Resolving LSID: my notebook

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 LSID

urn:lsid:ubio.org:namebank:11815

ubio.org is the authority.It is followed by a database and an id.
We need to resolve this authority to find some metadata about this LSID object. On unix, we put _lsid._tcp before this authority and the host command is used to ask the "DNS for the lsid service record for pdb.org with TCP as the network protocol" (I'm not really sure of what it really means, and I guess this can be a problem for the other bioinformaticians too).

%host -t srv _lsid._tcp.ubio.org
_lsid._tcp.ubio.org has SRV record 1 0 80 ANIMALIA.ubio.org.

So http://ANIMALIA.ubio.org the is location of the LSID service. We append /authority and we get a WSDL file at http://animalia.ubio.org/authority/ (This WSDL is another issue for me, is there so many bioinformaticians knowing how to read such format ?).

<wsdl:definitions targetNamespace="http://www.hyam.net/lsid/Authority">
<import namespace="http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings"
location="LSIDAuthorityServiceHTTPBindings.wsdl"
/>
<wsdl:service name="MyAuthorityHTTPService">
<wsdl:port name="MyAuthorityHTTPPort" binding="httpsns:LSIDAuthorityHTTPBinding">
<httpsns:address location="http://animalia.ubio.org/authority/index.php"/>
</wsdl:port>
</wsdl:service>
</wsdl:definitions>

At http://animalia.ubio.org/authority/LSIDAuthorityServiceHTTPBindings.wsdl we get the Http bindings.

</><definitions targetNamespace="http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings">
<import namespace="http://www.omg.org/LSID/2003/Standard/WSDL" location="LSIDPortTypes.wsdl"/>
<binding name="LSIDAuthorityHTTPBinding" type="sns:LSIDAuthorityServicePortType">
<http:binding verb="GET"/>
<operation name="getAvailableServices">
<http:operation location="/authority/"/>
<input>
<http:urlEncoded/>
</input>
<output>
<mime:multipartRelated>
<mime:part>
<mime:content part="wsdl" type="application/octet-stream"/>
</mime:part>
</mime:multipartRelated>
</output>
</operation>
</binding>
</definitions>

This WSDL tells us that http://animalia.ubio.org/authority/ is the URL where we can find some metadata about the LSID and using http+GET. And, by appending metadata.php (why this php extension ? this is not clear for me ) you'll get the following RDF metadata about urn:lsid:ubio.org:namebank:11815 (Very cool, I like this idea of getting a RDF from one identifier). The process of resolving the WSDL can be achieved once and cached.

<rdf:RDF>
<rdf:Description rdf:about="urn:lsid:ubio.org:namebank:11815">
<dc:identifier>urn:lsid:ubio.org:namebank:11815</dc:identifier>
<dc:creator rdf:resource="http://www.ubio.org"/>
<dc:subject>Pternistis leucoscepus (Gray, GR) 1867</dc:subject>
<ubio:taxonomicGroup>Aves</ubio:taxonomicGroup>
<ubio:recordVersion>4</ubio:recordVersion>
<ubio:canonicalName>Pternistis leucoscepus</ubio:canonicalName>
<dc:title>Pternistis leucoscepus</dc:title>
<dc:type>Scientific Name</dc:type>
<ubio:lexicalStatus>Unknown (Default)</ubio:lexicalStatus>
<gla:rank>Species</gla:rank>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:954940"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:954941"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:1564236"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:783787"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:1580313"/>
<gla:mapping rdf:resource="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=classification&BLCHID=12-4498"/>
<gla:mapping rdf:resource="http://www.cbif.gc.ca/pls/itisca/next?v_tsn=553857&taxa=&p_format=&p_ifx=cbif&p_lang="/>
<gla:hasBasionym rdf:resource="urn:lsid:ubio.org:namebank:12292"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:12292"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762007"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762032"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762051"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:3408791"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1116259"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1137821"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1173817"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1174615"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1416177"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1672192"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:2233032"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:13853963"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1909656"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:2304281"/>
<dcterms:bibliographicCitation>Sclater, W.L., Systema Avium Ethiopicarum, p. 91</dcterms:bibliographicCitation>
</rdf:Description>
</rdf:RDF>

notebook EOF.

Taxonomy and Semantic Web: writing an extension for ARQ/SPARQL

In this post I'll show how I've implemented a custom function in ARQ, the SPARQL/Jena engine for querying a RDF graph. The new function implemented tests if a node in the NCBI-taxonomy hierarchy as a given ancestor.

