology of Geographic Region (OGR);Ontology of Glucose Metabolism Disorder (OGMD);Ontology for Genetic Interval (OGI) GeneticDiatebetes: an Integrated Relational Database on Genetics of Diabetes</doac:subject>
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<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=1510707"/>
<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=41305706"/>
<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=13686406"/>
<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=34770184"/>
<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=16314219"/>
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<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=35979245"/>
<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=37942607"/>
<foaf:member rdf:resource="http://www.linkedin.com/ppl/webprofile?id=4631981"/>
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</rdf:RDF>

That's it
Pierre