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March 30, 2012, at 08:01 AM by 138.100.11.51 -
Changed lines 21-24 from:
ftp://bioinformatics.org/pub/RDFBuilder/ or http://ftp.bioinformatics.org/pub/RDFBuilder/

(If both these links are down please use http://achucarro.dia.fi.upm.es:8080/RDFBuilder/)
to:
http://www.bioinformatics.org/ftp/pub/RDFBuilder/

(If this link is down please use http://achucarro.dia.fi.upm.es:8080/RDFBuilder/)
March 30, 2012, at 07:51 AM by 138.100.11.51 -
Changed lines 21-26 from:
ftp://bioinformatics.org/pub/RDFBuilder/

or

http://ftp.bioinformatics.org/pub/RDFBuilder/
to:
ftp://bioinformatics.org/pub/RDFBuilder/ or http://ftp.bioinformatics.org/pub/RDFBuilder/

(If both these links are down please use http://achucarro.dia.fi.upm.es:8080/RDFBuilder/)
September 05, 2011, at 06:07 AM by 138.100.11.51 -
Changed lines 121-122 from:
<limit-experiment-count>300</limit-experiment-count>
<limit-vector-ranges>10000</limit-vector-ranges>
to:
<limit-experiment-count>5</limit-experiment-count>
<limit-vector-ranges>100</limit-vector-ranges>
September 05, 2011, at 06:07 AM by 138.100.11.51 -
Changed line 42 from:
Using RDFbuilder, a researchers can submit SPARQL queries for ArrayExpress and receive results in SPARQL results
to:
Using RDFbuilder, researchers can submit SPARQL queries for ArrayExpress and receive results in SPARQL results
Changed line 86 from:
String experimentId = "E-GEOD-21068"; \\
to:
String experimentId = "E-GEOD-1509"; \\
Changed lines 101-103 from:
Inside this tag there is one mandatory tag named <base-dir>, and two optional tags named limit-experiment-count and
limit-vector-ranges.
to:
Inside this tag there is one mandatory tag named <base-dir>, and two optional tags named <limit-experiment-count> and <limit-vector-ranges>.
August 25, 2011, at 05:55 AM by 138.100.11.51 -
Changed lines 107-108 from:
"mage-rdf-model-empty.obm" that comes bundled with the library.
to:
August 25, 2011, at 05:52 AM by 138.100.11.51 -
Added lines 21-24:
ftp://bioinformatics.org/pub/RDFBuilder/

or
Changed lines 27-33 from:
or

ftp://bioinformatics.org/pub/RDFBuilder/

Please read the README.TXT file contained in this ftp to learn the purpose of the available files.

to:
Please read the README.TXT file contained in this ftp to learn the purpose of the available files, or read the subsection "Standalone installation" below.

August 25, 2011, at 05:47 AM by 138.100.11.51 -
Changed lines 19-20 from:
There is a README.TXT file in the project root which explains how to use the library, plus several examples. Precompiled jars can also be downloaded from the project's download directory, available at:
to:
There is a README.TXT file in the project root which explains how to use the library, plus several examples. Precompiled jars, documentation and files needed for installation can also be downloaded from the project's download directory, available at:
Added lines 23-29:
or

ftp://bioinformatics.org/pub/RDFBuilder/

Please read the README.TXT file contained in this ftp to learn the purpose of the available files.

