https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=WhetzelNCBO Wiki - User contributions [en]2026-06-05T12:08:01ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12615NCBO Hackathon 20132013-04-24T20:37:53Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* Rm LK005 (ground floor) Project Classroom, La Ka Shing Center Center for Learning, 291 Campus Drive, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
Start time: 9:00am PDT<br />
End time: 6:00pm PDT <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION (NEW API):'''<br />
* ''Coming soon!''<br />
<br />
'''SOFTWARE DOCUMENTATION (''Old API''):'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
'''PARTICIPANTS:'''<br />
* Robert Muller, TAIR/Carnegie Institution for Science <br />
* David Huang, Carnegie Institution for Science<br />
* Hari Rekapalli, UCSF<br />
* Andrew Nguyen, BodyData Systems, Inc.<br />
* Sean Mooney, Buck Institute for Research on Aging<br />
* Reza Alemy, Patesco <br />
* Sina Madani, MD Anderson Cancer Center<br />
* Colin Watanabe, Genentech<br />
* Oren Schaedel, Bionetbook <br />
* Marcus Breese, Buck Institute for Research on Aging<br />
* Kevin Cohen, U. Colorado School of Medicine <br />
* Yongqun Oliver He, University of Michigan</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12614NCBO Hackathon 20132013-04-22T19:45:29Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* Rm LK005 (ground floor) Project Classroom, La Ka Shing Center Center for Learning, 291 Campus Drive, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
Start time: 9:00am PDT<br />
End time: 6:00pm PDT <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION (NEW API):'''<br />
* ''Coming soon!''<br />
<br />
'''SOFTWARE DOCUMENTATION (''Old API''):'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
'''PARTICIPANTS:'''<br />
* Robert Muller, TAIR/Carnegie Institution for Science <br />
* David Huang, Carnegie Institution for Science<br />
* Ketty Mobed, UCSF<br />
* Andrew Nguyen, BodyData Systems, Inc.<br />
* Sean Mooney, Buck Institute for Research on Aging<br />
* Reza Alemy, Patesco <br />
* Sina Madani, MD Anderson Cancer Center<br />
* Colin Watanabe, Genentech<br />
* Oren Schaedel, Bionetbook <br />
* Marcus Breese, Buck Institute for Research on Aging<br />
* Kevin Cohen, U. Colorado School of Medicine <br />
* Yongqun Oliver He, University of Michigan</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12613NCBO Hackathon 20132013-04-22T19:43:41Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
Start time: 9:00am PDT<br />
End time: 6:00pm PDT <br />
<br />
'''Location:''' <br />
Room LK005 (ground floor) Project Classroom, La Ka Shing Center Center for Learning, 291 Campus Drive, Stanford University<br />
http://www.certain.com/system/profile/web/index.cfm?PKwebID=0x430788ad1d&varPage=location<br />
<br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION (NEW API):'''<br />
* ''Coming soon!''<br />
<br />
'''SOFTWARE DOCUMENTATION (''Old API''):'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
'''PARTICIPANTS:'''<br />
* Robert Muller, TAIR/Carnegie Institution for Science <br />
* David Huang, Carnegie Institution for Science<br />
* Ketty Mobed, UCSF<br />
* Andrew Nguyen, BodyData Systems, Inc.<br />
* Sean Mooney, Buck Institute for Research on Aging<br />
* Reza Alemy, Patesco <br />
* Sina Madani, MD Anderson Cancer Center<br />
* Colin Watanabe, Genentech<br />
* Oren Schaedel, Bionetbook <br />
* Marcus Breese, Buck Institute for Research on Aging<br />
* Kevin Cohen, U. Colorado School of Medicine <br />
* Yongqun Oliver He, University of Michigan</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12612NCBO Hackathon 20132013-04-22T19:42:24Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
Start time: 9:00am PDT<br />
End time: 6:00pm PDT <br />
<br />
'''Location:''' <br />
http://www.certain.com/system/profile/web/index.cfm?PKwebID=0x430788ad1d&varPage=location<br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION (NEW API):'''<br />
* ''Coming soon!''<br />
<br />
'''SOFTWARE DOCUMENTATION (''Old API''):'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
'''PARTICIPANTS:'''<br />
* Robert Muller, TAIR/Carnegie Institution for Science <br />
* David Huang, Carnegie Institution for Science<br />
* Ketty Mobed, UCSF<br />
* Andrew Nguyen, BodyData Systems, Inc.<br />
* Sean Mooney, Buck Institute for Research on Aging<br />
* Reza Alemy, Patesco <br />
* Sina Madani, MD Anderson Cancer Center<br />
* Colin Watanabe, Genentech<br />
* Oren Schaedel, Bionetbook <br />
* Marcus Breese, Buck Institute for Research on Aging<br />
* Kevin Cohen, U. Colorado School of Medicine <br />
* Yongqun Oliver He, University of Michigan</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12611NCBO Hackathon 20132013-04-22T19:40:15Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
Start time: 9:00am PDT<br />
End time: 6:00pm PDT <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION (NEW API):'''<br />
* ''Coming soon!''<br />
<br />
'''SOFTWARE DOCUMENTATION (''Old API''):'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
'''PARTICIPANTS:'''<br />
* Robert Muller, TAIR/Carnegie Institution for Science <br />
* David Huang, Carnegie Institution for Science<br />
* Ketty Mobed, UCSF<br />
* Andrew Nguyen, BodyData Systems, Inc.<br />
* Sean Mooney, Buck Institute for Research on Aging<br />
* Reza Alemy, Patesco <br />
* Sina Madani, MD Anderson Cancer Center<br />
* Colin Watanabe, Genentech<br />
* Oren Schaedel, Bionetbook <br />
* Marcus Breese, Buck Institute for Research on Aging<br />
* Kevin Cohen, U. Colorado School of Medicine <br />
* Yongqun Oliver He, University of Michigan</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Category:NCBO_Virtual_Appliance&diff=12610Category:NCBO Virtual Appliance2013-04-17T13:20:39Z<p>Whetzel: /* Getting Started */</p>
<hr />
<div>The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system. The image was created using VMWare and is available for download by contacting support@bioontology.org.<br />
<br />
The following software is included on the image:<br />
* NCBO Web Services (BioPortal Core)<br />
* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
* Annotator<br />
* Resource Index<br />
<br />
Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.<br />
<br />
== Getting Started ==<br />
* To obtain the Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support] and include your BioPortal account username. You can create a BioPortal account at: http://bit.ly/bioportal-account<br />
* The download is provided as a tar archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].<br />
* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.<br />
* '''Change default passwords'''<br />
** Operating System<br />
*** Username: <code>root</code><br />
*** Password: password is prompted on the first boot<br />
** BioPortal Admin User<br />
*** Username: <code>admin</code><br />
*** Password: <code>changeme</code><br />
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new<br />
** BioPortal Ontology Services can be configured to automatically process new ontologies every hour at 30 minutes past the hour (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:<br />
*** Parsing any new, unparsed ontologies<br />
*** Calculating a set of metrics for these ontologies<br />
*** Indexing these ontologies for use with search<br />
* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example:8080/bioportal_admin<br />
* REST services are available at the following locations. The URLs below are for the root of the REST service and generally will not return information. Please read the documentation for guidelines on how to interact with the services, including sample URLs:<br />
** NCBO Web Services - http://example:8080/bioportal ([http://www.bioontology.org/wiki/index.php/BioPortal_REST_services documentation])<br />
** Annotator - http://example:8080/obs/annotator ([http://www.bioontology.org/wiki/index.php/Annotator_User_Guide documentation])<br />
** Resource Index - http://example:8080/resource_index ([http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide documentation])<br />
<br />
== System Requirements ==<br />
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.<br />
<br />
'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.<br />
<br />
* Minimum<br />
** 1 CPU (2 GHz)<br />
** 4GB RAM<br />
** Hard disk space: 3GB<br />
<br />
* Recommended for heavier usage<br />
** 2 CPU (3 GHz)<br />
** 6GB RAM (When using more than 4GB RAM, you should configure Tomcat to use the additional memory)<br />
** Hard disk space: 10GB (or more depending on number/size of ontologies)<br />
<br />
== Population Workflows ==<br />
When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.<br />
<br />
<br />
NOTE: Loading ontologies [1] developed using the NCI version of Protege will require an additional manual pre-processing step to remove XML tags added into the synonym and definition property values. This pre-processing step is especially important for populating the correct synonym value into the Annotator workflow. The code to pre-process ontologies developed using the NCI version of Protege is located at:<br />
https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F, the code can be checked out via anonymous SVN. <br />
<br />
[1] The NCI Thesaurus and the NanoParticle Ontology are developed using the NCI version of Protege<br />
<br />
== Image Format and Operating System Details ==<br />
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.<br />
<br />
The operating system is CentOS 5.7 64-bit running Tomcat 6.0.26, Java 6, MySQL 5.1.x, PHP 5.1.6, Rails 2.3.x, and Ruby Enterprise Edition 1.8.7, and memcached.<br />
<br />
The following applications use these services/runtime environments:<br />
* Tomcat, Java<br />
** BioPortal Ontology Services (BioPortal Core)<br />
** BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
** Annotator and Recommender<br />
** Resource Index<br />
* Rails, Ruby, memcached<br />
** BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* PHP<br />
** Resource Index UI<br />
* 4store<br />
** Mappings<br />
<br />
== Basic System Administration ==<br />
* Most of our administration scripts and build environment assume that you will be running as the root user.<br />
* Helper commands:<br />
** <code>ncbostart</code>: the required services are started on boot automatically, but if they need to be started automatically<br />
** <code>ncbostop</code>: manually stop services<br />
** <code>ncborestart</code>: manually start/stop services<br />
* Start individual services:<br />
** <code>/sbin/service httpd start</code><br />
** <code>/sbin/service memcached start</code><br />
** <code>/sbin/service tomcat6 start</code><br />
** <code>/sbin/service mgrep start</code><br />
** <code>/sbin/service 4store start</code><br />
* Stop individual services:<br />
** <code>/sbin/service httpd stop</code><br />
** <code>/sbin/service memcached stop</code><br />
** <code>/sbin/service tomcat6 stop</code><br />
** <code>/sbin/service mgrep stop</code><br />
** <code>/sbin/service 4store stop</code><br />
<br />
== License ==<br />
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Category:NCBO_Virtual_Appliance&diff=12609Category:NCBO Virtual Appliance2013-04-17T13:20:07Z<p>Whetzel: /* Getting Started */</p>
<hr />
<div>The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system. The image was created using VMWare and is available for download by contacting support@bioontology.org.<br />
<br />
The following software is included on the image:<br />
* NCBO Web Services (BioPortal Core)<br />
* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
* Annotator<br />
* Resource Index<br />
<br />
Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.<br />
<br />
== Getting Started ==<br />
* To obtain the Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support] and include your BioPortal username. You can create a BioPortal account at: http://bit.ly/bioportal-account<br />
* The download is provided as a tar archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].<br />
* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.<br />
* '''Change default passwords'''<br />
** Operating System<br />
*** Username: <code>root</code><br />
*** Password: password is prompted on the first boot<br />
** BioPortal Admin User<br />
*** Username: <code>admin</code><br />
*** Password: <code>changeme</code><br />
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new<br />
** BioPortal Ontology Services can be configured to automatically process new ontologies every hour at 30 minutes past the hour (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:<br />
*** Parsing any new, unparsed ontologies<br />
*** Calculating a set of metrics for these ontologies<br />
*** Indexing these ontologies for use with search<br />
* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example:8080/bioportal_admin<br />
* REST services are available at the following locations. The URLs below are for the root of the REST service and generally will not return information. Please read the documentation for guidelines on how to interact with the services, including sample URLs:<br />
** NCBO Web Services - http://example:8080/bioportal ([http://www.bioontology.org/wiki/index.php/BioPortal_REST_services documentation])<br />
** Annotator - http://example:8080/obs/annotator ([http://www.bioontology.org/wiki/index.php/Annotator_User_Guide documentation])<br />
** Resource Index - http://example:8080/resource_index ([http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide documentation])<br />
<br />
== System Requirements ==<br />
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.<br />
<br />
'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.<br />
<br />
* Minimum<br />
** 1 CPU (2 GHz)<br />
** 4GB RAM<br />
** Hard disk space: 3GB<br />
<br />
* Recommended for heavier usage<br />
** 2 CPU (3 GHz)<br />
** 6GB RAM (When using more than 4GB RAM, you should configure Tomcat to use the additional memory)<br />
** Hard disk space: 10GB (or more depending on number/size of ontologies)<br />
<br />
== Population Workflows ==<br />
When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.<br />
<br />
<br />
NOTE: Loading ontologies [1] developed using the NCI version of Protege will require an additional manual pre-processing step to remove XML tags added into the synonym and definition property values. This pre-processing step is especially important for populating the correct synonym value into the Annotator workflow. The code to pre-process ontologies developed using the NCI version of Protege is located at:<br />
https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F, the code can be checked out via anonymous SVN. <br />
<br />
[1] The NCI Thesaurus and the NanoParticle Ontology are developed using the NCI version of Protege<br />
<br />
== Image Format and Operating System Details ==<br />
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.<br />
<br />
The operating system is CentOS 5.7 64-bit running Tomcat 6.0.26, Java 6, MySQL 5.1.x, PHP 5.1.6, Rails 2.3.x, and Ruby Enterprise Edition 1.8.7, and memcached.<br />
<br />
The following applications use these services/runtime environments:<br />
* Tomcat, Java<br />
** BioPortal Ontology Services (BioPortal Core)<br />
** BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
** Annotator and Recommender<br />
** Resource Index<br />
* Rails, Ruby, memcached<br />
** BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* PHP<br />
** Resource Index UI<br />
* 4store<br />
** Mappings<br />
<br />
== Basic System Administration ==<br />
* Most of our administration scripts and build environment assume that you will be running as the root user.<br />
* Helper commands:<br />
** <code>ncbostart</code>: the required services are started on boot automatically, but if they need to be started automatically<br />
** <code>ncbostop</code>: manually stop services<br />
** <code>ncborestart</code>: manually start/stop services<br />
* Start individual services:<br />
** <code>/sbin/service httpd start</code><br />
** <code>/sbin/service memcached start</code><br />
** <code>/sbin/service tomcat6 start</code><br />
** <code>/sbin/service mgrep start</code><br />
** <code>/sbin/service 4store start</code><br />
* Stop individual services:<br />
** <code>/sbin/service httpd stop</code><br />
** <code>/sbin/service memcached stop</code><br />
** <code>/sbin/service tomcat6 stop</code><br />
** <code>/sbin/service mgrep stop</code><br />
** <code>/sbin/service 4store stop</code><br />
<br />
== License ==<br />
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Category:NCBO_Virtual_Appliance&diff=12608Category:NCBO Virtual Appliance2013-04-17T13:12:54Z<p>Whetzel: /* Getting Started */</p>
<hr />