Requirements

• Jena/ARQ: http://jena.sourceforge.net/ARQ/
• A java 1.6 compiler
• nodes.dmp , the ncbi taxonomy downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/

Here are a sample of the very first lines of nodes.dmp: the first column is the node-id of the taxon, the second column is its parent-id.

cat nodes.dmp | cut -c 1-20 | head
1 | 1 | no rank | |
2 | 131567 | superki
6 | 335928 | genus |
7 | 6 | species | AC
9 | 32199 | species
10 | 135621 | genus
11 | 10 | species |
13 | 203488 | genus
14 | 13 | species |
16 | 32011 | genus |

The input

our input is a RDF file:

<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:tax="http://species.lindenb.org"
>

<tax:Individual rdf:about="http://fr.wikipedia.org/wiki/Tintin">
<dc:title xml:lang="fr">Tintin</dc:title>
<dc:title xml:lang="en">Tintin</dc:title>
<tax:taxon rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:9606"/>
</tax:Individual>

<tax:Individual rdf:about="http://fr.wikipedia.org/wiki/Babar">
<dc:title xml:lang="fr">Babar</dc:title>
<dc:title xml:lang="en">Babar</dc:title>
<tax:taxon rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:9785"/>
</tax:Individual>

<tax:Individual rdf:about="http://fr.wikipedia.org/wiki/Milou">
<dc:title xml:lang="fr">Milou</dc:title>
<dc:title xml:lang="en">Snowy</dc:title>
<tax:taxon rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:9615"/>
</tax:Individual>

<tax:Individual rdf:about="http://fr.wikipedia.org/wiki/Donald_Duck">
<dc:title xml:lang="fr">Donald</dc:title>
<dc:title xml:lang="en">Donald Duck</dc:title>
<tax:taxon rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:8839"/>
</tax:Individual>

<tax:Individual rdf:about="http://fr.wikipedia.org/wiki/Le_L%C3%A9zard">
<dc:title xml:lang="fr">Lezard</dc:title>
<dc:title xml:lang="en">Lizard</dc:title>
<dc:title xml:lang="fr">Curt Connors</dc:title>
<dc:title xml:lang="en">Curt Connors</dc:title>
<tax:taxon rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:9606"/>
<tax:taxon rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:8504"/>
</tax:Individual>

</rdf:RDF>

Images via wikipedia

Tintin & Snowy

Babar

Donald

The Lizard

Basically this file describes

• 4 individuals: Tintin (human), Snowy (dog), Donal (duck) , Babar (Elephant) and Dr Connors/The Lizard (spiderman's foe)
• Each individual unambigously identified by his URI in wikipedia
• Each individual is named in english and in french
• For each individual, is ID in the NCBI hierarchy is specified using a simple URI (here I've tried to use a LSID, but it could have been something else (a URL... ))

A basic query

The following SPARQL query retrieve the URI, the taxonomy and the english name for each individuals.

The query

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX tax: <http://species.lindenb.org>

SELECT ?individual ?taxon ?title
{
?individual a tax:Individual .
?individual dc:title ?title .
?individual tax:taxon ?taxon .
FILTER langMatches( lang(?title), "en" )
}

Invoking ARQ

arq --query query01.rq --data taxonomy.rdf

Result

-------------------------------------------------------------------------------------------------------------
| individual | taxon | title |
=============================================================================================================
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:8504> | "Curt Connors"@en |
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:9606> | "Curt Connors"@en |
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:8504> | "Lizard"@en |
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:9606> | "Lizard"@en |
| <http://fr.wikipedia.org/wiki/Donald_Duck> | <lsid:ncbi.nlm.nih.gov:taxonomy:8839> | "Donald Duck"@en |
| <http://fr.wikipedia.org/wiki/Milou> | <lsid:ncbi.nlm.nih.gov:taxonomy:9615> | "Snowy"@en |
| <http://fr.wikipedia.org/wiki/Babar> | <lsid:ncbi.nlm.nih.gov:taxonomy:9785> | "Babar"@en |
| <http://fr.wikipedia.org/wiki/Tintin> | <lsid:ncbi.nlm.nih.gov:taxonomy:9606> | "Tintin"@en |
-------------------------------------------------------------------------------------------------------------

Adding a custom function

Now, I want to add a new function in sparql. This function 'isA' will take as input to parameters: the taxon/LSID of the child and the taxon/LSID of the parent and it will return a boolean 'true' if the 'child' has the 'parent' in his phylogeny. This new function is implemented by extending the class com.hp.hpl.jena.sparql.function.FunctionBase2. This new class contains an associative array child2parent mapping each taxon-id to its parent. This map is loaded as described bellow:

Pattern pat= Pattern.compile("[ \t]*\\|[ \t]*");
String line;
BufferedReader r= new BufferedReader(new FileReader(TAXONOMY_NODES_PATH));
while((line=r.readLine())!=null)
{
String tokens[]=pat.split(line, 3);
this.child2parent.put(
Integer.parseInt(tokens[0]),
Integer.parseInt(tokens[1])
);
}
r.close();
(...)