Changed lines 60-61 from:
the following web page: http://servet.dia.fi.upm.es:8080/ArrayExpressWrapperWeb/.
to:
the following web page: ftp://bioinformatics.org/pub/RDFBuilder/.
August 22, 2011, at 02:53 PM by 138.100.11.51 -
Changed lines 59-64 from:
- The JavaDoc documentation of the API
- An example configuration file named aewrapperConfig.xml, contained in the directory /AEWRAPPER_CONFIG
- The file mage-rdf-model-empty.obm, contained in the directory /baseRDFModel
- The mage-rdf-model-empty.owl file, containing the RDF-based schema of ArrayExpress (this schema defines the
valid SPARQL queries)
to:
- The JavaDoc documentation of the API, inside the javadoc.rar file
- An example configuration file, named aewrapperConfig.xml (see instructions below for editing and placing this file)
- The file mage-rdf-model-empty.obm, for internal use of the library. After a directory has been configured as cache directory for the library, this file must be placed inside that directory.
- The mage-rdf-model-empty.owl file, containing the RDF-based schema of ArrayExpress (this schema defines the valid SPARQL queries)
August 22, 2011, at 02:40 PM by 138.100.11.51 -
Changed lines 110-111 from:
In this example, the file mage-rdf-model-empty.obm should be placed inside C:\ArrayExpressWrapper\ \\
to:
In this example, the file mage-rdf-model-empty.obm should be placed inside C:\ArrayExpressWrapper\ \\\
August 22, 2011, at 02:39 PM by 138.100.11.51 -
Changed lines 110-111 from:
In this example, the file mage-rdf-model-empty.obm should be placed inside C:\ArrayExpressWrapper\
to:
In this example, the file mage-rdf-model-empty.obm should be placed inside C:\ArrayExpressWrapper\ \\
August 22, 2011, at 02:39 PM by 138.100.11.51 -
Changed lines 99-100 from:
directory and it is necessary for the proper functioning of the library.
Inside this directory there must by another directory named "baseRDFModel", containing the file
to:
directory and it is necessary for the proper functioning of the library. Inside this directory we must also place
the "mage-rdf-model-empty.obm" file that comes bundled with this library.
Changed lines 110-111 from:
In this example, the file mage-rdf-model-empty.obm should be placed in C:\ArrayExpressWrapper\baseRDFModel\
to:
In this example, the file mage-rdf-model-empty.obm should be placed inside C:\ArrayExpressWrapper\
August 22, 2011, at 02:29 PM by 138.100.11.51 -
Deleted lines 132-137:
Inside this tag there is only one tag named <base-dir>. The content of this tag must be the directory in which we
want RDFbuilder to place the cache (for example, <base-dir>C:\AEWrapper</base-dir>). Inside the cache directory we
must place the /baseRDFModel bundled in the API download (and the file mage-rdf-model-empty.obm should be inside it).
In our example, we should have the following path: C:/AEWrapper/baseRDFModel/mage-rdf-model-empty.obm.

August 22, 2011, at 02:28 PM by 138.100.11.51 -
Deleted lines 111-112:
///////////////////////////////////////////////////////////////////////////
August 22, 2011, at 02:27 PM by 138.100.11.51 -
Added lines 94-134:

Inside this tag there is one mandatory tag named <base-dir>, and two optional tags named limit-experiment-count and
limit-vector-ranges.

The value in the base-dir tag indicates the directory where the cache will be placed. This must be a valid
directory and it is necessary for the proper functioning of the library.
Inside this directory there must by another directory named "baseRDFModel", containing the file
"mage-rdf-model-empty.obm" that comes bundled with the library.

Example of config file (for a windows system with the cache base dir in C:\ArrayExpressWrapper)

<?xml version="1.0" encoding="UTF-8"?>
<aewrapper-config>
<base-dir>C:\ArrayExpressWrapper</base-dir>
</aewrapper-config>

In this example, the file mage-rdf-model-empty.obm should be placed in C:\ArrayExpressWrapper\baseRDFModel\

///////////////////////////////////////////////////////////////////////////

Another example of config file, including the two optional tags:

<?xml version="1.0" encoding="UTF-8"?>
<aewrapper-config>
<base-dir>C:\ArrayExpressWrapper</base-dir>
<limit-experiment-count>300</limit-experiment-count>
<limit-vector-ranges>10000</limit-vector-ranges>
</aewrapper-config>

In this example, with the optional tags we add two restrictions:

- We limit the number of experiments that are retrieved from the array express database to 300. This is to prevent
the retrieval of too many databases in order to solve queries with keywords. For example, if a query is submitted
with the keyword "organism", more than 23000 related experiments are found. Only downloading this amount of
data could take several days. This value limit the number of downloaded experiments for answering a single query