<div>The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system. The image was created using VMWare and is available for download by contacting support@bioontology.org.<br />
<br />
The following software is included on the image:<br />
* NCBO Web Services (BioPortal Core)<br />
* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
* Annotator<br />
* Resource Index<br />
<br />
Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.<br />
<br />
== Getting Started ==<br />
* To obtain the Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support] and include your BioPortal username. You can create a BioPortal account at: http://bioportal.bioontology.org/accounts/new<br />
* The download is provided as a tar archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].<br />
* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.<br />
* '''Change default passwords'''<br />
** Operating System<br />
*** Username: <code>root</code><br />
*** Password: password is prompted on the first boot<br />
** BioPortal Admin User<br />
*** Username: <code>admin</code><br />
*** Password: <code>changeme</code><br />
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new<br />
** BioPortal Ontology Services can be configured to automatically process new ontologies every hour at 30 minutes past the hour (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:<br />
*** Parsing any new, unparsed ontologies<br />
*** Calculating a set of metrics for these ontologies<br />
*** Indexing these ontologies for use with search<br />
* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example:8080/bioportal_admin<br />
* REST services are available at the following locations. The URLs below are for the root of the REST service and generally will not return information. Please read the documentation for guidelines on how to interact with the services, including sample URLs:<br />
** NCBO Web Services - http://example:8080/bioportal ([http://www.bioontology.org/wiki/index.php/BioPortal_REST_services documentation])<br />
** Annotator - http://example:8080/obs/annotator ([http://www.bioontology.org/wiki/index.php/Annotator_User_Guide documentation])<br />
** Resource Index - http://example:8080/resource_index ([http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide documentation])<br />
<br />
== System Requirements ==<br />
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.<br />
<br />
'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.<br />
<br />
* Minimum<br />
** 1 CPU (2 GHz)<br />
** 4GB RAM<br />
** Hard disk space: 3GB<br />
<br />
* Recommended for heavier usage<br />
** 2 CPU (3 GHz)<br />
** 6GB RAM (When using more than 4GB RAM, you should configure Tomcat to use the additional memory)<br />
** Hard disk space: 10GB (or more depending on number/size of ontologies)<br />
<br />
== Population Workflows ==<br />
When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.<br />
<br />
<br />
NOTE: Loading ontologies [1] developed using the NCI version of Protege will require an additional manual pre-processing step to remove XML tags added into the synonym and definition property values. This pre-processing step is especially important for populating the correct synonym value into the Annotator workflow. The code to pre-process ontologies developed using the NCI version of Protege is located at:<br />
https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F, the code can be checked out via anonymous SVN. <br />
<br />
[1] The NCI Thesaurus and the NanoParticle Ontology are developed using the NCI version of Protege<br />
<br />
== Image Format and Operating System Details ==<br />
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.<br />
<br />
The operating system is CentOS 5.7 64-bit running Tomcat 6.0.26, Java 6, MySQL 5.1.x, PHP 5.1.6, Rails 2.3.x, and Ruby Enterprise Edition 1.8.7, and memcached.<br />
<br />
The following applications use these services/runtime environments:<br />
* Tomcat, Java<br />
** BioPortal Ontology Services (BioPortal Core)<br />
** BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
** Annotator and Recommender<br />
** Resource Index<br />
* Rails, Ruby, memcached<br />
** BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* PHP<br />
** Resource Index UI<br />
* 4store<br />
** Mappings<br />
<br />
== Basic System Administration ==<br />
* Most of our administration scripts and build environment assume that you will be running as the root user.<br />
* Helper commands:<br />
** <code>ncbostart</code>: the required services are started on boot automatically, but if they need to be started automatically<br />
** <code>ncbostop</code>: manually stop services<br />
** <code>ncborestart</code>: manually start/stop services<br />
* Start individual services:<br />
** <code>/sbin/service httpd start</code><br />
** <code>/sbin/service memcached start</code><br />
** <code>/sbin/service tomcat6 start</code><br />
** <code>/sbin/service mgrep start</code><br />
** <code>/sbin/service 4store start</code><br />
* Stop individual services:<br />
** <code>/sbin/service httpd stop</code><br />
** <code>/sbin/service memcached stop</code><br />
** <code>/sbin/service tomcat6 stop</code><br />
** <code>/sbin/service mgrep stop</code><br />
** <code>/sbin/service 4store stop</code><br />
<br />
== License ==<br />
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12603NCBO Hackathon 20132013-04-04T04:34:16Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION (NEW API):'''<br />
* ''Coming soon!''<br />
<br />
'''SOFTWARE DOCUMENTATION (''Old API''):'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
'''PARTICIPANTS:'''<br />
* Robert Muller, TAIR/Carnegie Institution for Science <br />
* David Huang, Carnegie Institution for Science<br />
* Ketty Mobed, UCSF<br />
* Andrew Nguyen, BodyData Systems, Inc.<br />
* Sean Mooney, Buck Institute for Research on Aging<br />
* Reza Alemy, Patesco <br />
* Sina Madani, MD Anderson Cancer Center<br />
* Colin Watanabe, Genentech<br />
* Oren Schaedel, Bionetbook <br />
* Marcus Breese, Buck Institute for Research on Aging<br />
* Kevin Cohen, U. Colorado School of Medicine <br />
* Yongqun Oliver He, University of Michigan</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12602NCBO Hackathon 20132013-04-04T04:33:25Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION:'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
'''PARTICIPANTS:'''<br />
* Robert Muller, TAIR/Carnegie Institution for Science <br />
* David Huang, Carnegie Institution for Science<br />
* Ketty Mobed, UCSF<br />
* Andrew Nguyen, BodyData Systems, Inc.<br />
* Sean Mooney, Buck Institute for Research on Aging<br />
* Reza Alemy, Patesco <br />
* Sina Madani, MD Anderson Cancer Center<br />
* Colin Watanabe, Genentech<br />
* Oren Schaedel, Bionetbook <br />
* Marcus Breese, Buck Institute for Research on Aging<br />
* Kevin Cohen, U. Colorado School of Medicine <br />
* Yongqun Oliver He, University of Michigan</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12601Dissemination Wiki2013-04-04T04:30:50Z<p>Whetzel: </p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[NCBO Hackathon 2013]]'''<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
* ''[http://www.certain.com/system/profile/web/index.cfm?PKwebID=0x430788962b&varPage=info Registration and Meeting Logistics here]''<br />
<br />
'''[http://wiki.plantontology.org/index.php/PRO-PO-GO_Meeting PRO-PO-GO Meeting]'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events from 2005]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=12600Main Page2013-04-04T04:30:08Z<p>Whetzel: </p>
<hr />
<div>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. <br />
Please visit our [http://www.bioontology.org Main Site] for more information and materials.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! style="background:#efefef;" | NCBO Links<br />
! style="background:#efefef;" | Shared Materials<br />
! style="background:#efefef;" | NCBC Links<br />
|-<br />
| [http://www.bioontology.org/ Home page]<br />
| [[Public Requirements Redirect|Public Requirements]]<br />
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]<br />
|-<br />
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]<br />
| [[Shared Materials]]<br />
| [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]<br />
|-<br />
| [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination]<br />
|-<br />
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]<br />
| [[Evaluation Activities]]<br />
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]<br />
|}<br />
<br />
<br />
=== Software ===<br />
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page for BioPortal Web site<br />
* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries<br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes BioPortal Software Release Announcements] <br />
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies<br />
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.<br />
<br />
=== User Support Documentation ===<br />
*[[BioPortal Help]] - General BioPortal help documentation. <br />
* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project<br />
<br />
=== Technical Documentation ===<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO REST Web services] - Listing of all NCBO web services with usage documentation<br />
* [http://www.bioontology.org/wiki/index.php/View_Extraction Ontology Subset Extraction Web service] - Documentation on how to extract subtree views from ontologies<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Term Mappings Web service] - Documentation & information about accessing term mapping data<br />
* [http://www.bioontology.org/wiki/index.php/Ontology_Notes Term Proposal Web service] - Documentation & information about posting and accessing comments and new term proposals <br />
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator<br />
* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender <br />
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index<br />
* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation<br />
* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages<br />
* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services <br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.<br />
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)<br />
<br />
=== Ontology Development Projects ===<br />
Below are links for ontology development projects that NCBO is involved in. <br />
*[[BRO:Main_Page]] - Biomedical Resource Ontology<br />
*[[TMO:]] - Translational Medicine Ontology <br />
*[[NPO:Main_Page]] - NanoParticle Ontology<br />
*[[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
*[[RO:Main_Page]] - OBO Relations ontology<br />
*[[CARO:Main_Page]] - Reference anatomical ontology<br />
*[[CL:Main_Page]] - OBO Cell ontology<br />
*[[SO:Main_Page]] - Sequence Ontology<br />
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br />
*[[OCI:Main_Page]] - Ontology of Clinical Investigation<br />
<br />
=== Research projects and Prototypes ===<br />
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)<br />
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)<br />
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)<br />
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)<br />
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)<br />
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)<br />
*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow. (Tejaswi Tenneti)</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=12599Main Page2013-04-04T04:29:20Z<p>Whetzel: </p>
<hr />
<div>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. <br />
Please visit our [http://www.bioontology.org Main Site] for more information and materials.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! style="background:#efefef;" | NCBO Links<br />
! style="background:#efefef;" | Shared Materials<br />
! style="background:#efefef;" | NCBC Links<br />
|-<br />
| [http://www.bioontology.org/ Home page]<br />
| [[Public Requirements Redirect|Public Requirements]]<br />
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]<br />
|-<br />
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]<br />
| [[Shared Materials]]<br />
| [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]<br />
|-<br />
| [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination]<br />
|-<br />
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]<br />
| [[Evaluation Activities]]<br />
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]<br />
|}<br />
<br />
<br />
=== Software ===<br />
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page for BioPortal Web site<br />
* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries<br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes BioPortal Software Release Announcements] <br />
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies<br />
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.<br />
<br />
=== User Support Documentation ===<br />
*[[BioPortal Help]] - General BioPortal help documentation. <br />
* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project<br />
<br />
=== Technical Documentation ===<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO REST Web services] - Listing of all NCBO web services with usage documentation<br />
* [http://www.bioontology.org/wiki/index.php/View_Extraction Ontology Subset Extraction Web service] - Documentation on how to extract subtree views from ontologies<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Term Mappings Web service] - Documentation & information about accessing term mapping data<br />
* [http://www.bioontology.org/wiki/index.php/Ontology_Notes Term Proposal Web service] - Documentation & information about posting and accessing comments and new term proposals <br />
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator<br />
* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender <br />
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index<br />
* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation<br />
* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages<br />
* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services <br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.<br />
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)<br />
<br />
=== Ontology Development Projects ===<br />
Below are links for ontology development projects that NCBO is involved in. <br />
*[[BRO:Main_Page]] - Biomedical Resource Ontology<br />
*[[TMO:]] - Translational Medicine Ontology <br />
*[[NPO:Main_Page]] - NanoParticle Ontology<br />
*[[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
*[[RO:Main_Page]] - OBO Relations ontology<br />
*[[CARO:Main_Page]] - Reference anatomical ontology<br />
*[[CL:Main_Page]] - OBO Cell ontology<br />
*[[SO:Main_Page]] - Sequence Ontology<br />
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br />
*[[OCI:Main_Page]] - Ontology of Clinical InvestigatioN<br />
<br />
=== Research projects and Prototypes ===<br />
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)<br />
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)<br />
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)<br />
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)<br />
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)<br />
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)<br />
*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow. (Tejaswi Tenneti)</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12597BioPortal REST services2013-04-02T19:31:37Z<p>Whetzel: /* Get term, including its properties, subclasses, and superclasses */</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use. See also work on wrapping Bioportal REST services as a [[CTS2_BioPortal_wrapper]].<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
Ontology files that were successfully parsed have a value of 3 for the <statusId> attribute in the XML response.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do work for ontology views also with the same signature.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}<br />
** To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
Examples using Alt Signature<br />
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
Examples using Alt Virtual Signature (uses ontology id and uri-encoded concept id)<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FO80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
** '''NOTE''': To ensure that the Web service works within your application, url-encode the concept id as some ontologies may contain terms where the concept id is a URI.<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12596BioPortal REST services2013-04-02T19:30:26Z<p>Whetzel: /* Get term, including its properties, subclasses, and superclasses */</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use. See also work on wrapping Bioportal REST services as a [[CTS2_BioPortal_wrapper]].<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
Ontology files that were successfully parsed have a value of 3 for the <statusId> attribute in the XML response.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do work for ontology views also with the same signature.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}<br />