The function 'exec' will check if the two arguments are an URI and will invoke the method isChildOf

public NodeValue exec(NodeValue childNode, NodeValue parentNode)
{
(...check the nodes are URI)
return NodeValue.makeBoolean(isChildOf(childId,parentId));
}

The function 'isChildOf' loops in the map child2parent to check if the parent is an ancestor of the child:

while(true)
{
Integer id= child2parent.get(childid);
if(id==null || id==childid) return false;
if(id==parentid) return true;
childid=id;
}

Here is the complete source code of this class:

package org.lindenb.arq4taxonomy;

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.regex.Pattern;

import com.hp.hpl.jena.sparql.expr.ExprEvalException;
import com.hp.hpl.jena.sparql.expr.NodeValue;
import com.hp.hpl.jena.sparql.function.FunctionBase2;

public class isA
extends FunctionBase2
{
public static final String LSID="lsid:ncbi.nlm.nih.gov:taxonomy:";
public static final String TAXONOMY_NODES_PATH="/home/lindenb/tmp/TAXONOMY_NCBI/nodes.dmp";
private Map<Integer, Integer> child2parent=null;

public isA()
{

}
/**
* return a associative map child.id -> parent.id
* @return
*/
private Map<Integer, Integer> getTaxonomy()
{
if(this.child2parent==null)
{
this.child2parent= new HashMap<Integer, Integer>();
try
{
Pattern pat= Pattern.compile("[ \t]*\\|[ \t]*");
String line;
BufferedReader r= new BufferedReader(new FileReader(TAXONOMY_NODES_PATH));
while((line=r.readLine())!=null)
{
String tokens[]=pat.split(line, 3);
this.child2parent.put(
Integer.parseInt(tokens[0]),
Integer.parseInt(tokens[1])
);
}
r.close();
System.err.println(this.child2parent.size());
}
catch(IOException err)
{
err.printStackTrace();
throw new ExprEvalException(err);
}
}
return this.child2parent;
}

private boolean isChildOf(int childid,int parentid)
{
if(childid==parentid) return true;
Map<Integer,Integer> map= getTaxonomy();
while(true)
{
Integer id= map.get(childid);
if(id==null || id==childid) return false;
if(id==parentid) return true;
childid=id;
}
}

@Override
public NodeValue exec(NodeValue childNode, NodeValue parentNode)
{

if( childNode.isLiteral() ||
parentNode.isLiteral() ||
childNode.asNode().isBlank() ||
parentNode.asNode().isBlank())
{
return NodeValue.makeBoolean(false);
}

String childURI = childNode.asNode().getURI();
if(!childURI.startsWith(LSID))
{
return NodeValue.makeBoolean(false);
}


String parentURI = parentNode.asNode().getURI();
if(!parentURI.startsWith(LSID))
{
return NodeValue.makeBoolean(false);
}

int childId=0;
try {
childId= Integer.parseInt(childURI.substring(LSID.length()));
}
catch (NumberFormatException e)
{
return NodeValue.makeBoolean(false);
}

int parentId=0;
try {
parentId= Integer.parseInt(parentURI.substring(LSID.length()));
}
catch (NumberFormatException e)
{
return NodeValue.makeBoolean(false);
}

return NodeValue.makeBoolean(isChildOf(childId,parentId));
}

}

This class is then compiled and packaged into the file tax.jar:

javac -cp $(ARQ_CLASSPATH):. -sourcepath src src/org/lindenb/arq4taxonomy/isA.java
jar cvf tax.jar -C src org

and we add this jar in the classpath:

export CP=$PWD/tax.jar

To tell ARQ about this new functio,n we just add its classpath as a new PREFIX in the SPARQL query:

PREFIX fn: <java:org.lindenb.arq4taxonomy.>

First test

the following SPARQL query retrieves all the Mammals (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=40674) in the data set.

The query

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX tax: <http://species.lindenb.org>
PREFIX fn: <java:org.lindenb.arq4taxonomy.>

SELECT ?individual ?taxon ?title
{
?individual a tax:Individual .
?individual dc:title ?title .
?individual tax:taxon ?taxon .
FILTER fn:isA(?taxon,<lsid:ncbi.nlm.nih.gov:taxonomy:40674> )
FILTER langMatches( lang(?title), "en" )
}

The command line

arq --query query02.rq --data taxonomy.rdf

The result

-------------------------------------------------------------------------------------------------------------
| individual | taxon | title |
=============================================================================================================
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:9606> | "Curt Connors"@en |
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:9606> | "Lizard"@en |
| <http://fr.wikipedia.org/wiki/Milou> | <lsid:ncbi.nlm.nih.gov:taxonomy:9615> | "Snowy"@en |
| <http://fr.wikipedia.org/wiki/Babar> | <lsid:ncbi.nlm.nih.gov:taxonomy:9785> | "Babar"@en |
| <http://fr.wikipedia.org/wiki/Tintin> | <lsid:ncbi.nlm.nih.gov:taxonomy:9606> | "Tintin"@en |
-------------------------------------------------------------------------------------------------------------

Second query

the following SPARQL query retrieves all the 'Sauropdias' (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=8457) in the RDF file.