- We limit the number of instances that are loaded from each MAGE-ML model (discarding the rest). This
is useful if we want to execute the software in machines with fairly limited RAM size. With a value of 10000,
the data should fit in a machine with 4GB of RAM. NOTE: adjust your java configuration to accept this amount
of memory. To do this see for example http://www.caucho.com/resin-3.0/performance/jvm-tuning.xtp
Added line 140:
August 22, 2011, at 01:10 PM by 138.100.11.51 -
Changed lines 1-2 from:
== Introduction ==
to:
! Introduction
August 22, 2011, at 01:10 PM by 138.100.11.51 -
Changed lines 1-2 from:
! Introduction
to:
== Introduction ==
August 22, 2011, at 08:47 AM by 138.100.11.51 -
Changed lines 1-2 from:
==Introduction==
to:
! Introduction
Changed lines 13-14 from:
==Downloads==
to:
! Downloads
August 22, 2011, at 08:46 AM by 138.100.11.51 -
Changed lines 13-14 from:
! Downloads
to:
==Downloads==
August 22, 2011, at 08:45 AM by 138.100.11.51 -
Changed lines 1-2 from:
! Introduction
to:
==Introduction==
August 22, 2011, at 08:40 AM by 138.100.11.51 -
Changed lines 71-78 from:
||String query = "PREFIX base: <http://aewrapper#>\n" \\
"SELECT ?id ?name ?desc_text\n" \\
"WHERE {\n" \\
"?exp base:identifier_string ?id .\n" \\
"?exp base:name_string ?name .\n" \\
"?exp a base:Experiment.Experiment .\n" \\
"?exp base:descriptions ?desc .\n" \\
"?desc base:text_string ?desc_text .\n" \\
to:
||String query = "PREFIX base: <http://aewrapper#>\n" + \\
"SELECT ?id ?name ?desc_text\n" + \\
"WHERE {\n" + \\
"?exp base:identifier_string ?id .\n" + \\
"?exp base:name_string ?name .\n" + \\
"?exp a base:Experiment.Experiment .\n" + \\
"?exp base:descriptions ?desc .\n" + \\
"?desc base:text_string ?desc_text .\n" + \\
August 22, 2011, at 08:39 AM by 138.100.11.51 -
Changed line 71 from:
|| String query = "PREFIX base: <http://aewrapper#>\n" \\
to:
||String query = "PREFIX base: <http://aewrapper#>\n" \\
August 22, 2011, at 08:39 AM by 138.100.11.51 -
Changed lines 71-83 from:
||-->String query = "PREFIX base: <http://aewrapper#>\n" \\
"SELECT ?id ?name ?desc_text\n" \\
"WHERE {\n" \\
"?exp base:identifier_string ?id .\n" \\
"?exp base:name_string ?name .\n" \\
"?exp a base:Experiment.Experiment .\n" \\
"?exp base:descriptions ?desc .\n" \\
"?desc base:text_string ?desc_text .\n" \\
"}"; \\
String experimentId = "E-GEOD-21068"; \\
// resultFile will contain the path to the file containing the results in SPARQL format \\
String resultFile = QueryProcessor.processQuery(query, experimentId); ||
to:
|| String query = "PREFIX base: <http://aewrapper#>\n" \\
"SELECT ?id ?name ?desc_text\n" \\
"WHERE {\n" \\
"?exp base:identifier_string ?id .\n" \\
"?exp base:name_string ?name .\n" \\
"?exp a base:Experiment.Experiment .\n" \\
"?exp base:descriptions ?desc .\n" \\
"?desc base:text_string ?desc_text .\n" \\
"}"; \\
String experimentId = "E-GEOD-21068"; \\
// resultFile will contain the path to the file containing the results in SPARQL format \\
String resultFile = QueryProcessor.processQuery(query, experimentId); ||
August 22, 2011, at 08:38 AM by 138.100.11.51 -
Changed lines 71-74 from:
|| cell 1 ||