** To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
Examples using Alt Signature<br />
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
Examples using Alt Virtual Signature<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FO80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
** '''NOTE''': To ensure that the Web service works within your application, url-encode the concept id as some ontologies may contain terms where the concept id is a URI.<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Release_Notes&diff=12587BioPortal Release Notes2013-02-21T01:43:46Z<p>Whetzel: /* BioPortal Release 3.12 */</p>
<hr />
<div>== BioPortal Release 3.12 ==<br />
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.<br />
* Improved some default layouts in the visualization system.<br />
* Updated automated mappings for all ontologies.<br />
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.<br />
* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].<br />
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.<br />
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.<br />
** NIF PubMed Health: Tests<br />
** NIF Drug Related Gene Database<br />
** NIF Gemma<br />
** NIF Integrated Disease View<br />
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.<br />
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.<br />
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.<br />
* Fixed Search to work correctly in MeSH.<br />
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses<br />
<br />
(Release February 2013)<br />
<br />
== BioPortal Release 3.10 ==<br />
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.<br />
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.<br />
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.<br />
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.<br />
<br />
(Release July 2012)<br />
<br />
== BioPortal Release 3.9 ==<br />
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *<br />
<br />
* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *<br />
<br />
* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!<br />
<br />
(Release June 2012)<br />
<br />
== BioPortal Release 3.8 == <br />
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*<br />
<br />
* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*<br />
<br />
* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*<br />
<br />
We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.<br />
<br />
<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release May 2012)<br />
<br />
== BioPortal Release 3.7 ==<br />
* Updated term mappings generated by LOOM <br />
* Added boolean functionality to Search Web service and UI<br />
* Updated ontology content for the Resource Index<br />
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org <br />
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*<br />
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release April 2012)<br />
<br />
== BioPortal Release 3.6 ==<br />
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:<br />
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org<br />
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org<br />
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org<br />
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org<br />
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org<br />
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org<br />
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org<br />
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org<br />
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.<br />
* Major Updates and Fixes<br />
** Updated the ontologies used by the Annotator Web Services*<br />
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release January 2012) <br />
<br />
== BioPortal Release 3.5 ==<br />
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display<br />
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation<br />
* Improved Annotator Web service response performance by 5-10x* <br />
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)* <br />
* Updated Ontology Recommender algorithm to provide better recommendations*<br />
* Added display of matched terms for Ontology Recommender*<br />
* Added Web service to get all namespaces for an ontology*<br />
* Bug Fixes <br />
** Display user-friendly names for RxNorm ontology properties<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release December 2011)<br />
<br />
== BioPortal Release 3.4 ==<br />
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*<br />
* Limited access to “Private” ontologies via the Browse and Search pages<br />
* Added backend support to allow multiple administrators for a single ontology*<br />
* Added ability to copy to the clipboard a permanent link to any BioPortal term* <br />
* Bug Fixes <br />
** Resolved issue causing search to not display all matching terms* <br />
** Fixed Term Mappings tab display for IE 7 & 8* <br />
** Fixed RDF Ontology Download Web service<br />
** Fixed link to the list of resources included in the Resource Index* <br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release October 2011) <br />
<br />
== BioPortal Release 3.3 == <br />
New features include updates to the Web interface and Web services:<br />
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services <br />
* Updated Search page to remove Flash<br />
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies. <br />
* Added Help documentation <br />
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.<br />
* Bug Fix<br />
** Fixed the Filter by Account on the Mappings tab<br />
<br />
(Release date September 2011)<br />
<br />
== BioPortal Release 3.2 ==<br />
New features include updates to the Web interface and Web services:<br />
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender <br />
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service<br />
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples<br />
* Added support for access control for viewing ontologies <br />
* Added link to subscribe to BioPortal Notes emails <br />
* Synchronized “Jump To” feature with ontology parsing and display <br />
* Added documentation on Ontology Groups<br />
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter <br />
* Removed the metric "Number of classes without an author" <br />
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release. <br />
* Bug Fix<br />
** Fixed calculation of “Classes with no definition” metric<br />
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results <br />
<br />
<br />
'''''Firefox Extension for NCBO API Key''''':<br />
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org. <br />
<br />
'''''Upcoming software license change''''':<br />
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.<br />
<br />
== BioPortal Release 3.1 ==<br />
New features include updates to the Web interface and Web services:<br />
* Support for loading OWL 2 ontologies<br />
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key. <br />
* Browsing of ontologies that contain large numbers of sibling terms<br />
* Icons for is_a and part_of are displayed for OBO format ontologies <br />
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology <br />
Bug Fix<br />
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response<br />
<br />
(Release date July 8, 2011)<br />
<br />
== BioPortal Release 3.0 ==<br />
New features include updates to the Web interface and Web services:<br />
* Web interface updates<br />
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology<br />
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology<br />
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.<br />
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms<br />
* Form auto-complete Widget - Option to include term definition in display<br />
* Resource Index<br />
** Data indexed with new ontologies from BioPortal<br />
** PubMed data now available for abstracts published in 2010 <br />
<br />
(Release date May 19, 2011)<br />
<br />
== BioPortal Release 2.6.4 ==<br />
New features include additional Web services and Web interface enhancements:<br />
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23'' <br />
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )<br />
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display<br />
* Annotator<br />
** Updated ontology content<br />
** Offsets corrected for non-ASCII characters<br />
** Link to Annotator Web interface using parameters<br />
** Web interface enhancements<br />
* Display of ontology development status<br />
* Hyperlinks on term details page<br />
* Ability to add comments on Mappings<br />
<br />
(Release date February 2011)<br />
<br />
== BioPortal Release 2.5 ==<br />
New features in this release include the following:<br />
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.<br />
<br />
* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)<br />
<br />
* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).<br />
<br />
* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org<br />
<br />
* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.<br />
<br />
* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.<br />
<br />
* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings<br />
<br />
[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services<br />
<br />
(Release date June 9, 2010)</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Release_Notes&diff=12576BioPortal Release Notes2013-02-06T20:29:59Z<p>Whetzel: /* BioPortal Release 3.12 */</p>
<hr />
<div>== BioPortal Release 3.12 ==<br />
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.<br />
* Improved some default layouts in the visualization system.<br />
* Updated automated mappings for all ontologies.<br />
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.<br />
* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].<br />
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.<br />
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.<br />
** NIF PubMed Health: Tests<br />
** NIF Drug Related Gene Database<br />
** NIF Gemma<br />
** NIF Integrated Disease View<br />
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.<br />
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.<br />
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.<br />
* Fixed Search to work correctly in MeSH.<br />
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses<br />
<br />
(Release February 2012)<br />
<br />
== BioPortal Release 3.10 ==<br />
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.<br />
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.<br />
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.<br />
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.<br />
<br />
(Release July 2012)<br />
<br />
== BioPortal Release 3.9 ==<br />
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *<br />
<br />
* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *<br />
<br />
* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!<br />
<br />
(Release June 2012)<br />
<br />
== BioPortal Release 3.8 == <br />
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*<br />
<br />
* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*<br />
<br />
* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*<br />
<br />
We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.<br />
<br />
<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release May 2012)<br />
<br />
== BioPortal Release 3.7 ==<br />
* Updated term mappings generated by LOOM <br />
* Added boolean functionality to Search Web service and UI<br />
* Updated ontology content for the Resource Index<br />
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org <br />
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*<br />
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release April 2012)<br />
<br />
== BioPortal Release 3.6 ==<br />
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:<br />
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org<br />
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org<br />
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org<br />
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org<br />
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org<br />
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org<br />
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org<br />
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org<br />
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.<br />
* Major Updates and Fixes<br />
** Updated the ontologies used by the Annotator Web Services*<br />
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release January 2012) <br />
<br />
== BioPortal Release 3.5 ==<br />
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display<br />
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation<br />
* Improved Annotator Web service response performance by 5-10x* <br />
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)* <br />
* Updated Ontology Recommender algorithm to provide better recommendations*<br />
* Added display of matched terms for Ontology Recommender*<br />
* Added Web service to get all namespaces for an ontology*<br />
* Bug Fixes <br />
** Display user-friendly names for RxNorm ontology properties<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release December 2011)<br />
<br />
== BioPortal Release 3.4 ==<br />
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*<br />
* Limited access to “Private” ontologies via the Browse and Search pages<br />
* Added backend support to allow multiple administrators for a single ontology*<br />
* Added ability to copy to the clipboard a permanent link to any BioPortal term* <br />
* Bug Fixes <br />
** Resolved issue causing search to not display all matching terms* <br />
** Fixed Term Mappings tab display for IE 7 & 8* <br />
** Fixed RDF Ontology Download Web service<br />
** Fixed link to the list of resources included in the Resource Index* <br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release October 2011) <br />
<br />
== BioPortal Release 3.3 == <br />
New features include updates to the Web interface and Web services:<br />
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services <br />
* Updated Search page to remove Flash<br />
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies. <br />
* Added Help documentation <br />
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.<br />
* Bug Fix<br />
** Fixed the Filter by Account on the Mappings tab<br />
<br />
(Release date September 2011)<br />
<br />
== BioPortal Release 3.2 ==<br />
New features include updates to the Web interface and Web services:<br />
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender <br />
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service<br />
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples<br />
* Added support for access control for viewing ontologies <br />
* Added link to subscribe to BioPortal Notes emails <br />
* Synchronized “Jump To” feature with ontology parsing and display <br />
* Added documentation on Ontology Groups<br />
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter <br />
* Removed the metric "Number of classes without an author" <br />
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release. <br />
* Bug Fix<br />
** Fixed calculation of “Classes with no definition” metric<br />
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results <br />
<br />
<br />
'''''Firefox Extension for NCBO API Key''''':<br />
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org. <br />
<br />
'''''Upcoming software license change''''':<br />
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.<br />
<br />
== BioPortal Release 3.1 ==<br />
New features include updates to the Web interface and Web services:<br />
* Support for loading OWL 2 ontologies<br />
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key. <br />
* Browsing of ontologies that contain large numbers of sibling terms<br />
* Icons for is_a and part_of are displayed for OBO format ontologies <br />
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology <br />
Bug Fix<br />
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response<br />
<br />
(Release date July 8, 2011)<br />
<br />
== BioPortal Release 3.0 ==<br />
New features include updates to the Web interface and Web services:<br />
* Web interface updates<br />