The SPARQL file

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX tax: <http://species.lindenb.org>
PREFIX fn: <java:org.lindenb.arq4taxonomy.>

SELECT ?individual ?taxon ?title
{
?individual a tax:Individual .
?individual dc:title ?title .
?individual tax:taxon ?taxon .
FILTER fn:isA(?taxon,<lsid:ncbi.nlm.nih.gov:taxonomy:8457> )
FILTER langMatches( lang(?title), "en" )
}

Command line

arq --query query03.rq --datataxonomy.rdf

The result

-------------------------------------------------------------------------------------------------------------
| individual | taxon | title |
=============================================================================================================
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:8504> | "Curt Connors"@en |
| <http://fr.wikipedia.org/wiki/Le_L%C3%A9zard> | <lsid:ncbi.nlm.nih.gov:taxonomy:8504> | "Lizard"@en |
| <http://fr.wikipedia.org/wiki/Donald_Duck> | <lsid:ncbi.nlm.nih.gov:taxonomy:8839> | "Donald Duck"@en |
-------------------------------------------------------------------------------------------------------------

Et hop ! voila ! That's it !

Seven deadly sins of bioinformatics

Via NodalPoint.
Keynote talk from Carole Goble at BOSC SIG from ISMB 2007 in Vienna, July 2007.

Inside LSID

This post is my notes about LSID but it has nothing todo with the current "LSID wars".

There is no or no good documentation about the life science identifiers(LSID). Did you just try to read the specs ? houch... I'm a biologist not a network engineer. Fortunately the sources of the firefox add-on for LSID where very informative. It shows what happen when you enter a LSID in the browser. (Note: Roderic Page has also implemented is own firefox extension for LSID, see http://lsid.mozdev.org/))

Say, you have a LSID identifier:

urn:lsid:ubio.org:namebank:11815

The third part of this uri (ubio.org) is called the authority. By default the plugin looks at http://ubio.org:9090/authority to find a "WSDL" file.

OK, and this is where I've got a problem: the default behavior of the firefox add-on failed in most cases I've tested.
For instance, dcc.hapmap.org:9090/authority does not work with urn:LSID:dcc.hapmap.org:Individual:JA18942:1. So I guess that there must be a way to find this authority from the LSID itself (biomoby?) but I still have not find how.

Here I added the server http://www.ubio.org/authority in the preferences of the add-ons just because I found the URL by chance

Here is the WSDL file found at http://www.ubio.org/authority:

<?xml version="1.0"?>
<wsdl:definitions xmlns:tns="http://www.hyam.net/lsid/Authority"
targetNamespace="http://www.hyam.net/lsid/Authority"
xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:httpsns="http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings">

<import namespace="http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings" location="LSIDAuthorityServiceHTTPBindings.wsdl" />

<wsdl:service name="MyAuthorityHTTPService">
<wsdl:port name="MyAuthorityHTTPPort" binding="httpsns:LSIDAuthorityHTTPBinding">
<httpsns:address location="http://www.ubio.org/authority/index.php" />
</wsdl:port>
</wsdl:service>

</wsdl:definitions>

Tthe prefix associated with the namespace http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings is then searched (There may be other bindings than HTTP: SOAP, FTP...). Here it is httpsns. The <wsdl:port> element having an attribute binding containing httpsns:LSIDAuthorityHTTPBinding" contains a child element with an attribute "location". Here the value of "location" is "http://www.ubio.org/authority/index.php". We then ask some informations about our LSID from this URL by adding a parameter "lsid=[the-lsid]" at the end of the URL: http://www.ubio.org/authority/index.php?lsid=urn:lsid:ubio.org:namebank:11815. The result is, again a WSDL file:

<?xml version="1.0"?>
<definitions xmlns:tns="http://www.example.org/SampleDataServices"
targetNamespace="http://www.example.org/SampleDataServices"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns="http://schemas.xmlsoap.org/wsdl/"
xmlns:http="http://schemas.xmlsoap.org/wsdl/http/"
xmlns:httpsns="http://www.omg.org/LSID/2003/DataServiceHTTPBindings"
>

<import namespace="http://www.omg.org/LSID/2003/DataServiceHTTPBindings" location="LSIDDataServiceHTTPBindings.wsdl" />

<!-- Example HTTP GET Services (urlEncoding) -->
<service name="MyDataHTTPService">
<port name="MyDataServiceHTTPPort" binding="httpsns:LSIDDataHTTPBinding">
<http:address location="http://www.ubio.org/authority/data.php" />
</port>
</service>
<service name="MyMetadataHTTPService">
<port name="MyMetadataServiceHTTPPort" binding="httpsns:LSIDMetadataHTTPBinding">
<http:address location="http://www.ubio.org/authority/metadata.php" />
</port>
</service>
</definitions>

Again, from this xml file, we obtain two URLs: http://www.ubio.org/authority/data.php and http://www.ubio.org/authority/metadata.php are the URL respectively used to fetch the data and the metadata about the LSID.

http://www.ubio.org/authority/data.php?lsid=urn:lsid:ubio.org:namebank:11815 returns
http://www.ubio.org/authority/data.php?lsid=urn:lsid:ubio.org:namebank:11815 (???)