|| border=1
||String query = "PREFIX base: <http://aewrapper#>\n" \\
to:
||-->String query = "PREFIX base: <http://aewrapper#>\n" \\
August 22, 2011, at 08:36 AM by 138.100.11.51 -
Changed line 74 from:
|| String query = "PREFIX base: <http://aewrapper#>\n" \\
to:
||String query = "PREFIX base: <http://aewrapper#>\n" \\
August 22, 2011, at 08:35 AM by 138.100.11.51 -
Changed lines 74-86 from:
|| String query = "PREFIX base: <http://aewrapper#>\n"
"SELECT ?id ?name ?desc_text\n"
"WHERE {\n"
"?exp base:identifier_string ?id .\n"
"?exp base:name_string ?name .\n"
"?exp a base:Experiment.Experiment .\n"
"?exp base:descriptions ?desc .\n"
"?desc base:text_string ?desc_text .\n"
"}";
String experimentId = "E-GEOD-21068"; /
// resultFile will contain the path to the file containing the results in SPARQL format
String resultFile = QueryProcessor.processQuery(query, experimentId); ||
to:
|| String query = "PREFIX base: <http://aewrapper#>\n" \\
"SELECT ?id ?name ?desc_text\n" \\
"WHERE {\n" \\
"?exp base:identifier_string ?id .\n" \\
"?exp base:name_string ?name .\n" \\
"?exp a base:Experiment.Experiment .\n" \\
"?exp base:descriptions ?desc .\n" \\
"?desc base:text_string ?desc_text .\n" \\
"}"; \\
String experimentId = "E-GEOD-21068"; \\
// resultFile will contain the path to the file containing the results in SPARQL format \\
String resultFile = QueryProcessor.processQuery(query, experimentId); ||
August 22, 2011, at 08:34 AM by 138.100.11.51 -
Changed lines 74-87 from:
|| String query = "PREFIX base: <http://aewrapper#>\n" + /
/ "SELECT ?id ?name ?desc_text\n" + /
/ "WHERE {\n" + /
/ "?exp base:identifier_string ?id .\n" + /
/ "?exp base:name_string ?name .\n" + /
/ "?exp a base:Experiment.Experiment .\n" + /
/ "?exp base:descriptions ?desc .\n" + /
/ "?desc base:text_string ?desc_text .\n" + /
/ "}"; /
/ String experimentId = "E-GEOD-21068"; /
/ // resultFile will contain the path to the file containing the results in SPARQL format /
/ String resultFile = QueryProcessor.processQuery(query, experimentId); /
||
to:
|| String query = "PREFIX base: <http://aewrapper#>\n"
"SELECT ?id ?name ?desc_text\n"
"WHERE {\n"
"?exp base:identifier_string ?id .\n"
"?exp base:name_string ?name .\n"
"?exp a base:Experiment.Experiment .\n"
"?exp base:descriptions ?desc .\n"
"?desc base:text_string ?desc_text .\n"
"}";
String experimentId = "E-GEOD-21068"; /
// resultFile will contain the path to the file containing the results in SPARQL format
String resultFile = QueryProcessor.processQuery(query, experimentId); ||
August 22, 2011, at 08:31 AM by 138.100.11.51 -
Changed lines 70-73 from:
||border=1
to:
|| border=1
|| cell 1 ||

|| border=1
August 22, 2011, at 08:30 AM by 138.100.11.51 -
Changed lines 70-72 from:
/-----------------------------------------------------------------------------------------------/
/ /
/ String query = "PREFIX base: <http://aewrapper#>\n" + /
to:
||border=1
|| String query = "PREFIX base: <http://aewrapper#>\n" + /
Changed lines 83-85 from:
/ /
/-----------------------------------------------------------------------------------------------/
to:
||
August 22, 2011, at 08:28 AM by 138.100.11.51 -
Changed lines 25-26 from:

to:
!! Introduction

This document explains how to use the RDFbuilder API for enabling RDF-based access to the ArrayExpress microarray
database. This API is written in Java 6.0, so any operating system that has a compatible Java Virtual machine is
supported. Please ensure that you have Java installed in the target machine before proceeding to use this API.
You can download the latest Java version from http://www.java.com/.