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology<br />
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology<br />
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.<br />
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms<br />
* Form auto-complete Widget - Option to include term definition in display<br />
* Resource Index<br />
** Data indexed with new ontologies from BioPortal<br />
** PubMed data now available for abstracts published in 2010 <br />
<br />
(Release date May 19, 2011)<br />
<br />
== BioPortal Release 2.6.4 ==<br />
New features include additional Web services and Web interface enhancements:<br />
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23'' <br />
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )<br />
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display<br />
* Annotator<br />
** Updated ontology content<br />
** Offsets corrected for non-ASCII characters<br />
** Link to Annotator Web interface using parameters<br />
** Web interface enhancements<br />
* Display of ontology development status<br />
* Hyperlinks on term details page<br />
* Ability to add comments on Mappings<br />
<br />
(Release date February 2011)<br />
<br />
== BioPortal Release 2.5 ==<br />
New features in this release include the following:<br />
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.<br />
<br />
* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)<br />
<br />
* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).<br />
<br />
* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org<br />
<br />
* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.<br />
<br />
* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.<br />
<br />
* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings<br />
<br />
[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services<br />
<br />
(Release date June 9, 2010)</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Release_Notes&diff=12575BioPortal Release Notes2013-02-06T20:29:12Z<p>Whetzel: /* BioPortal Release 3.12 */</p>
<hr />
<div>== BioPortal Release 3.12 ==<br />
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization<br />
* Improved some default layouts in the visualization system<br />
* Updated automated mappings for all ontologies<br />
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.<br />
* Implemented support for federated queries in the BioPortal SPARQL endpoint<br />
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.<br />
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.<br />
** NIF PubMed Health: Tests<br />
** NIF Drug Related Gene Database<br />
** NIF Gemma<br />
** NIF Integrated Disease View<br />
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.<br />
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.<br />
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.<br />
* Fixed Search to work correctly in MeSH.<br />
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses<br />
<br />
(Release February 2012)<br />
<br />
== BioPortal Release 3.10 ==<br />
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.<br />
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.<br />
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.<br />
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.<br />
<br />
(Release July 2012)<br />
<br />
== BioPortal Release 3.9 ==<br />
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *<br />
<br />
* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *<br />
<br />
* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!<br />
<br />
(Release June 2012)<br />
<br />
== BioPortal Release 3.8 == <br />
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*<br />
<br />
* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*<br />
<br />
* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*<br />
<br />
We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.<br />
<br />
<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release May 2012)<br />
<br />
== BioPortal Release 3.7 ==<br />
* Updated term mappings generated by LOOM <br />
* Added boolean functionality to Search Web service and UI<br />
* Updated ontology content for the Resource Index<br />
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org <br />
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*<br />
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release April 2012)<br />
<br />
== BioPortal Release 3.6 ==<br />
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:<br />
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org<br />
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org<br />
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org<br />
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org<br />
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org<br />
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org<br />
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org<br />
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org<br />
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.<br />
* Major Updates and Fixes<br />
** Updated the ontologies used by the Annotator Web Services*<br />
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release January 2012) <br />
<br />
== BioPortal Release 3.5 ==<br />
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display<br />
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation<br />
* Improved Annotator Web service response performance by 5-10x* <br />
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)* <br />
* Updated Ontology Recommender algorithm to provide better recommendations*<br />
* Added display of matched terms for Ontology Recommender*<br />
* Added Web service to get all namespaces for an ontology*<br />
* Bug Fixes <br />
** Display user-friendly names for RxNorm ontology properties<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release December 2011)<br />
<br />
== BioPortal Release 3.4 ==<br />
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*<br />
* Limited access to “Private” ontologies via the Browse and Search pages<br />
* Added backend support to allow multiple administrators for a single ontology*<br />
* Added ability to copy to the clipboard a permanent link to any BioPortal term* <br />
* Bug Fixes <br />
** Resolved issue causing search to not display all matching terms* <br />
** Fixed Term Mappings tab display for IE 7 & 8* <br />
** Fixed RDF Ontology Download Web service<br />
** Fixed link to the list of resources included in the Resource Index* <br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release October 2011) <br />
<br />
== BioPortal Release 3.3 == <br />
New features include updates to the Web interface and Web services:<br />
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services <br />
* Updated Search page to remove Flash<br />
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies. <br />
* Added Help documentation <br />
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.<br />
* Bug Fix<br />
** Fixed the Filter by Account on the Mappings tab<br />
<br />
(Release date September 2011)<br />
<br />
== BioPortal Release 3.2 ==<br />
New features include updates to the Web interface and Web services:<br />
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender <br />
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service<br />
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples<br />
* Added support for access control for viewing ontologies <br />
* Added link to subscribe to BioPortal Notes emails <br />
* Synchronized “Jump To” feature with ontology parsing and display <br />
* Added documentation on Ontology Groups<br />
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter <br />
* Removed the metric "Number of classes without an author" <br />
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release. <br />
* Bug Fix<br />
** Fixed calculation of “Classes with no definition” metric<br />
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results <br />
<br />
<br />
'''''Firefox Extension for NCBO API Key''''':<br />
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org. <br />
<br />
'''''Upcoming software license change''''':<br />
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.<br />
<br />
== BioPortal Release 3.1 ==<br />
New features include updates to the Web interface and Web services:<br />
* Support for loading OWL 2 ontologies<br />
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key. <br />
* Browsing of ontologies that contain large numbers of sibling terms<br />
* Icons for is_a and part_of are displayed for OBO format ontologies <br />
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology <br />
Bug Fix<br />
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response<br />
<br />
(Release date July 8, 2011)<br />
<br />
== BioPortal Release 3.0 ==<br />
New features include updates to the Web interface and Web services:<br />
* Web interface updates<br />
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology<br />
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology<br />
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.<br />
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms<br />
* Form auto-complete Widget - Option to include term definition in display<br />
* Resource Index<br />
** Data indexed with new ontologies from BioPortal<br />
** PubMed data now available for abstracts published in 2010 <br />
<br />
(Release date May 19, 2011)<br />
<br />
== BioPortal Release 2.6.4 ==<br />
New features include additional Web services and Web interface enhancements:<br />
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23'' <br />
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )<br />
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display<br />
* Annotator<br />
** Updated ontology content<br />
** Offsets corrected for non-ASCII characters<br />
** Link to Annotator Web interface using parameters<br />
** Web interface enhancements<br />
* Display of ontology development status<br />
* Hyperlinks on term details page<br />
* Ability to add comments on Mappings<br />
<br />
(Release date February 2011)<br />
<br />
== BioPortal Release 2.5 ==<br />
New features in this release include the following:<br />
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.<br />
<br />
* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)<br />
<br />
* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).<br />
<br />
* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org<br />
<br />
* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.<br />
<br />
* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.<br />
<br />
* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings<br />
<br />
[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services<br />
<br />
(Release date June 9, 2010)</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Release_Notes&diff=12574BioPortal Release Notes2013-02-06T20:11:03Z<p>Whetzel: /* BioPortal Release 3.12 */</p>
<hr />
<div>== BioPortal Release 3.12 ==<br />
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.<br />
* Improved some default layouts in the visualization system.<br />
* Updated automated mappings for all ontologies.<br />
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.<br />
* Implemented support for federated queries in the BioPortal SPARQL endpoint.<br />
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.<br />
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.<br />
** NIF PubMed Health: Tests<br />
** NIF Drug Related Gene Database<br />
** NIF Gemma<br />
** NIF Integrated Disease View<br />
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.<br />
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.<br />
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.<br />
* Fixed Search to work correctly in MeSH.<br />
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses<br />
<br />
(Release February 2012)<br />
<br />
== BioPortal Release 3.10 ==<br />
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.<br />
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.<br />
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.<br />
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.<br />
<br />
(Release July 2012)<br />
<br />
== BioPortal Release 3.9 ==<br />
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *<br />
<br />
* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *<br />
<br />
* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!<br />
<br />
(Release June 2012)<br />
<br />
== BioPortal Release 3.8 == <br />
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*<br />
<br />
* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*<br />
<br />
* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*<br />
<br />
We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.<br />
<br />
<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release May 2012)<br />
<br />
== BioPortal Release 3.7 ==<br />
* Updated term mappings generated by LOOM <br />
* Added boolean functionality to Search Web service and UI<br />
* Updated ontology content for the Resource Index<br />
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org <br />
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*<br />
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release April 2012)<br />
<br />
== BioPortal Release 3.6 ==<br />
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:<br />
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org<br />
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org<br />
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org<br />
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org<br />
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org<br />
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org<br />
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org<br />
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org<br />
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.<br />
* Major Updates and Fixes<br />
** Updated the ontologies used by the Annotator Web Services*<br />
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release January 2012) <br />
<br />
== BioPortal Release 3.5 ==<br />
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display<br />
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation<br />
* Improved Annotator Web service response performance by 5-10x* <br />
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)* <br />
* Updated Ontology Recommender algorithm to provide better recommendations*<br />
* Added display of matched terms for Ontology Recommender*<br />
* Added Web service to get all namespaces for an ontology*<br />
* Bug Fixes <br />
** Display user-friendly names for RxNorm ontology properties<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release December 2011)<br />
<br />
== BioPortal Release 3.4 ==<br />
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*<br />
* Limited access to “Private” ontologies via the Browse and Search pages<br />
* Added backend support to allow multiple administrators for a single ontology*<br />
* Added ability to copy to the clipboard a permanent link to any BioPortal term* <br />
* Bug Fixes <br />
** Resolved issue causing search to not display all matching terms* <br />
** Fixed Term Mappings tab display for IE 7 & 8* <br />
** Fixed RDF Ontology Download Web service<br />
** Fixed link to the list of resources included in the Resource Index* <br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release October 2011) <br />
<br />
== BioPortal Release 3.3 == <br />
New features include updates to the Web interface and Web services:<br />
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services <br />
* Updated Search page to remove Flash<br />
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies. <br />
* Added Help documentation <br />
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.<br />
* Bug Fix<br />
** Fixed the Filter by Account on the Mappings tab<br />
<br />
(Release date September 2011)<br />
<br />
== BioPortal Release 3.2 ==<br />
New features include updates to the Web interface and Web services:<br />
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender <br />
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service<br />
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples<br />
* Added support for access control for viewing ontologies <br />
* Added link to subscribe to BioPortal Notes emails <br />
* Synchronized “Jump To” feature with ontology parsing and display <br />
* Added documentation on Ontology Groups<br />
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter <br />
* Removed the metric "Number of classes without an author" <br />
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release. <br />
* Bug Fix<br />