Here is the Metadata/RDF file fetched from http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:11815

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:ubio="urn:lsid:ubio.org:predicates:"
xmlns:gla="urn:lsid:lsid.zoology.gla.ac.uk:predicates:"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">

<rdf:Description rdf:about="urn:lsid:ubio.org:namebank:11815">
<dc:identifier>urn:lsid:ubio.org:namebank:11815</dc:identifier>
<dc:creator rdf:resource="http://www.ubio.org"/>
<dc:subject>Pternistis leucoscepus (Gray, GR) 1867</dc:subject>
<ubio:taxonomicGroup>Aves</ubio:taxonomicGroup>
<ubio:recordVersion>4</ubio:recordVersion>
<ubio:canonicalName>Pternistis leucoscepus</ubio:canonicalName>
<dc:title>Pternistis leucoscepus</dc:title>
<dc:type>Scientific Name</dc:type>
<ubio:lexicalStatus>Unknown (Default)</ubio:lexicalStatus>
<gla:rank>Species</gla:rank>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:954940"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:954941"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:1564236"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:783787"/>
<gla:vernacularName rdf:resource="urn:lsid:ubio.org:namebank:1580313"/>
<gla:mapping rdf:resource="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=classification&amp;BLCHID=12-4498"/>
<gla:mapping rdf:resource="http://www.cbif.gc.ca/pls/itisca/next?v_tsn=553857&amp;taxa=&p_format=&p_ifx=cbif&p_lang="/>
<gla:hasBasionym rdf:resource="urn:lsid:ubio.org:namebank:12292"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:12292"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762007"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762032"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:1762051"/>
<gla:objectiveSynonym rdf:resource="urn:lsid:ubio.org:namebank:3408791"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1116259"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1137821"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1173817"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1174615"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1416177"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1672192"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:2233032"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:12798879"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:1909656"/>
<ubio:hasCAVConcept rdf:resource="urn:lsid:ubio.org:classificationbank:2304281"/>
<dcterms:bibliographicCitation>Sclater, W.L., Systema Avium Æthiopicarum, p. 91</dcterms:bibliographicCitation>
</rdf:Description>
</rdf:RDF>

URL +1, LSID -1

"URL +1, LSID -1" is the name of the current thread on "public-semweb-lifesci":
http://www.mail-archive.com/public-semweb-lifesci@w3.org/index.html#02766
This discussion (worth looking) is about the life science identifier 'LSID) and it was started by Eric Jain:

In the latest release of UniProt (11.3), all URIs of the form:

urn:lsid:uniprot.org:{db}:{id}

have been replaced with URLs:

http://purl.uniprot.org/{db}/{id}

In general, these URLs can be resolved to a human readable web page (a few are still broken, will be fixed). Some of these web pages may (or may not) be linked to a machine-readable representation via link-rel=alternate.

As an optimization for "Semantic Web" crawlers, there is experimental support for "Accept" headers (i.e. set it to "application/rdf+xml").

Some examples:

http://purl.uniprot.org/uniprot/P12345
http://purl.uniprot.org/taxonomy/9606
http://purl.uniprot.org/pdb/1BRC

Among the protagonists we can find Roderic Page, Michel Dumontier, Mark Wilkinson, Alan Ruttenberg, Dany Ayers, etc...

---

Life Science Identifiers (LSIDs) are persistent, location-independent, resource identifiers for uniquely naming biologically significant resources including species names, concepts, occurrences, genes or proteins, or data objects that encode information about them. To put it simply, LSIDs are a way to identify and locate pieces of biological information on the web.

As far I understand LSID, we all should use lsid:ncbi.nlm.nih.gov:pubmed:12507336 instead of http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=12507336&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum or http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&uid=12507336. (Note that the two later URL are not the same but they point to the same article). An LSID resolver can also be used to find/discover some other (RDF based) properties about your object.

In the thread a firefox extension resolving lSID uri was described: I just installed it on my firefox and it looks nice and the code looks really interesting: it shows how to create a firefox extension which will insert a new handler for a new internet protocol named "lsidres:".


(...)
LsidModule.registerSelf = function (compMgr, location, loaderStr, type){

// http://developer.mozilla.org/xpcom/api/nsIComponentRegistrar/
compMgr = compMgr.QueryInterface(Components.interfaces.nsIComponentRegistrar);
compMgr.registerFactoryLocation(LSIDPROT_HANDLER_CID,
"Protocol handler for LSID",
"@mozilla.org/network/protocol;1?name=lsidres",
location, loaderStr, type);

}
(...)



Then when a hyperlink in a HTML page (such as lsidres:urn:lsid:ubio.org:namebank:11815) is activated, firefox open a new window, calls a remote LSID resolver and displays the properties of your object.

Pierre

Systems-Biology using GoogleGears: my notebook

Google gears is an open source browser extension that enables web applications to provide offline functionality. The data are stored locally in a fully-searchable relational database using the sqlite engine.