The goal of RDFbuilder is to enable RDF-based access to the ArrayExpress databases. These public databases store
microarray data. The employed format is MAGE-ML, a language for representing microarray experiments data developed
by the ArrayExpress consortium. The only way to query these data is to access a simple web-interface with some forms.
Using RDFbuilder, a researchers can submit SPARQL queries for ArrayExpress and receive results in SPARQL results
format. Enabling RDF-based access to ArrayExpress will facilitate its integration with other biomedical data
(e.g. clinical data).


!! Web-based access to the tool

The functionality of this API can be used and tested through a web-based graphical interface. Please go to the
following address to access the tool:

http://servet.dia.fi.upm.es:8080/ArrayExpressWrapperWeb/

The website includes the necessary instructions for using the tool online.


!! Standalone installation

The API can be used in a standalone application. All its functionality is bundled in the JAR that can be downloaded at
the following web page: http://servet.dia.fi.upm.es:8080/ArrayExpressWrapperWeb/.

The download includes the following items:

- A README.TXT file (this document) with use and installation instructions
- A jar file with the java code of the RDFbuilder API
- The JavaDoc documentation of the API
- An example configuration file named aewrapperConfig.xml, contained in the directory /AEWRAPPER_CONFIG
- The file mage-rdf-model-empty.obm, contained in the directory /baseRDFModel
- The mage-rdf-model-empty.owl file, containing the RDF-based schema of ArrayExpress (this schema defines the
valid SPARQL queries)

The jar file contains all the pre-compiled classes that compose the RDFbuilder. To learn how to use these classes,
please refer to the attached JavaDoc files. In addition, the file es.upm.gib.aewrapper.queryprocessing.test.SimpleTest
contains a main method with the code needed to launch a query using RDFbuilder. The following code snippet shows how
the API can be invoked:

/-----------------------------------------------------------------------------------------------/
/ /
/ String query = "PREFIX base: <http://aewrapper#>\n" + /
/ "SELECT ?id ?name ?desc_text\n" + /
/ "WHERE {\n" + /
/ "?exp base:identifier_string ?id .\n" + /
/ "?exp base:name_string ?name .\n" + /
/ "?exp a base:Experiment.Experiment .\n" + /
/ "?exp base:descriptions ?desc .\n" + /
/ "?desc base:text_string ?desc_text .\n" + /
/ "}"; /
/ String experimentId = "E-GEOD-21068"; /
/ // resultFile will contain the path to the file containing the results in SPARQL format /
/ String resultFile = QueryProcessor.processQuery(query, experimentId); /
/ /
/-----------------------------------------------------------------------------------------------/

In this code, the API is invoked with a SPARQL query (String) and a single experiment id (String). RDFbuilder translates
the data of the specified experiment into RDF and performs the given SPARQL query, producing a file with SPARQL results
format. There are some more options available when performing queries, such as the possibility of specifying a set
of keywords instead of a single experiment. Please refer to the JavaDoc to get further details.

The API makes use of the disk drive of the computer where it executes to cache data from ArrayExpress. The directory
for this cache is configurable through an xml configuration file. This configuration file must be named
aewrapperConfig.xml, and must be placed inside a directory named /AEWRAPPER_CONFIG, which must be inside the
base execution directory. For example, if our base execution directory is C:/executionDir/, then the xml configuration
file should be in C:/executionDir/AEWRAPPER_CONFIG/aewrapperConfig.xml. The config file root tag is <aewrapper-config>.
Inside this tag there is only one tag named <base-dir>. The content of this tag must be the directory in which we
want RDFbuilder to place the cache (for example, <base-dir>C:\AEWrapper</base-dir>). Inside the cache directory we
must place the /baseRDFModel bundled in the API download (and the file mage-rdf-model-empty.obm should be inside it).
In our example, we should have the following path: C:/AEWrapper/baseRDFModel/mage-rdf-model-empty.obm.