** Fixed calculation of “Classes with no definition” metric<br />
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results <br />
<br />
<br />
'''''Firefox Extension for NCBO API Key''''':<br />
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org. <br />
<br />
'''''Upcoming software license change''''':<br />
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.<br />
<br />
== BioPortal Release 3.1 ==<br />
New features include updates to the Web interface and Web services:<br />
* Support for loading OWL 2 ontologies<br />
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key. <br />
* Browsing of ontologies that contain large numbers of sibling terms<br />
* Icons for is_a and part_of are displayed for OBO format ontologies <br />
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology <br />
Bug Fix<br />
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response<br />
<br />
(Release date July 8, 2011)<br />
<br />
== BioPortal Release 3.0 ==<br />
New features include updates to the Web interface and Web services:<br />
* Web interface updates<br />
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology<br />
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology<br />
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.<br />
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms<br />
* Form auto-complete Widget - Option to include term definition in display<br />
* Resource Index<br />
** Data indexed with new ontologies from BioPortal<br />
** PubMed data now available for abstracts published in 2010 <br />
<br />
(Release date May 19, 2011)<br />
<br />
== BioPortal Release 2.6.4 ==<br />
New features include additional Web services and Web interface enhancements:<br />
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23'' <br />
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )<br />
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display<br />
* Annotator<br />
** Updated ontology content<br />
** Offsets corrected for non-ASCII characters<br />
** Link to Annotator Web interface using parameters<br />
** Web interface enhancements<br />
* Display of ontology development status<br />
* Hyperlinks on term details page<br />
* Ability to add comments on Mappings<br />
<br />
(Release date February 2011)<br />
<br />
== BioPortal Release 2.5 ==<br />
New features in this release include the following:<br />
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.<br />
<br />
* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)<br />
<br />
* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).<br />
<br />
* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org<br />
<br />
* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.<br />
<br />
* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.<br />
<br />
* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings<br />
<br />
[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services<br />
<br />
(Release date June 9, 2010)</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Release_Notes&diff=12573BioPortal Release Notes2013-02-06T20:10:34Z<p>Whetzel: </p>
<hr />
<div>== BioPortal Release 3.12 ==<br />
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.<br />
* Improved some default layouts in the visualization system.<br />
* Updated automated mappings for all ontologies.<br />
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.<br />
* Implemented support for federated queries in the BioPortal SPARQL endpoint.<br />
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.<br />
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.<br />
** NIF PubMed Health: Tests<br />
** NIF Drug Related Gene Database<br />
** NIF Gemma<br />
** NIF Integrated Disease View<br />
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.<br />
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.<br />
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.<br />
* Fixed Search to work correctly in MeSH.<br />
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses<br />
<br />
<br />
== BioPortal Release 3.10 ==<br />
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.<br />
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.<br />
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.<br />
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.<br />
<br />
(Release July 2012)<br />
<br />
== BioPortal Release 3.9 ==<br />
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *<br />
<br />
* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *<br />
<br />
* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list. Thank you for your comments and suggestions!<br />
<br />
(Release June 2012)<br />
<br />
== BioPortal Release 3.8 == <br />
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*<br />
<br />
* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*<br />
<br />
* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*<br />
<br />
We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.<br />
<br />
<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release May 2012)<br />
<br />
== BioPortal Release 3.7 ==<br />
* Updated term mappings generated by LOOM <br />
* Added boolean functionality to Search Web service and UI<br />
* Updated ontology content for the Resource Index<br />
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org <br />
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*<br />
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release April 2012)<br />
<br />
== BioPortal Release 3.6 ==<br />
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:<br />
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org<br />
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org<br />
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org<br />
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org<br />
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org<br />
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org<br />
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org<br />
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org<br />
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.<br />
* Major Updates and Fixes<br />
** Updated the ontologies used by the Annotator Web Services*<br />
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!<br />
<br />
(Release January 2012) <br />
<br />
== BioPortal Release 3.5 ==<br />
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display<br />
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation<br />
* Improved Annotator Web service response performance by 5-10x* <br />
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)* <br />
* Updated Ontology Recommender algorithm to provide better recommendations*<br />
* Added display of matched terms for Ontology Recommender*<br />
* Added Web service to get all namespaces for an ontology*<br />
* Bug Fixes <br />
** Display user-friendly names for RxNorm ontology properties<br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release December 2011)<br />
<br />
== BioPortal Release 3.4 ==<br />
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*<br />
* Limited access to “Private” ontologies via the Browse and Search pages<br />
* Added backend support to allow multiple administrators for a single ontology*<br />
* Added ability to copy to the clipboard a permanent link to any BioPortal term* <br />
* Bug Fixes <br />
** Resolved issue causing search to not display all matching terms* <br />
** Fixed Term Mappings tab display for IE 7 & 8* <br />
** Fixed RDF Ontology Download Web service<br />
** Fixed link to the list of resources included in the Resource Index* <br />
<br />
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions! <br />
<br />
(Release October 2011) <br />
<br />
== BioPortal Release 3.3 == <br />
New features include updates to the Web interface and Web services:<br />
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services <br />
* Updated Search page to remove Flash<br />
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies. <br />
* Added Help documentation <br />
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.<br />
* Bug Fix<br />
** Fixed the Filter by Account on the Mappings tab<br />
<br />
(Release date September 2011)<br />
<br />
== BioPortal Release 3.2 ==<br />
New features include updates to the Web interface and Web services:<br />
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender <br />
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service<br />
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples<br />
* Added support for access control for viewing ontologies <br />
* Added link to subscribe to BioPortal Notes emails <br />
* Synchronized “Jump To” feature with ontology parsing and display <br />
* Added documentation on Ontology Groups<br />
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter <br />
* Removed the metric "Number of classes without an author" <br />
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release. <br />
* Bug Fix<br />
** Fixed calculation of “Classes with no definition” metric<br />
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results <br />
<br />
<br />
'''''Firefox Extension for NCBO API Key''''':<br />
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org. <br />
<br />
'''''Upcoming software license change''''':<br />
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.<br />
<br />
== BioPortal Release 3.1 ==<br />
New features include updates to the Web interface and Web services:<br />
* Support for loading OWL 2 ontologies<br />
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key. <br />
* Browsing of ontologies that contain large numbers of sibling terms<br />
* Icons for is_a and part_of are displayed for OBO format ontologies <br />
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology <br />
Bug Fix<br />
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response<br />
<br />
(Release date July 8, 2011)<br />
<br />
== BioPortal Release 3.0 ==<br />
New features include updates to the Web interface and Web services:<br />
* Web interface updates<br />
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology<br />
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology<br />
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.<br />
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms<br />
* Form auto-complete Widget - Option to include term definition in display<br />
* Resource Index<br />
** Data indexed with new ontologies from BioPortal<br />
** PubMed data now available for abstracts published in 2010 <br />
<br />
(Release date May 19, 2011)<br />
<br />
== BioPortal Release 2.6.4 ==<br />
New features include additional Web services and Web interface enhancements:<br />
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23'' <br />
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )<br />
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display<br />
* Annotator<br />
** Updated ontology content<br />
** Offsets corrected for non-ASCII characters<br />
** Link to Annotator Web interface using parameters<br />
** Web interface enhancements<br />
* Display of ontology development status<br />
* Hyperlinks on term details page<br />
* Ability to add comments on Mappings<br />
<br />
(Release date February 2011)<br />
<br />
== BioPortal Release 2.5 ==<br />
New features in this release include the following:<br />
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.<br />
<br />
* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)<br />
<br />
* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).<br />
<br />
* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org<br />
<br />
* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.<br />
<br />
* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.<br />
<br />
* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings<br />
<br />
[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services<br />
<br />
(Release date June 9, 2010)</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12572NCBO Hackathon 20132013-01-29T01:54:45Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& '''register soon'''!] <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION:'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
----</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12571NCBO Hackathon 20132013-01-29T01:53:59Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& register] soon! <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''SOFTWARE DOCUMENTATION:'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''PROJECTS:'''<br />
* ''Based on participant interest''<br />
<br />
----</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12565NCBO Hackathon 20132013-01-24T08:01:26Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so [http://www.certain.com/system/profile/form/index.cfm?PKformID=0x1436515d8e3& register] soon! <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''DOCUMENTATION:'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''AGENDA:'''<br />
* ''Detailed Agenda to be posted soon!''<br />
<br />
----</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12564Dissemination Wiki2013-01-24T08:00:32Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
'''[[NCBO Hackathon 2013]]'''<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
* ''[http://www.certain.com/system/profile/web/index.cfm?PKwebID=0x430788962b&varPage=info Registration and Meeting Logistics here]''<br />
<br />
'''[http://wiki.plantontology.org/index.php/PRO-PO-GO_Meeting PRO-PO-GO Meeting]'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12559NCBO Hackathon 20132013-01-19T01:12:26Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so register soon! <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''DOCUMENTATION:'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''AGENDA:'''<br />
* ''Detailed Agenda to be posted soon!''<br />
<br />
----</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12558NCBO Hackathon 20132013-01-19T01:12:08Z<p>Whetzel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so register soon! <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''DOCUMENTATION:'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''AGENDA:'''<br />
''* Detailed Agenda to be posted soon!''<br />
<br />
----</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Hackathon_2013&diff=12557NCBO Hackathon 20132013-01-19T01:11:40Z<p>Whetzel: Created page with "The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dis..."</p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Hackathon as one of our [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination and Outreach] events. <br />
<br />
'''Venue:''' [http://stanford.edu Stanford University]<br />
* La Ka Shing Center Center for Learning, 291 Campus Drive, Rm LK005 (ground floor) Project Classroom, Stanford, CA 94305-5479<br />
* [http://bmir.stanford.edu/pages/view.php/maps_and_information Maps]<br />
<br />
'''Date:''' '''April 29-30, 2013''' <br />
<br />
'''Organization:''' [mailto:whetzel@stanford.edu Trish Whetzel] (NCBO / Stanford University) <br />
<br />
'''Registration:''' Early registration is $25, but spots are limited so register soon! <br />
<br />
The '''NCBO Hackathon''' will consist of two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from high-level application design to low-level coding. You will be able to:<br />
* Brainstorm ideas for applications<br />
* Discuss coding issues, performance tuning, and future development plans<br />
* Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)<br />
* Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language<br />
<br />
'''DOCUMENTATION:'''<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_REST_services NCBO Web services documentation]<br />
* [http://sparql.bioontology.org/examples BioPortal SPARQL query examples]<br />
* [http://www.bioontology.org/wiki/index.php/File:Whetzel_NCBO-Hackathon.pdf Slides] - this includes links to Sample code examples, GoogleDoc examples, and applications using the Web services.<br />
* [http://www.stanford.edu/~manuelso/ncbohack/index.html#%281%29 BioPortal SPARQL Endpoint Slides] - this includes information on the BioPortal SPARQL endpoint<br />
* [http://www.bioontology.org/wiki/index.php/File:Hackathon_Programming_TaskswithSPARQL.pdf Programming Tasks]<br />
<br />
'''AGENDA:'''''<br />
* Detailed Agenda to be posted soon!''<br />
<br />
----</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12556Dissemination Wiki2013-01-19T01:09:27Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
'''[[NCBO Hackathon 2013]]'''<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
* ''Registration link coming soon''<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12555Dissemination Wiki2013-01-19T01:08:46Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