My Biological Network is a tool I created as a test to play with Google gears: it is used to build a network of protein-protein interactions. It uses Google Gears to record your entries on the local disk, so Gears needs to be installed on your computer. Programming with gears with JAVASCRIPT is really cool as you don't have to implement the storage of the data on the server side and you're using some standard SQL statements to handle the data.

http://www.urbigene.com/gears/mynetwork/

Screenshots

Tutorial

Open the tab Organism (fig. 4): add one or more organism. (Homo Sapiens already inserted by default)

Open the tab Protein (fig. 1): add one or more protein.

Open the tab Paper (fig. 3): add one or more article that will be used as an evidence for an interaction.

Open the tab Technology (fig. 2): add one or more technology that was used to characterize an interaction.

Open the tab Component: add one or more cellular component using Gene Ontology (GO:0005575 \"cellular component\" was inserted by default)

Open the tab Interaction (fig. 5):

• Name and describe this interaction


• Select one or more protein and/or one or more previously defined proteic complex. You Cannot describe self interactions with this tool.
• 
  
• (optional) choose one or more paper/technology/component...

Open the RDF table (fig. 6): I choose to display the content of the database using RDF. Such format can then be validated and visualized using the W3C RDF validator, or transformed using XSLT, etc.... I also used the life science identifier (LSID) as an URI for my resources.

On my computer, the database is stored in /env/islande/home/lindenb/.mozilla/firefox/<profile-id>/Google Gears for Firefox/islande/<host>/mynetwork#database. The database can be manualy accessed using sqlite3:

sqlite3 mynetwork#database
SQLite version 3.4.0
Enter '.help' for instructions
sqlite> .tables
component        interactionhash  paper            technology
interaction      organism         prote
sqlite> .schema organism
CREATE TABLE organism(id integer  primary key ,name varchar(50) not null unique);
sqlite> select * from organism;
9606|Homo Sapiens
sqlite>

Internals

We the page is loaded, we check that gears was installed

  if (!window.google || !google.gears) {
    debug("NOTE:  You must install Google Gears first.")

We then create the database if does not exist. The file is created in firefox in ${HOME}/.mozilla/firefox/<profile-id>/Google Gears for Firefox/<server>/mynetwork#database

connection = google.gears.factory.create("beta.database","1.0");

I create the tables just by invoking some standards SQL 'CREATE TABLE' statements. I also insert some default values (e.g. human organism)

        connection.execute("create table  if not exists  organism(id integer  primary key ,name varchar(50) not null unique)");
        connection.execute("insert or ignore into organism(id,name) values(9606,\"Homo Sapiens\")");
        connection.execute("create table if not exists protein(id integerprimary key autoincrement,name varchar(50)  not null,taxId int  not null,acn varchar(50)  not null unique)");
        connection.execute("create table if not exists paper(pmid integerprimary key ,title varchar(255)  not null,citation varchar(255)  not null,firstAuthor varchar(50)  not null)");
        connection.execute("create table if not exists component(id integer primary key autoincrement,go varchar(50)  not null unique, name varchar(50)  not null unique)");

        connection.execute("insert or ignore into component(go,name) values(\"GO:0005575\",\"cellular component\")");
        connection.execute("insert or ignore into component(go,name) values(\"GO:0008372\",\"cellular component unknown\")");

        connection.execute("create table if not exists technology(id integer  primary key autoincrement,name varchar(50) not null unique, description varchar(255)  not null)");

        connection.execute("insert or ignore into technology(name,description) values(\"Y2H\",\"Yeast Two Hybrid System\")");
        connection.execute("insert or ignore into technology(name,description) values(\"CoIP\",\"Co-Immuno Precipitation\")");


        connection.execute("create table if not exists interaction(id integer  primary key autoincrement, name varchar(50)  not null  unique,description varchar(255)  not null)");
        connection.execute("create table if not exists interactionhash(id integer  primary key autoincrement,LINK_interaction int ,type varchar(20) not null,child int  not null)");

When a data is about to be inserted we check all the fields and we insert them using SQL: INSERT INTO

var id= getById("organism-input-id");
if(!isInteger(id.value))
        {
        debug("TaxId not a Number");
        return;
        }
var name=getById("organism-input-name");
if(trim(name.value).length==0)
        {
        debug("Taxon Name empty");
        return;
        }

try
        {
        connection.execute("insert into organism(id,name) values("+sqlescape(trim(id.value))+","+sqlquote(trim(name.value))+")");
        id.value="";
        name.value="";
        }
catch(err)
        {
        debug(err.message);
        return;
        }

a simple SELECT is used to retrieve the data and insert them in a HTML table

 var rs= connection.execute("select id,name from organism order by name");
 while (rs.isValidRow())
  {
  var tr= ce("tr");
  table.appendChild(tr);
  var td= ce("td");
  tr.appendChild(td);
  td.appendChild(ct(rs.field(0)));

  td= ce("td");
  tr.appendChild(td);
  var a= ce("a");
  a.setAttribute("title","Open in NCBI");
  a.setAttribute("target","tax"+rs.field(0));
  a.setAttribute("href","http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+rs.field(0));
  td.appendChild(a);
  a.appendChild(ct(rs.field(1)));
  rs.next();
  }
 rs.close();

That's it !