Once the configuration file is properly set and placed, we can invoke the Java methods contained in the API. The
software will create a directory called localExps inside the cache directory for storing downloaded data. This
directory can be erased at any moment, thus clearing the cache. In addition, for each query submitted, the API will
create a session directory inside the cache dir, looking something like query_session__2011-06-02--12-36-53__0.
These directories store files created to answer submitted queries, and the result files for such queries.
They can be erased after the results have been acquired.


August 22, 2011, at 08:27 AM by 138.100.11.51 -
Changed lines 15-16 from:
The source code of RDFBuilder is available in the following svn repository:
to:
The source code of RDFBuilder is available in the following svn repository (accessible with the anonymous user):
Changed lines 19-20 from:
accessible with the anonymous user. There is a README.TXT file in the project root which explains how to use the library, plus several examples. Precompiled jars can also be downloaded from the project's download directory, available at:
to:
There is a README.TXT file in the project root which explains how to use the library, plus several examples. Precompiled jars can also be downloaded from the project's download directory, available at:
August 22, 2011, at 08:26 AM by 138.100.11.51 -
Changed lines 1-2 from:
! RDFBuilder
to:
! Introduction
August 22, 2011, at 08:26 AM by 138.100.11.51 -
Added lines 13-14:
! Downloads
Added lines 23-26:
! Library instructions


August 22, 2011, at 08:25 AM by 138.100.11.51 -
Changed lines 1-2 from:
=RDFBuilder=
to:
! RDFBuilder
Changed lines 21-22 from:
=Contact=
to:
! Contact
August 22, 2011, at 08:22 AM by 138.100.11.51 -
Changed lines 1-2 from:
=RDFBuilder
to:
=RDFBuilder=
Changed lines 21-22 from:
=Contact:
to:
=Contact=
August 22, 2011, at 08:20 AM by 138.100.11.51 -
Changed lines 1-2 from:
RDFBuilder
to:
=RDFBuilder
Changed lines 21-22 from:
Contact:
to:
=Contact:
August 22, 2011, at 08:18 AM by 138.100.11.51 -
Added lines 13-23:
The source code of RDFBuilder is available in the following svn repository:

svn://bioinformatics.org/svnroot/rdfbuilder/trunk

accessible with the anonymous user. There is a README.TXT file in the project root which explains how to use the library, plus several examples. Precompiled jars can also be downloaded from the project's download directory, available at:

http://ftp.bioinformatics.org/pub/RDFBuilder/

Contact:

For any comments, questions or suggestions, please write an email to aanguita@infomed.dia.fi.upm.es
August 22, 2011, at 08:09 AM by 138.100.11.51 -
Changed lines 5-12 from:
Through the methods contained in this library, SPARQL queries can be submitted againt the ArrayExpress repositories, producing results in SPARQL format. The schema for constructing the queries is an RDF that resembles the MAGE-OM object model.
to:
Through the methods contained in this library, SPARQL queries can be submitted againt the ArrayExpress repositories, producing results in SPARQL format. The schema for constructing the queries is an RDF that resembles the MAGE-OM object model.

At the same time, we developed a web-application for easily testing the offered functionallity. This application can be accessed on the following URL:

http://servet.dia.fi.upm.es:8080/ArrayExpressWrapperWeb/

Instructions for using the application can be found in the same address.
August 22, 2011, at 07:58 AM by 138.100.11.51 -
Added lines 1-5:
RDFBuilder

RDFBuilder is a Java library designed to enable RDF-based access to the ArrayExpress public microarray repositories. The library and its source code are freely available through the Bioinformatics.org web.

Through the methods contained in this library, SPARQL queries can be submitted againt the ArrayExpress repositories, producing results in SPARQL format. The schema for constructing the queries is an RDF that resembles the MAGE-OM object model.