'''NCBO Hackathon 2013'''<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
* ''Registration link coming soon''<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12548Dissemination Wiki2013-01-02T14:06:30Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
'''NCBO Hackathon'''<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
* ''Registration link coming soon''<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12547Dissemination Wiki2013-01-02T14:04:34Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
'''NCBO Hackathon'''<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12546Dissemination Wiki2013-01-02T14:04:20Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
'''NCBO Hackathon'''<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12545Dissemination Wiki2013-01-02T14:04:06Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
NCBO Hackathon<br />
* Stanford University, Stanford, CA, April 29-30, 2013<br />
<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12544Dissemination Wiki2013-01-02T03:02:16Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
* This course is aimed at those working in the development and implementation of biomedical applications and who wish to understand how ontologies can help with tasks such as annotation of data, searching and data integration. The course is suitable for both academics and industry alike, including advanced PhD students, research scientists and software developers. It is expected that those attending the course will already have some basic familiarity with what an ontology is though an overview of the basic features of an ontology will be given. There will be some exercises involving the use of Java and with using RESTful Web services so some understanding of Java would be required if you wish to participate in these exercises.<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12543Dissemination Wiki2013-01-02T03:01:30Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''[http://www.ebi.ac.uk/training/course/biomedical-ontologies#course_registration Building Applications with Biomedical Ontologies]'''<br />
* European Bioinformatics Institute, Hinxton, UK, April 18-19, 2013<br />
<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Category:NCBO_Virtual_Appliance&diff=12542Category:NCBO Virtual Appliance2012-12-27T18:42:23Z<p>Whetzel: </p>
<hr />
<div>The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system. The image was created using VMWare and is available for download by contacting support@bioontology.org.<br />
<br />
The following software is included on the image:<br />
* NCBO Web Services (BioPortal Core)<br />
* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
* Annotator<br />
* Resource Index<br />
<br />
Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.<br />
<br />
== Getting Started ==<br />
* To obtain the Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support]<br />
* The download is provided as a tar archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].<br />
* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.<br />
* '''Change default passwords'''<br />
** Operating System<br />
*** Username: <code>root</code><br />
*** Password: password is prompted on the first boot<br />
** BioPortal Admin User<br />
*** Username: <code>admin</code><br />
*** Password: <code>changeme</code><br />
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new<br />
** BioPortal Ontology Services can be configured to automatically process new ontologies every hour at 30 minutes past the hour (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:<br />
*** Parsing any new, unparsed ontologies<br />
*** Calculating a set of metrics for these ontologies<br />
*** Indexing these ontologies for use with search<br />
* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example:8080/bioportal_admin<br />
* REST services are available at the following locations. The URLs below are for the root of the REST service and generally will not return information. Please read the documentation for guidelines on how to interact with the services, including sample URLs:<br />
** NCBO Web Services - http://example:8080/bioportal ([http://www.bioontology.org/wiki/index.php/BioPortal_REST_services documentation])<br />
** Annotator - http://example:8080/obs/annotator ([http://www.bioontology.org/wiki/index.php/Annotator_User_Guide documentation])<br />
** Resource Index - http://example:8080/resource_index ([http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide documentation])<br />
<br />
== System Requirements ==<br />
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.<br />
<br />
'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.<br />
<br />
* Minimum<br />
** 1 CPU (2 GHz)<br />
** 4GB RAM<br />
** Hard disk space: 3GB<br />
<br />
* Recommended for heavier usage<br />
** 2 CPU (3 GHz)<br />
** 6GB RAM (When using more than 4GB RAM, you should configure Tomcat to use the additional memory)<br />
** Hard disk space: 10GB (or more depending on number/size of ontologies)<br />
<br />
== Population Workflows ==<br />
When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.<br />
<br />
<br />
NOTE: Loading ontologies [1] developed using the NCI version of Protege will require an additional manual pre-processing step to remove XML tags added into the synonym and definition property values. This pre-processing step is especially important for populating the correct synonym value into the Annotator workflow. The code to pre-process ontologies developed using the NCI version of Protege is located at:<br />
https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F, the code can be checked out via anonymous SVN. <br />
<br />
[1] The NCI Thesaurus and the NanoParticle Ontology are developed using the NCI version of Protege<br />
<br />
== Image Format and Operating System Details ==<br />
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.<br />
<br />
The operating system is CentOS 5.7 64-bit running Tomcat 6.0.26, Java 6, MySQL 5.1.x, PHP 5.1.6, Rails 2.3.x, and Ruby Enterprise Edition 1.8.7, and memcached.<br />
<br />
The following applications use these services/runtime environments:<br />
* Tomcat, Java<br />
** BioPortal Ontology Services (BioPortal Core)<br />
** BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
** Annotator and Recommender<br />
** Resource Index<br />
* Rails, Ruby, memcached<br />
** BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* PHP<br />
** Resource Index UI<br />
* 4store<br />
** Mappings<br />
<br />
== Basic System Administration ==<br />
* Most of our administration scripts and build environment assume that you will be running as the root user.<br />
* Helper commands:<br />
** <code>ncbostart</code>: the required services are started on boot automatically, but if they need to be started automatically<br />
** <code>ncbostop</code>: manually stop services<br />
** <code>ncborestart</code>: manually start/stop services<br />
* Start individual services:<br />
** <code>/sbin/service httpd start</code><br />
** <code>/sbin/service memcached start</code><br />
** <code>/sbin/service tomcat6 start</code><br />
** <code>/sbin/service mgrep start</code><br />
** <code>/sbin/service 4store start</code><br />
* Stop individual services:<br />
** <code>/sbin/service httpd stop</code><br />
** <code>/sbin/service memcached stop</code><br />
** <code>/sbin/service tomcat6 stop</code><br />
** <code>/sbin/service mgrep stop</code><br />
** <code>/sbin/service 4store stop</code><br />
<br />
== License ==<br />
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Category:NCBO_Virtual_Appliance&diff=12541Category:NCBO Virtual Appliance2012-12-27T18:41:39Z<p>Whetzel: /* Getting Started */</p>
<hr />
<div>The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system. The image was created using VMWare and is available for download by contacting support@bioontology.org.<br />
<br />
The following software is included on the image:<br />
* BioPortal Ontology Services (BioPortal Core)<br />
* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
* Annotator<br />
* Resource Index<br />
<br />
Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.<br />
<br />
== Getting Started ==<br />
* To obtain the Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support]<br />
* The download is provided as a tar archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].<br />
* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.<br />
* '''Change default passwords'''<br />
** Operating System<br />
*** Username: <code>root</code><br />
*** Password: password is prompted on the first boot<br />
** BioPortal Admin User<br />
*** Username: <code>admin</code><br />
*** Password: <code>changeme</code><br />
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new<br />
** BioPortal Ontology Services can be configured to automatically process new ontologies every hour at 30 minutes past the hour (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:<br />
*** Parsing any new, unparsed ontologies<br />
*** Calculating a set of metrics for these ontologies<br />
*** Indexing these ontologies for use with search<br />
* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example:8080/bioportal_admin<br />
* REST services are available at the following locations. The URLs below are for the root of the REST service and generally will not return information. Please read the documentation for guidelines on how to interact with the services, including sample URLs:<br />
** NCBO Web Services - http://example:8080/bioportal ([http://www.bioontology.org/wiki/index.php/BioPortal_REST_services documentation])<br />
** Annotator - http://example:8080/obs/annotator ([http://www.bioontology.org/wiki/index.php/Annotator_User_Guide documentation])<br />
** Resource Index - http://example:8080/resource_index ([http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide documentation])<br />
<br />
== System Requirements ==<br />
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.<br />
<br />
'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.<br />
<br />
* Minimum<br />
** 1 CPU (2 GHz)<br />
** 4GB RAM<br />
** Hard disk space: 3GB<br />
<br />
* Recommended for heavier usage<br />
** 2 CPU (3 GHz)<br />
** 6GB RAM (When using more than 4GB RAM, you should configure Tomcat to use the additional memory)<br />
** Hard disk space: 10GB (or more depending on number/size of ontologies)<br />
<br />
== Population Workflows ==<br />
When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.<br />
<br />
<br />
NOTE: Loading ontologies [1] developed using the NCI version of Protege will require an additional manual pre-processing step to remove XML tags added into the synonym and definition property values. This pre-processing step is especially important for populating the correct synonym value into the Annotator workflow. The code to pre-process ontologies developed using the NCI version of Protege is located at:<br />
https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F, the code can be checked out via anonymous SVN. <br />
<br />
[1] The NCI Thesaurus and the NanoParticle Ontology are developed using the NCI version of Protege<br />
<br />
== Image Format and Operating System Details ==<br />
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.<br />
<br />
The operating system is CentOS 5.7 64-bit running Tomcat 6.0.26, Java 6, MySQL 5.1.x, PHP 5.1.6, Rails 2.3.x, and Ruby Enterprise Edition 1.8.7, and memcached.<br />
<br />
The following applications use these services/runtime environments:<br />
* Tomcat, Java<br />
** BioPortal Ontology Services (BioPortal Core)<br />
** BioPortal Admin (a UI for administering BioPortal Ontology Services)<br />
** Annotator and Recommender<br />
** Resource Index<br />
* Rails, Ruby, memcached<br />
** BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)<br />
* PHP<br />
** Resource Index UI<br />
* 4store<br />
** Mappings<br />
<br />
== Basic System Administration ==<br />
* Most of our administration scripts and build environment assume that you will be running as the root user.<br />
* Helper commands:<br />
** <code>ncbostart</code>: the required services are started on boot automatically, but if they need to be started automatically<br />
** <code>ncbostop</code>: manually stop services<br />
** <code>ncborestart</code>: manually start/stop services<br />
* Start individual services:<br />
** <code>/sbin/service httpd start</code><br />
** <code>/sbin/service memcached start</code><br />
** <code>/sbin/service tomcat6 start</code><br />
** <code>/sbin/service mgrep start</code><br />
** <code>/sbin/service 4store start</code><br />
* Stop individual services:<br />
** <code>/sbin/service httpd stop</code><br />
** <code>/sbin/service memcached stop</code><br />
** <code>/sbin/service tomcat6 stop</code><br />
** <code>/sbin/service mgrep stop</code><br />
** <code>/sbin/service 4store stop</code><br />
<br />
== License ==<br />
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12540BioPortal REST services2012-12-19T15:55:58Z<p>Whetzel: /* List all the latest version of ontologies */</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
Ontology files that were successfully parsed have a value of 3 for the <statusId> attribute in the XML response.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do work for ontology views also with the same signature.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}<br />
** To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
Examples using Alt Signature<br />
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
Examples using Alt Virtual Signature<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
** '''NOTE''': To ensure that the Web service works within your application, url-encode the concept id as some ontologies may contain terms where the concept id is a URI.<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12539BioPortal REST services2012-12-19T15:53:53Z<p>Whetzel: /* Download the latest ontology file */</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do work for ontology views also with the same signature.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}<br />
** To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
Examples using Alt Signature<br />
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
Examples using Alt Virtual Signature<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
** '''NOTE''': To ensure that the Web service works within your application, url-encode the concept id as some ontologies may contain terms where the concept id is a URI.<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=12538BioPortal REST services2012-12-19T15:51:30Z<p>Whetzel: /* Download an ontology file */</p>
<hr />
<div>The list below documents the NCBO Web services. For questions on how to use these Web services or to request features, contact [mailto:support@bioontology.org Support]. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/<br />
<br />
* '''<font color='red'>Note</font>''': All NCBO Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, [http://bioportal.bioontology.org/login login to BioPortal] and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter. <br />
<br />
* '''''Note for Application Developers''''': Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.<br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. <br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Sample Code Cookbook = <br />
*Examples of using the Web services in sample code can be found [http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook here]<br />
**Sample code is located within the [https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F NCBO Gforge repository] and can be checked out via anonymous SVN access<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] are located on the pages documenting these Web services<br />
<br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Service Output Formats =<br />
''JSON output scheduled for mid-December release''<br />
Currently, BioPortal services allow for two output formats: <strong>XML</strong> (default) and <strong>JSON</strong> (currently works only for ontology and concept services).<br />
<br />
* '''XML''': no special parameters required. This is the default REST services output format. It assumes the media type as <strong>application/xml</strong>.<br />
* '''JSON''': requires an "Accept" request-header with the following value: <strong>application/json</strong>. <br />
<br />
If both <strong>application/xml</strong> and <strong>application/json</strong> media types are present in the Accept header, the output format will be determined based on the higher "q" parameter indicating a relative quality factor of each media type. For more info, please refer to: http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html<br />
<br />
