NCBO Wiki - User contributions [en]

PURL Server

2009-05-11T10:44:15Z

Nipunb: New page: ==Set Up== *2 Windows boxes. *Machine 1 - Master *IP: master.ip *Has MySQL 5.1 *Installing PURL using MySQL as the backend on Machine 1. **1. Download PULR 1.4 **2. Install specifying My...

==Set Up==
*2 Windows boxes.
*Machine 1 - Master
*IP: master.ip
*Has MySQL 5.1

*Installing PURL using MySQL as the backend on Machine 1.
**1. Download PULR 1.4
**2. Install specifying MySQL as your backend.Imp Note: You would have a create a database schema'purls' on your MySQL using command line. The PURL installation would not do that for you. In other words, the PURL installation expects you to have a schema called 'purls'. This is will be used as the backend for storing the URLs.
**3. Go to the folder where you installed PURL, by default it is: C:\Program Files\PURLZ-Server-1.4
**4. Navigate to the bin folder, click on startup.bat to start the server. Imp Note: Default username password for the PURL server is: admin/password
**5. Create a backup of purls on Machine 1. On the command line, execute the following command:
mysqldump --user=root --password --opt purls > c:\purls_backup.sql

*Machine 2 - Slave
*IP: slave.ip
*Has MySQL 5.1

==Instructions for creating the replication==

*1. On Machine 1:
**Log on to MySQL
mysql -u root -p

*2. On Machine 1:
**Run the command
grant replication slave, replication client on *.* to 'replicator'@'slave.ip' identified by 'password';

*3. On Machine 1:
**Configure the master:Add the following lines to my.ini file in C:\Program Files\MySQL\MySQL 5.1 folder. Add the lines in the section [mysqld] after the line that specifies the port

server-id=1
log-bin="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/bin.log"
log-error="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/error.log"
log-bin-index="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/log-bin.index"
binlog-do-db=purls

*4.Restart the MySQL service on the master

*5. On Machine 2:
**Create a new empty database 'purls'

*6. On Machine 2:
**Restore the purls database
**On the command promt run the command
mysql -u root -p purls < C:\path_to_purls_backup\purls_backup.sql

*7. On Machine 2: Configure the slave: Add the following lines to my.ini file in C:\Program Files\MySQL\MySQL 5.1 folder. Add the lines in the section [mysqld] after the line that specifies the port

server-id=2
master-host=171.65.32.120
master-port=3306
master-user=replicator
master-password=password
replicate-do-db=purls

log-bin="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/bin.log"
log-bin-index="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/log-bin.index"
log-error="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/error.log"
relay-log="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/relay.log"
relay-log-info-file="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/relay-log.info"
relay-log-index="C:/Documents and Settings/All Users/Application Data/MySQL/MySQL Server 5.1/Data/relay-log.index"

*8.Restart the MySQL service on the slave

*9. On the slave, log into MySQl
**i) start slave;
**ii)show slave status\G;
Make sure slave I/O running is yes
Make sure slave_SQL_running is yes

Main Page

2009-05-11T10:36:27Z

Nipunb: /* Software Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]
*[http://www.bioontology.org/wiki/index.php/News_Events_Publications NCBO News, Events and Publications]

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders

*[[OCI:Main_Page]] - Ontology of Clinical Investigation

*[[NPO:Main_Page]] - NanoParticle Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== NCBO Biomedical Resources index ===

NCBO has indexed some biomedical resources with ontology concepts from BioPortal and UMLS. The index is based on semantic annotation of biomedical data. It enable users to locate biomedical data resources related to particular ontology concepts. Learn more about the the resource index here: [[NCBO Biomedical Resources Index]].

=== Software Development Area ===

*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
*[[Processing_OBR_Resources]] - Notes on resources being processed
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services
*[[Tag Cloud Generation]] - Project to consume the OBS REST services and generated cumulative count using the path to root
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redudancy

=== NCBO Web services ===

* [[BioPortal REST services]] - Documentation on how to use BioPortal functionality as Web services
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Resources Index Web services]] - Documentation & information about the annotation-based NCBO resources index
* [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

Main Page

2009-05-11T10:31:05Z

Nipunb: /* Software Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]
*[http://www.bioontology.org/wiki/index.php/News_Events_Publications NCBO News, Events and Publications]

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders

*[[OCI:Main_Page]] - Ontology of Clinical Investigation

*[[NPO:Main_Page]] - NanoParticle Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== NCBO Biomedical Resources index ===

NCBO has indexed some biomedical resources with ontology concepts from BioPortal and UMLS. The index is based on semantic annotation of biomedical data. It enable users to locate biomedical data resources related to particular ontology concepts. Learn more about the the resource index here: [[NCBO Biomedical Resources Index]].

=== Software Development Area ===

*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
*[[Processing_OBR_Resources]] - Notes on resources being processed
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services
*[[Tag Cloud Generation]] - Project to consume the OBS REST services and generated cumulative count using the path to root

=== NCBO Web services ===

* [[BioPortal REST services]] - Documentation on how to use BioPortal functionality as Web services
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Resources Index Web services]] - Documentation & information about the annotation-based NCBO resources index
* [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

Main Page

2009-05-11T10:08:04Z

Nipunb: /* Software Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]
*[http://www.bioontology.org/wiki/index.php/News_Events_Publications NCBO News, Events and Publications]

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders

*[[OCI:Main_Page]] - Ontology of Clinical Investigation

*[[NPO:Main_Page]] - NanoParticle Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== NCBO Biomedical Resources index ===

NCBO has indexed some biomedical resources with ontology concepts from BioPortal and UMLS. The index is based on semantic annotation of biomedical data. It enable users to locate biomedical data resources related to particular ontology concepts. Learn more about the the resource index here: [[NCBO Biomedical Resources Index]].

=== Software Development Area ===

*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
*[[Processing_OBR_Resources]] - Notes on resources being processed
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services

=== NCBO Web services ===

* [[BioPortal REST services]] - Documentation on how to use BioPortal functionality as Web services
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Resources Index Web services]] - Documentation & information about the annotation-based NCBO resources index
* [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

File:Triple Stores.pdf

2009-05-01T21:53:27Z

Nipunb:

File:RDFTripleStore.ppt

2009-05-01T21:13:26Z

Nipunb:

Main Page

2009-05-01T19:45:41Z

Nipunb: /* Software Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]
*[http://www.bioontology.org/wiki/index.php/News_Events_Publications NCBO News, Events and Publications]

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders

*[[OCI:Main_Page]] - Ontology of Clinical Investigation

*[[NPO:Main_Page]] - NanoParticle Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== Software Development Area ===

*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
*[[Processing_OBR_Resources]] - Notes on resources being processed
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores

=== NCBO Web services ===

* [[BioPortal REST services]] - Documentation on how to use BioPortal functionality as Web services
* [[UMLS_REST_Services]] - Documentation on how to use our prototype UMLS services (NetKernel)
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Resources index Web services]] - Documentation & information about the annotation-based NCBO resources index