Pierre

updated 2010-08-12: source code

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<script type="text/javascript" src="gears_init.js"></script>
<script type="text/javascript" src="network.js"></script>
<link rel="stylesheet" type="text/css" href="./network.css" />
<title>My Biological Network</title>
</head>
<body onload="init()">
<h1>My Biological Network</h1>
<p>Pierre Lindenbaum PhD <a href="mailto:plindenbaum@yahoo.fr">plindenbaum@yahoo.fr</a><br/><a href="http://plindenbaum.blogspot.com">http://plindenbaum.blogspot.com</a><br/><address>Bioinformatics department<br/><a href="http://www.integragen.com">Integragen S.A.</a><br/>Evry, France</address></p>
<p/>
<div>
<button onclick="javascript:showCard('home-pane');">Home</button>
<button onclick="showOrganismPane()">Organisms</button>
<button onclick="showProteinPane()">Proteins</button>
<button onclick="showPaperPane()">Papers</button>
<button onclick="showTechnologyPane()">Technology</button>
<button onclick="showComponentPane()">Component</button>
<button onclick="showInteractionPane()">Interactions</button>
<button onclick="showRDFPane()">RDF</button>
</div>
<div style="color:red;" id="stderr"></div>
<p/>

<!-- ====================================== ORGANISM ====================================== -->
<div style="display:none;" id="organism-pane">
<table>
<caption>Add an Organism</caption>
<tr><th>NCBI Taxon ID <i>(e.g. 10912)</i></th><td><input id="organism-input-id" length="10"/></td></tr>
<tr><th>NCBI Taxon Name <i>(e.g. Rotavirus)</i></th><td><input id="organism-input-name" length="10"/></td></tr>
<tr><th/><td><button onclick="addOrganism()">Add</button></td></tr>
</table>

<hr/>

<table width="80%">
<caption>All Organisms</caption>
<thead>
<tr><th>Taxon ID</th><th>Taxon Name</th></tr></tr>
</thead>
<tbody id="organism-table">
</tbody>
</table>

</div>

<!-- ====================================== COMPONENT ====================================== -->
<div style="display:none;" id="component-pane">
<table>
<caption>Add a Component</caption>
<tr><th>Name</th><td><input id="component-input-name" length="10"/></td></tr>
<tr><th>GO</th><td><input id="component-input-go" length="10"/></td></tr>
<tr><th/><td><button onclick="addComponent()">Add</button></td></tr>
</table>

<hr/>

<table width="80%">
<caption>All Components</caption>
<thead>
<tr><th>Name</th><th>GO</th></tr>
</thead>
<tbody id="component-table">
</tbody>
</table>

</div>

<!-- ====================================== TECHNOLOGY ====================================== -->
<div style="display:none;" id="technology-pane">
<table>
<caption>Add a Technology</caption>
<tr><th>Name</th><td><input id="technology-input-name" length="50"/></td></tr>
<tr><th>Description</th><td><input id="technology-input-desc" length="50"/></td></tr>
<tr><th/><td><button onclick="addTechnology()">Add</button></td></tr>
</table>

<hr/>

<table width="80%">
<caption>All Technologies</caption>
<thead>
<tr><th>Name</th><th>Description</th></tr></tr>
</thead>
<tbody id="technology-table">
</tbody>
</table>

</div>


<!-- ====================================== PROTEIN ====================================== -->

<div style="display:none;" id="protein-pane">
<table>
<caption>Add a Protein</caption>
<tr><th>Uniprot accession number <i>(e.g. Q3T8J2)</i></th><td><input id="protein-input-acn" length="10"/></td></tr>
<tr><th>Uniprot Name <i>(e.g. Replicase polyprotein 1ab)</i></th><td><input id="protein-input-name" length="10"/></td></tr>
<tr><th>Organism</th><td><select id="protein-input-taxon" length="10"><option>A</option></select></td></tr>
<tr><th/><td><button onclick="addProtein()">Add</button></td></tr>
</table>

<hr/>

<table width="80%">
<caption>All Proteins</caption>
<thead>
<tr><th>Primary accession</th><th>Name</th><th>Taxon</th></tr></tr>
</thead>
<tbody id="protein-table">
</tbody>
</table>

</div>

<!-- ====================================== PAPER ====================================== -->
<div style="display:none;" id="paper-pane">
<table>
<caption>Add a Paper</caption>
<tr><th>PMID</th><td><input id="paper-input-pmid" length="10"/></td></tr>
<tr><th>Title</th><td><input id="paper-input-title" length="50"/></td></tr>
<tr><th>Citation</th><td><input id="paper-input-citation" length="50"/></td></tr>
<tr><th>First Author</th><td><input id="paper-input-author" length="50"/></td></tr>
<tr><th/><td><button onclick="addPaper()">Add</button></td></tr>
</table>