'''NOTE:''' JSON output is currently not available for Annotator Service.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Description''': Return a list of ontologies in BioPortal. To get information on Ontology Views, use the "List the latest version of all Views" Web service call. <br />
* '''Signature''': ./ontologies?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey<br />
** NOTE: The element <id> contains the value for the ontology version identifier.<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?apikey=YourAPIKey<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?apikey=YourAPIKey<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?apikey=YourAPIKey<br />
<br />
== Get Metrics for an ontology version ==<br />
* '''Signature''': ./ontologies/metrics/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey<br />
* More documentation: http://www.bioontology.org/wiki/index.php/Ontology_Metrics<br />
<br />
== Get all the namespace prefixes for an ontology version ==<br />
* '''Signature''': ./ontologies/namespaces/{ontology version id}?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/namespaces/44450?apikey=YourAPIKey<br />
<br />
== List all ontology categories == <br />
* '''Signature''': ./categories?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories?apikey=YourAPIKey<br />
<br />
== List all ontology groups ==<br />
* '''Signature''': ./groups?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups?apikey=YourAPIKey<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do work for ontology views also with the same signature.<br />
<br />
== Download a specific ontology view based on the ontology view version id ==<br />
* '''Signature''': ./ontologies/download/{ontology version id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey<br />
* '''Note''': File downloads can include zip archives. Where multiple files are included in the archive, BioPortal uses the following algorithm to determine the primary file: 1) look for a file named the same as the archive with a different extension (IE .owl instead of .zip) and 2) if no similarly-named file exists, use the first file in the list when sorted alphabetically.<br />
<br />
== Get all view versions of a virtual view == <br />
<br />
* '''Signature''': ./ontologies/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/2070?apikey=YourAPIKey<br />
<br />
<br />
However, there are a few Web services that are distinct for views. <br />
<br />
== List the latest version of all Views == <br />
* '''Signature''': ./views?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?apikey=YourAPIKey<br />
<br />
== Get all versions of views from a virtual ontology id == <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?apikey=YourAPIKey<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/?query={uri-encoded query}[&{optional args}]&apikey={YourAPIKey}<br />
* '''Deprecated Signature''': ./search/{query}[?{optional args}]&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&apikey=YourAPIKey<br />
<br />
* '''Boolean Search Options:'''<br />
** () parentheses allow to enclose multiple terms joined by OR<br />
*** <pre>Example: "(foo bar)" will expand to "foo* OR bar*"</pre><br />
** - the minus sign preceding a term indicates NOT<br />
*** <pre>Example: "foo bar -baz" will expand to "foo* AND bar* AND NOT baz*"</pre><br />
** No prefix means MUST (required).<br />
<br />
* '''Optional Arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
** objecttypes=<class,individual,property> - limits the results returned to these types, multitple types can be included in the parameter, e.g. class,individual.<br />
** includedefinitions={true} - if a search result is a hit for a term, adding this parameter will include the definition in the search result xml. '''Note''': Including the definition results in a slight performance hit.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Field Values'''<br />
** The '<recordType></recordType>' entries can be: PREFERRED_NAME = "apreferredname", CONCEPT_ID = "bconceptid", SYNONYM = "csynonym", and PROPERTY = "dproperty".<br />
** The '<objectType></objectType>' entries are concept types, which can be: "class", "property", or "individual".<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/?query=Gene&ontologyids=1032&isexactmatch=1&apikey=YourAPIKey<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/search/</accessedResource><br />
<accessDate>2012-07-06 10:31:44.413 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>2</pageSize><br />
<numResultsPage>2</numResultsPage><br />
<numResultsTotal>2</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>apreferredname</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene</conceptId><br />
<conceptIdShort>Gene</conceptIdShort><br />
<preferredName>Gene</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>0</isObsolete><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<recordType>csynonym</recordType><br />
<objectType>class</objectType><br />
<conceptId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Object</conceptId><br />
<conceptIdShort>Gene_Object</conceptIdShort><br />
<preferredName>Gene Object</preferredName><br />
<contents>Gene</contents><br />
<isObsolete>1</isObsolete><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>47638</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel>NCI Thesaurus</ontologyDisplayLabel><br />
<numHits>2</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
<numHitsTotal>3</numHitsTotal><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term, including its properties, subclasses, and superclasses ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?apikey={YourAPIKey}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&apikey={YourAPIKey}<br />
* '''Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}/{concept id}&apikey={YourAPIKey}<br />
* '''Alt Virtual Signature''' (always uses most recent version of the ontology): ./virtual/ontology/{ontology id}?conceptid={uri-encoded concept id}<br />
** To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
** maxnumchildren - an integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
Examples using Alt Signature<br />
* http://rest.bioontology.org/bioportal/concepts/44103?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/concepts/44450?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
Examples using Alt Virtual Signature<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1516?conceptid=O80-O84.9&apikey=YourAPIKey<br />
* http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey<br />
<br />
<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8"?><br />
<success><br />
<accessedResource>/bioportal/concepts/44103</accessedResource><br />
<accessDate>2010-12-08 16:57:43.763 PST</accessDate><br />
<data><br />
<classBean><br />
<id>O80-O84.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId><br />
<br />
<label>Delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<br />
<id>O84</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId><br />
<label>Multiple delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O83</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId><br />
<br />
<label>Other assisted single delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>7</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O82</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId><br />
<label>Single delivery by caesarean section</label><br />
<type>Class</type><br />
<br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>5</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<br />
<id>O81</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId><br />
<label>Single delivery by forceps and vacuum extractor</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>6</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<id>O80</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId><br />
<br />
<label>Single spontaneous delivery</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<int>4</int><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>PAR</string><br />
<list><br />
<classBean><br />
<br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<entry><br />
<string>ChildCount</string><br />
<br />
<int>5</int><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Therapeutic or Preventive Procedure</string><br />
</list><br />
<br />
</entry><br />
<entry><br />
<string>TUI</string><br />
<list><br />
<string>T061</string><br />
</list><br />
</entry><br />
<entry><br />
<br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0011209</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SuperClass</string><br />
<br />
<list><br />
<classBean><br />
<id>O00-O99.9</id><br />
<fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId><br />
<label>Pregnancy, childbirth and the puerperium</label><br />
<type>Class</type><br />
<relations><br />
<br />
<entry><br />
<string>ChildCount</string><br />
<int>8</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
<br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?apikey=YourAPIKey<br />
<br />
== Get a path between a term and the root ==<br />
<br />
* '''Signature''': ./path/{ontology_version_id}/?source={concept1_id}&target=root&apikey=YourAPIKey<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/path/42838/?source=Transitional_Epithelium&target=root&apikey=YourAPIKey<br />
* Note: If there is no path between the specified term and the set of nodes designated as "roots" then this method just returns the root node. Note that "root" here is defined as a set of classes which have been designated as "roots". It is not defined as a node which as no parents.<br />
* Note: This service only returns a '''single path''' between a term and the root. There is a [[NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology|service that returns '''all paths''' from a term to the root]] for most ontologies. Alternatively, all paths can be calculated by recursively calling [[NCBO_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses|the term service]].<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&apikey=YourAPIKey<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
*** '''maxnumchildren:''' An integer that sets threshold on the number of children in the SubClass relation for a term. If a term contains more children than the "maxnumchildren", the SubClass relation returns an empty list. The ChildCount relation still contains the correct number of children.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Property Services =<br />
<br />
== Get all available ontology properties using the specific ontology version id ==<br />
* '''Signature''': ./ontologies/properties/{ontlogyVersionId}?apikey={YourAPIKey} <br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey<br />
* '''Description''': returns all properties for a given ontology version.<br />
* '''Sample Output:'''<br />
<pre><br />
<success><br />
<accessedResource>/bioportal/ontologies/properties/38801<br />
</accessedResource><br />
<accessDate>2011-09-22 15:47:46.309 PDT</accessDate><br />
<data><br />
<list><br />
<propertyBean><br />
<id>has_value</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_value<br />
</fullId><br />
<label>has_value</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_description</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_description<br />
</fullId><br />
<label>has_description</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</propertyBean><br />
<propertyBean><br />
<id>has_pages</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#has_pages<br />
</fullId><br />
<label>has_pages</label><br />
<type>property</type><br />
<isObsolete>0</isObsolete><br />
<relations><br />
<entry><br />
<string>Domain</string><br />
<classBean><br />
<id>BibliographicReference</id><br />
<fullId>http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference<br />
</fullId><br />
<label>BibliographicReference</label><br />
<type>class</type><br />
<isObsolete>0</isObsolete><br />
<relations /><br />
</classBean><br />
</entry><br />
</relations><br />
</propertyBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}?conceptid={uri-encoded concept id}[&{optional args}]&apikey={YourAPIKey} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=10&pagenum=1&apikey=YourAPIKey<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}?instanceid={instanceid}&apikey={YourAPIKey}<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&apikey=YourAPIKey<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services provide access to pre-computed term hierarchy information via a single web service call. The pre-computed hierarchy data is generated for only one version of an ontology and is periodically updated. Therefore, if using the Hierarchy Web services, it is best to use the form of the call with the virtual ontology id. To get hierarchy information for any version of an ontology, use the Term Web service to traverse the ontology structure. <br />
<br />
* '''<font color='red'>NOTE: </font>To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Neoplasm?apikey=YourAPIKey<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?apikey=YourAPIKey (returns an empty list since the term Melanoma is a leaf node)<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** delim=<string> – use a custom delimiter between returned terms. Default is a period (.).<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology available via the Hierarchy web services. To see which ontology versions are available, see the '''<font color='red'>NOTE</font>''' above for the [http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hierarchy_Services Hierarchy web services].<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?apikey={YourAPIKey}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?apikey=YourAPIKey<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Ontology Recommender =<br />
The Ontology Recommender is a Web service that provides information on what ontology is best covered by your text metadata. An in-depth description and links to the Web service documentation and sample clients can be found at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
<br />
<br />
= RDF Term Service =<br />
<br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id}&apikey=YourAPIKey<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/?conceptid={concept id},{concept id},...,{concept id}&apikey=YourAPIKey<br />
** '''NOTE''': To ensure that the Web service works within your application, url-encode the concept id as some ontologies may contain terms where the concept id is a URI.<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/?conceptid=NEMO_0000024&apikey=YourAPIKey<br />
** http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO#"<br />
xml:base="http://purl.bioontology.org/ontology/NEMO"<br />
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"<br />
xmlns:BPMetadata="http://purl.bioontology.org/ontology/BPMetadata#"<br />
xmlns:owl="http://www.w3.org/2002/07/owl#"<br />
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"<br />
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br />
xmlns:NEMO="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#"<br />
xmlns:ontology="http://omv.ontoware.org/2005/05/ontology/"<br />
xmlns:skos="http://www.w3.org/2004/02/skos/core#"<br />
xmlns:ontology2="http://purl.bioontology.org/NEMO/ontology#"><br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO"><br />
<ontology:name>Neural ElectroMagnetic Ontologies</ontology:name><br />
<ontology:acronym>NEMO</ontology:acronym><br />
<ontology:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</ontology:description><br />
<BPMetadata:id>45141</BPMetadata:id><br />
<ontology:hasOntologyLanguage rdf:resource="http://omv.ontoware.org/2005/05/ontology#owl"/><br />
</owl:Ontology><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Annotation properties<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/name"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_synonym"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_definition"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#definition"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/ontology/BPMetadata#id"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#broader"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subClassOf"/><br />
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/NEMO/ontology#NEMO_pref_label"><br />
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/><br />
</owl:AnnotationProperty><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/acronym"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#notation"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/description"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/><br />
<owl:AnnotationProperty rdf:about="http://omv.ontoware.org/2005/05/ontology/hasOntologyLanguage"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#subPropertyOf"/><br />
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/><br />
<br />
<br />
<br />
<!-- <br />
///////////////////////////////////////////////////////////////////////////////////////<br />
//<br />
// Classes<br />
//<br />
///////////////////////////////////////////////////////////////////////////////////////<br />
--><br />
<br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<br />
<br />
<br />
<!-- http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024 --><br />
<br />
<owl:Class rdf:about="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000024"><br />
<rdfs:label>left_posterotemporal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
<skos:prefLabel>left_posterotemporal_scalp_surface_region</skos:prefLabel><br />
<skos:notation>NEMO_0000024</skos:notation><br />
<ontology2:NEMO_pref_label>left_posterotemporal_scalp_surface_region</ontology2:NEMO_pref_label><br />
<skos:broader rdf:resource="http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_0000010"/><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1451) http://owlapi.sourceforge.net --><br />
<br />
<br />
</pre><br />
<br />
= RDF Download Service =<br />
<br />
* '''Signature''': ./bioportal/virtual/ontology/rdf/download/{ontology id}?apikey=YourAPIKey<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/ontology/rdf/download/1537?apikey=YourAPIKey<br />
''NOTE:'' If using the Web service calls from Firefox, disable the Tabulator Add-on in order to download the files. <br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
= Notes Service (Term Proposals and Comments) =<br />
* The Notes Web service is described here: http://www.bioontology.org/wiki/index.php/Ontology_Notes.<br />
<br />
= Mapping Service = <br />
* The Mapping Web service is described here: http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service. <br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|Term]] and [[#Hierarchy_Services|Hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12537BioPortal Mappings2012-12-10T22:26:56Z<p>Whetzel: /* Survey of BioPortal Mappings */</p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping sources and common relationships in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
= Mapping Sources =<br />
<br />
* [http://www.bioontology.org/ The National Center for Biomedical Ontology (NCBO)] <br />
** '''NCBO lexical mapping (loom)''': Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded. These mappings are represented by the mapping relationship '''skos:closeMatch'''.<br />
** '''NCBO Identical URI (loom)''': Mapping for terms with the same URI from different ontologies. These mappings are represented by the mapping relationship '''skos:exactMatch'''.<br />
<br />
* [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS)]<br />
** '''NLM UMLS (CUI)''': Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM. These mappings are represented by the mapping relationship '''skos:closeMatch'''.<br />
** '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data. These mappings are represented by the mapping relationship '''skos:closeMatch'''.<br />
<br />
* [http://obofoundry.org/ The Open Biological and Biomedical Ontologies (OBO)]<br />
** '''OBO xref''': Mappings between ontology terms related by an OBO xref property. These mappings are represented by the mapping relationship '''skos:relatedMatch'''.<br />
** See also, [http://obofoundry.org/index.cgi?show=mappings OBO mappings]<br />
<br />
= Mapping Relationships =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| skos:relatedMatch||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Mappings&diff=12536BioPortal Mappings2012-12-10T22:22:37Z<p>Whetzel: /* Mapping Sources */</p>
<hr />
<div>= BioPortal Mapping Notes =<br />
<br />
This page documents mapping sources and common relationships in the [http://bioportal.bioontology.org NCBO BioPortal], with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to [mailto:support@bioontology.org support@bioontology.org].<br />
<br />
== Related Mapping Documents ==<br />
<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]<br />
* [http://bioportal.bioontology.org/mappings BioPortal Mappings]<br />
<br />
= Mapping Sources =<br />
<br />
* [http://www.bioontology.org/ The National Center for Biomedical Ontology (NCBO)] <br />
** '''NCBO lexical mapping (loom)''': Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded. These mappings are represented by the mapping relationship '''skos:closeMatch'''.<br />
** '''NCBO Identical URI (loom)''': Mapping for terms with the same URI from different ontologies. These mappings are represented by the mapping relationship '''skos:exactMatch'''.<br />
<br />
* [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS)]<br />
** '''NLM UMLS (CUI)''': Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM. These mappings are represented by the mapping relationship '''skos:closeMatch'''.<br />
** '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data. These mappings are represented by the mapping relationship '''skos:closeMatch'''.<br />
<br />
* [http://obofoundry.org/ The Open Biological and Biomedical Ontologies (OBO)]<br />
** '''OBO xref''': Mappings between ontology terms related by an OBO xref property. These mappings are represented by the mapping relationship '''skos:relatedMatch'''.<br />
** See also, [http://obofoundry.org/index.cgi?show=mappings OBO mappings]<br />
<br />
= Mapping Relationships =<br />
<br />
There are mappings of the following types in BioPortal:<br />
<br />
* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]<br />
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual<br />
<br />
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]<br />
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource. <br />
<br />
* '''related match''': [http://www.w3.org/2004/02/skos/core#relatedMatch skos:relatedMatch]<br />
** '''Definition''': (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:relatedMatch</tt> is used to state an associative mapping link between two concepts; <tt>skos:relatedMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>. <br />
** '''Symmetry''': <tt>skos:relatedMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:relatedMatch <conceptB> .<br />
<conceptB> skos:relatedMatch <conceptA> .<br />
<br />
* '''close match''': [http://www.w3.org/2004/02/skos#closeMatch skos:closeMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property. The <tt>skos:closeMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:closeMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:closeMatch <conceptB> .<br />
<conceptB> skos:closeMatch <conceptA> .<br />
<br />
* '''exact match''': [http://www.w3.org/2004/02/skos#exactMatch skos:exactMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The <tt>skos:exactMatch</tt> it is a sub-property of <tt>skos:closeMatch</tt> and, in addition, it is an instance of <tt>owl:TransitiveProperty</tt>. Also, <tt>skos:exactMatch</tt> is disjoint with each of the properties <tt>skos:relatedMatch</tt>, <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt>.<br />
** '''Symmetry''': <tt>skos:exactMatch</tt> is an instance of <tt>owl:SymmetricProperty</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:exactMatch <conceptB> .<br />
<conceptB> skos:exactMatch <conceptA> .<br />
<br />
* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:broadMatch <conceptB> .<br />
<conceptB> skos:narrowMatch <conceptA> .<br />
<br />
* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]<br />
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.<br />
** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:<br />
<br />
<conceptA> skos:narrowMatch <conceptB> .<br />
<conceptB> skos:broadMatch <conceptA> .<br />
<br />
* '''homologous to''' (for anatomical terms): ''not defined yet''<br />
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).<br />
<br />
= Survey of BioPortal Mappings =<br />
The table below presents the statistics and examples of BioPortal mappings as of July 2010.<br />
<br />
{| border="1" cellpadding="2"<br />
| align="center" style="background:#f0f0f0;"|'''relationship'''<br />
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''<br />
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''<br />
| align="center" style="background:#f0f0f0;"|'''Source'''<br />
| align="center" style="background:#f0f0f0;"|'''Total mappings'''<br />
| width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''<br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings<br />
<br />
<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings<br />
<br />
<tt>select * from mappings where map_source = "exact match or synonym match";</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Manual||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology<br />
<br />
<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt><br />
|-<br />
| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt><br />
|-<br />
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms<br />
<br />
<tt>select * from mappings where map_source = "OBO xref";</tt><br />
|-<br />
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs<br />
<br />
<tt>select * from mappings where map_source = "DbXref";</tt><br />
|-<br />
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO<br />
<br />
<tt>select * from mappings where map_source = "Upload"; </tt><br />
|-<br />
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt><br />
|-<br />
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface<br />
<br />
<tt>select * from mappings where map_source = "BioPortal UI"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT <br />
<br />
<tt>select * from mappings where map_source = "NCICB"</tt><br />
|-<br />
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity<br />
<br />
<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt><br />
|-<br />
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT<br />
<br />
<tt>select * from mappings where map_source = "NLM"</tt><br />
|}</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=SWAT4LS2012_Tutorial&diff=12535SWAT4LS2012 Tutorial2012-11-29T16:58:55Z<p>Whetzel: Created page with "Tutorial documentation to be added here. <pre> Example queries --> Slide 27 -- Select count of all terms from ABA. Result is 913 rows returned. PREFIX owl: <http://www.w3.or..."</p>
<hr />
<div>Tutorial documentation to be added here.<br />
<br />
<pre><br />
Example queries<br />
--> Slide 27<br />
-- Select count of all terms from ABA. Result is 913 rows returned.<br />
PREFIX owl: <http://www.w3.org/2002/07/owl#><br />
SELECT (count(*) as ?c)<br />
FROM <http://bioportal.bioontology.org/ontologies/ABA><br />
WHERE {<br />
?s a owl:Class .<br />
}<br />
<br />
-- Select count of all terms from ABA and HP. Result is 10855 rows returned.<br />
PREFIX owl: <http://www.w3.org/2002/07/owl#><br />
SELECT (count(*) as ?c)<br />
FROM <http://bioportal.bioontology.org/ontologies/ABA><br />
FROM <http://bioportal.bioontology.org/ontologies/HP><br />
WHERE {<br />
?s a owl:Class .<br />
}<br />
<br />
-- Select all distinct triples that have the specified URI as a subject<br />
PREFIX owl: <http://www.w3.org/2002/07/owl#><br />
SELECT DISTINCT *<br />
WHERE {<br />
<http://purl.obolibrary.org/obo/BFO_0000001> ?p ?o .<br />
}<br />
<br />
<br />
--> Slide 29<br />
-- Select the URI and preferred name from ABA (OWL format) and HP (OBO format) using the "globals" graph<br />
PREFIX owl: <http://www.w3.org/2002/07/owl#><br />
PREFIX skos: <http://www.w3.org/2004/02/skos/core#><br />
SELECT DISTINCT ?termURI ?prefLabel<br />
FROM <http://bioportal.bioontology.org/ontologies/ABA><br />
FROM <http://bioportal.bioontology.org/ontologies/HP><br />
FROM <http://bioportal.bioontology.org/ontologies/globals> <br />
WHERE {<br />
?termURI a owl:Class;<br />
skos:prefLabel ?prefLabel .<br />
} <br />
LIMIT 20 //limit added for demo query<br />
<br />
<br />
--> Slide 30<br />
-- Select all ontology graphs<br />
PREFIX meta: <http://bioportal.bioontology.org/metadata/def/><br />
SELECT DISTINCT ?graph <br />
WHERE {<br />
[] meta:hasDataGraph ?graph <br />
}<br />
ORDER BY ?graph<br />
<br />
--> No slide<br />
-- Select the count of all graphs<br />
PREFIX meta: <http://bioportal.bioontology.org/metadata/def/> <br />
SELECT (COUNT(?graph) as ?c)<br />
WHERE { <br />
[] meta:hasDataGraph ?graph<br />
}<br />
<br />
<br />
--> Slide 31<br />
-- Describe SNOMEDCT<br />
DESCRIBE <http://bioportal.bioontology.org/ontologies/46896><br />
<br />
<br />
--> Slide 32<br />
-- Select all ontologies updated since some DATE<br />
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#><br />
PREFIX meta: <http://bioportal.bioontology.org/metadata/def/><br />
PREFIX omv: <http://omv.ontoware.org/2005/05/ontology#><br />
<br />
SELECT ?version ?name ?creation WHERE { <br />
?version a omv:Ontology .<br />
?version omv:name ?name .<br />
?version meta:timestampCreation ?creation .<br />
FILTER (xsd:dateTime(?creation) > "2012-10-01T00:00:00"^^xsd:dateTime)<br />
} ORDER BY ?name<br />
<br />
<br />
--> Slide 33<br />
-- Select the latest versions of all ontologies<br />
PREFIX meta: <http://bioportal.bioontology.org/metadata/def/> <br />
PREFIX omv: <http://omv.ontoware.org/2005/05/ontology#><br />
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#><br />
<br />
SELECT ?ont ?name ?acr ?creationDate ?contactName ?terms<br />
WHERE { <br />
?ont a omv:Ontology;<br />
omv:acronym ?acr;<br />
omv:name ?name;<br />
meta:timestampCreation ?creationDate .<br />
OPTIONAL { ?ont meta:hasContactName ?contactName . }<br />
OPTIONAL { ?ont omv:numberOfClasses ?terms . }<br />
} ORDER BY DESC(xsd:dateTime(?creationDate))<br />
<br />
<br />
--> No slide <br />
-- List unique graphs and their metadata<br />
PREFIX meta: <http://bioportal.bioontology.org/metadata/def/> <br />
PREFIX omv: <http://omv.ontoware.org/2005/05/ontology#><br />
SELECT ?ont ?name ?acronym<br />
WHERE { <br />
?ont meta:hasDataGraph ?graph .<br />
?ont a omv:Ontology .<br />
?ont omv:name ?name .<br />
?ont omv:acronym ?acronym .<br />
}<br />
ORDER BY ?acronym<br />
LIMIT 10 //limit added for demo<br />
<br />
<br />
--> No slide<br />
-- Download an ontology<br />
CONSTRUCT { ?s ?p ?o } WHERE {<br />
GRAPH <http://bioportal.bioontology.org/ontologies/1580> {<br />
?s ?p ?o .<br />
}<br />
}<br />
<br />
<br />
--> Slide 34 <br />
-- Select all graphs that contain a term URI<br />
PREFIX owl: <http://www.w3.org/2002/07/owl#><br />
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#><br />
<br />
SELECT DISTINCT ?graph WHERE {<br />
GRAPH ?graph {<br />
<http://mouse.brain-map.org/atlas/index.html#RHP> a owl:Class .<br />
}<br />
}<br />
</pre></div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12534Dissemination Wiki2012-11-29T16:58:02Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS2012 Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12533Dissemination Wiki2012-11-29T16:57:43Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS Tutorial | SWAT4LS2012 Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12532Dissemination Wiki2012-11-29T16:57:26Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS Tutorial | SWAT4LS Tutorial]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12531Dissemination Wiki2012-11-29T16:56:40Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''[[SWAT4LS Tutorial | ]]'''<br />
* Paris, November 29, 2012<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12530Dissemination Wiki2012-11-29T16:54:20Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''SWAT4LS Tutorial'''<br />
* Paris, November 29, 2012<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12529Dissemination Wiki2012-11-29T16:54:10Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''SWAT4LSTutorial'''<br />
* Paris, November 29, 2012<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzelhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=12528Dissemination Wiki2012-11-29T16:52:46Z<p>Whetzel: /* NCBO Dissemination and Outreach: Future Events */</p>
<hr />
<div>== NCBO Dissemination and Outreach: Future Events == <br />
<br />
'''SWAT4LS Tutorial'''<br />
* Paris, November 29, 2012<br />
<br />
'''PRO-PO-GO Meeting'''<br />
*Buffalo, NY, May 15-16, 2013<br />
*The goal of this meeting is to enhance ontology coordination in relation to plant genomics, proteomics and related fields. A special focus will be the ontological treatment of diseases and phenotypes in relation to all organisms.<br />
<br />
'''NCBO Webinar Series'''<br />
* The full list of Webinar presentations and recordings for past presentations is available [http://www.bioontology.org/webinar-series here]<br />
<br />
==Past Events==<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005 - 2012)]]'''<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/learning-about-ontologies here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations]]</div>Whetzel