<hr/>

<table width="80%">
<caption>All Papers</caption>
<thead>
<tr><th>PMID</th><th>Citation</th><th>First Author</th><th>Title</th></tr></tr>
</thead>
<tbody id="paper-table">
</tbody>
</table>

</div>

<!-- ====================================== INTERACTION ====================================== -->


<div style="display:none;" id="interaction-pane">

<table>
<caption>Add an Interaction</caption>
<tr><th>Name</th><td colspan="4"><input id="interaction-input-name" length="50"/></td></tr>
<tr><th>Description</th><td colspan="4"><input id="interaction-input-desc" length="50"/></td></tr>
<tr>
<th>Protein</th>
<th>Interactors</th>
<th>Methods</th>
<th>Evidences</th>
<th>Components</th></tr>
<tr>
<td><select id="interactors-input-proteins" size="5" multiple="true"/></td>
<td><select id="interactors-input-interactors" size="5" multiple="true"></td>
<td><select id="interactors-input-technologies" size="5" multiple="true"></td>
<td><select id="interactors-input-evidences" size="5" multiple="true"></td>
<td><select id="interactors-input-components" size="5" multiple="true"></td>
</tr>
<tr><th colspan="4"/><td><button onclick="addInteraction()">Add</button></td></tr>
</table>

<hr/>

<table width="80%">
<caption>All Interactions</caption>
<thead>
<tr><th>Name</th><th>Description</th></tr></tr>
</thead>
<tbody id="interaction-table">
</tbody>
</table>

</div>

<!-- ====================================== RDF ====================================== -->
<div style="display:none;" id="rdf-pane">
<h2>RDF Pane</h2>
<textarea wrap="off" id="rdf-area" rows="20" cols="80"></textarea>

</div>

<!-- ====================================== HOME ====================================== -->
<div style="display:none;" id="home-pane">
<h3>About My Biological Network</h3>
<p><a href="http://gears.google.com/">Google gears</a> is an open source browser extension that enables web applications to provide offline functionality. The data are stored locally in a fully-searchable relational database using the <a href="http://www.sqlite.org/">sqlite engine</a>.</p>
<p><b>My Biological Network</b> is a tool I created as a test to play with Google gears: it is used to build a network of protein-protein interactions. It uses Google Gears to record your entries on the <u>local disk</u>, so Gears needs to be installed on your computer. </p>

<p>
Open the tab <b>Organism</b>: add one or more organism. (Homo Sapiens already inserted by default)<br/>
Open the tab <b>Protein</b>: add one or more protein.<br/>
Open the tab <b>Paper</b>: add one or more article that will be used as an evidence for an interaction.<br/>
Open the tab <b>Technology</b>: add one or more technology that was used to characterize an interaction.<br/>
Open the tab <b>Component</b>: add one or more cellular component using Gene Ontology (GO:0005575 \"cellular component\" was inserted by default)<br/>
Open the tab <b>Interaction</b>:<ul>
<li>Name and describe this interaction</li>
<li>Select one or more protein and/or one or more previously defined proteic complex. You <i>Cannot</i> describe self interactions with this tool.<li>
<li>(optional) choose one or more paper/technology/component...</li>
</ul><br/>
Open the <b>RDF table</b>: I choose to display the content of the database using <a href="http://www.w3.org/RDF/">RDF</a>. Such format can then be validated and visualized using the <a href="http://www.w3.org/RDF/Validator/">W3C RDF validator</a>, or transformed using <a href="http://www.w3.org/TR/xslt">XSLT</a>, etc.... I also used the <a href="http://lsid.sourceforge.net/">life science identifier (LSID)</a> as an URI for my resources.<br/>

</p>

<p>On my computer, the database is stored in <code>$HOME/.mozilla/firefox/&lt;profile-id&gt;/Google Gears for Firefox/&lt;host&gt;/mynetwork#database</code>. The database can be manualy accessed using <a href="http://www.sqlite.org/">sqlite3</a>:<pre style='color:black;border:1pt solid;background:lightgray;'>sqlite3 mynetwork#database
SQLite version 3.4.0
Enter &apos;.help&apos; for instructions
sqlite&gt; .tables
component interactionhash paper technology
interaction organism prote
sqlite&gt; .schema organism
CREATE TABLE organism(id integer primary key ,name varchar(50) not null unique);
sqlite&gt; select * from organism;
9606|Homo Sapiens
sqlite&gt;</pre>

</p>

</div>


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Wilkinson's "The Declaration of Semantic Web Independence"

Mark Wilkison has posted a :

Declaration of Semantic Web Independence

For more details see: ttp://biordf.org/wilkinsonlab/index.php/all/2007/05/17/semantic_declaration_of_independence

1. Ontologies are a path to a goal, not the goal itself.
   
   • Ontologies are World Views
   • World Views are Hypotheses
   • Hypotheses are Queries
   • Queries are Disposable
   • Therefore Ontologies are (should be) Disposable!


2. Reasoning is your problem, not mine!


3. LSIDs provide a great way of solving the ontology-segmentation problem


4. Ontological predicates can be thought of as, and mapped to, Web Service