NCBO Wiki - User contributions [en]

Annotator Web service

2009-05-06T16:56:01Z

Benjamindai:

''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations
''

=== Presentation & Demonstration ===

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.

[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]

=== Contacts ===

* Community & usage: [[mailto:whetzel@stanford.edu Trish Whetzel]]
* Design, utility & applications: [[mailto:nigam@stanford.edu Nigam Shah]] and [[mailto:jonquet@stanford.edu Clement Jonquet]]
* Technical support: [[mailto:cyoun@stanford.edu Cherie Youn]]

=== Documentation ===

* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]

* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.

=== Versions (prototypes & releases) ===

* April 2009 - First production release.

* March 2009 - Prototype user interface has been deployed on the BioPortal staging server. Please contact us to try it.

* October 2008 - The new prototype (v1.1) has bee released for testing and evaluation. Please check it out: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]

* May 2008 - First prototype (v1.0) - Has been removed from servers.

=== Community ===

After 8 months of existence OBA counts already 8 academic groups (Univ. of California, San Francisco, Univ. of Indiana, Jackson Lab) that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resources index Web services]]).

Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]

Annotator Web service

2009-05-05T23:38:46Z

Benjamindai: /* Annotator Web Service Documentation */

''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations
''
=== Annotator Web Service Documentation ===

The following link presents the user guide documentation on how to access and use the Annotator services:

[http://www.bioontology.org/wiki/index.php/Annotator_User_Guide Annotator User Guide]

=== Presentation & Demonstration ===

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.

[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]

=== Contacts ===

* Community & usage: [[mailto:whetzel@stanford.edu Trish Whetzel]]
* Design, utility & applications: [[mailto:nigam@stanford.edu Nigam Shah]] and [[mailto:jonquet@stanford.edu Clement Jonquet]]
* Technical support: [[mailto:cyoun@stanford.edu Cherie Youn]]

=== Documentation ===

* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.

* Annotator Restlet User's Guide [[Annotator_User_Guide]]

=== Versions (prototypes & releases) ===

* April 2009 - First production version to come.

* March 2009 - Prototype user interface has been deployed on the BioPortal staging server. Please contact us to try it.

* October 2008 - The new prototype (v1.1) has bee released for testing and evaluation. Please check it out: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]

* May 2008 - First prototype (v1.0) - Has been removed from servers.

=== Community ===

After 8 months of existence OBA counts already 8 academic groups (Univ. of California, San Francisco, Univ. of Indiana, Jackson Lab) that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resources index Web services]]).

Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]

Annotator Web service

2009-05-05T23:38:20Z

Benjamindai: /* Annotator Web Service Documentation */

''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations
''
=== Annotator Web Service Documentation ===

The following link presents the user guide documentation on how to access and use the Annotator services:

[http://www.bioontology.org/wiki/index.php/Annotator_User_Guide]

=== Presentation & Demonstration ===

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.

[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]

=== Contacts ===

* Community & usage: [[mailto:whetzel@stanford.edu Trish Whetzel]]
* Design, utility & applications: [[mailto:nigam@stanford.edu Nigam Shah]] and [[mailto:jonquet@stanford.edu Clement Jonquet]]
* Technical support: [[mailto:cyoun@stanford.edu Cherie Youn]]

=== Documentation ===

* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.

* Annotator Restlet User's Guide [[Annotator_User_Guide]]

=== Versions (prototypes & releases) ===

* April 2009 - First production version to come.

* March 2009 - Prototype user interface has been deployed on the BioPortal staging server. Please contact us to try it.

* October 2008 - The new prototype (v1.1) has bee released for testing and evaluation. Please check it out: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]

* May 2008 - First prototype (v1.0) - Has been removed from servers.

=== Community ===

After 8 months of existence OBA counts already 8 academic groups (Univ. of California, San Francisco, Univ. of Indiana, Jackson Lab) that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resources index Web services]]).

Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]

Annotator Web service

2009-05-05T23:38:05Z

Benjamindai:

''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations
''
=== Annotator Web Service Documentation ===

The following link presents the user guide documentation on how to access and use the Annotator services.
[http://www.bioontology.org/wiki/index.php/Annotator_User_Guide Annotator]

=== Presentation & Demonstration ===

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.

[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]

=== Contacts ===

* Community & usage: [[mailto:whetzel@stanford.edu Trish Whetzel]]
* Design, utility & applications: [[mailto:nigam@stanford.edu Nigam Shah]] and [[mailto:jonquet@stanford.edu Clement Jonquet]]
* Technical support: [[mailto:cyoun@stanford.edu Cherie Youn]]

=== Documentation ===

* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.

* Annotator Restlet User's Guide [[Annotator_User_Guide]]

=== Versions (prototypes & releases) ===

* April 2009 - First production version to come.

* March 2009 - Prototype user interface has been deployed on the BioPortal staging server. Please contact us to try it.

* October 2008 - The new prototype (v1.1) has bee released for testing and evaluation. Please check it out: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]

* May 2008 - First prototype (v1.0) - Has been removed from servers.

=== Community ===

After 8 months of existence OBA counts already 8 academic groups (Univ. of California, San Francisco, Univ. of Indiana, Jackson Lab) that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resources index Web services]]).

Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]

Main Page

2009-05-05T23:20:54Z

Benjamindai: /* NCBO Web services */

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

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

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

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

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

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

=== Ontology Development Area ===

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

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

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

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

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

*[[SO:Main_Page]] - Sequence Ontology

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

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

*[[NPO:Main_Page]] - NanoParticle Ontology

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

=== Software Development Area ===

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

=== NCBO Web services ===

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

Main Page

2009-05-05T23:20:37Z

Benjamindai: /* NCBO Web services */

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

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

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

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

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

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

=== Ontology Development Area ===

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

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

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

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

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

*[[SO:Main_Page]] - Sequence Ontology

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

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

*[[NPO:Main_Page]] - NanoParticle Ontology

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

=== Software Development Area ===

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

=== NCBO Web services ===

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

Main Page

2009-05-05T23:20:28Z

Benjamindai: /* NCBO Web services */

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

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

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

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

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

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

=== Ontology Development Area ===

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

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

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

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

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

*[[SO:Main_Page]] - Sequence Ontology

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

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

*[[NPO:Main_Page]] - NanoParticle Ontology

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

=== Software Development Area ===

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

=== NCBO Web services ===

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

BioPortal 2.1 (Core 1014; UI 1019) Release Notes

2009-05-01T22:02:26Z

Benjamindai: /* Resolved Bugs */

BioPortal 2.1 consists of two NCBO software packages: BioPortal Core (Label 1014) and BioPortal UI (Label 1019).

=New Features=
* New Annotator service
* New All Resources UI
* New Search UI
* New BioPortal Look and Feel
* New labels on relations in the tree
* Adding reviews and projects
* Ontology list on the Browse page
* Add column on main page for group
* Add syndication for a specific ontology
* Filter out "[R].." relationships

=Resolved Bugs=
*1153 Navigation Visualization doesn't scale correctly in IE
*1157 Need to add "alpha" to "All Resources" tab
*1159 Clicking on a Project in Projects tab results in an error
*1113 RSS feed for OBI has wrong id for URL
*1107 Send Feedback page
*1101 Email address usage for Support on BioPortal
*1100 Request to remove Group MSI
*1099 Explore button doesn't work on the new home page
*1096 Filter mappings doesn't work on stage
*1072 Need relationships on full path to root
*1060 Unable to subscribe to overall BioPortal RSS feed
*1059 OBO ontologies parse errors causing wrong search results
*1015 Need to add a note in order to see the past one
*971 When a user creates a note, it does not show up right away
*957 Concepts with IDs starting with "@_" cannot be visualized in the UI
*1194 Request to remove ontology
*1188 Need isFoundry added to /ontologies response XML
*709 Additional inverse relationships gets introduced for OBO ontologies (has subclass and has part)
*1131 Explore button on home page should take you to the metadata page for ontologies that are not explorable
*1151 Full text name and/or description of resource
*1180 Wrong relations returned by a concept service in OBO ontologies
*1175 Category "Taxonomic Classification" has no instances
*1023 Ontology ID mismatch on metadata page and URL
*1154 Wrong hierarchy when going directly to a concept in OWL ontologies
*1171 The children hierarchy service returns children only at the specified level, rather than *up to* specified level
*1148 Ontology selection - missing scroll bar
*1150 Max Results slider
*1163 Gene ontology not explorable on stage
*1161 Gene ontology not explorable
*1132 Class details do not work in IE on Windows (hangs the browser)
*1145 OBO ontologies not explorable on the dev server
*1108 [R]regulates link appear as "regulates" link in FlexViz
*1097 Edit Metadata button - unable to add multiple categories
*1127 NPO ontology is stuck in parsing
*1118 Project page - updates needed for EFO project
*1109 Don't show "Thing" concept in Full FlexViz
*1110 Search of NCIT - not pointing to latest version
*1117 EFO - stuck in Parsing
*1098 Typo in message following ontology submission
*1121 Update the version number for NPO
*807 Ontology for disease genetic investigation Broken
*1092 Request to remove ontology - NIF Gross Anatomy
*1084 STAGE - Error with term Clarke's nuclei in Jump to and Search
*1095 Notes Column Overlap in IE and Safari
*999 MySQL exceptions when requesting too many services
*990 Update on ontologies with problem with the REST services
*801 Ontology 38633 does not support UI
*953 We should preserve namespaces with concepts in OWL ontologies, even when we use preferred names
*510 Adding ontologies to a project, maximize dialog doesn't use full screen
*1057 More concepts with problem (after processing of OBS DB)
*835 Plus/Minus sign usage in Visualization full window is inconsistent
*486 A spurious phone number appears after user registration
*991 Link to filter by group, should select menu highlight group filtered by?
*800 Ontology 28837 does not support UI
*961 Update on ontologies which has some conceptIDs as URL
*1032 Duplication of ontology abbreviation on Home page for Gene Regulation ontology
*984 Highly nested ontologies and tree-view
*1038 Notes expanded past note panel
*1006 DermLex - issue with display of preferred name
*974 Display of BioPortal metadata ontology?
*596 In the Visualization tree: a click a node doesn't take move to that node
*1043 Repeated labels in OBI - {definition, definition}
*511 Add Ontologies To Project dialog has too many scrollbars!!
*551 Ontology review display and editing use ontology ID instead of ontology name
*925 Mapping not reciprocal - not shown for mapped to term
*554 When editing marginal notes the create link button doesn't work
*613 Expanding tree view frame causing odd behaviour
*497 If I select a particular tab (e.g., Details), then this tab should open when I click on a different class
*547 Clicking on a node on the graph view should open the corresponding concept.
*543 Need to stay on the same tab when exploring an ontology
*648 Concept tree navigation should be centered on the concept of focus
*552 Ontology review feature is not working from the main ontology list
*587 When window width is reduced, columns jump to the bottom of it
*595 A clicked term has always the tab Details shown
*628 Marginal Note - Title Field in Comment Display is too short (i.e., Comment Editor is significantly longer than display) and Missing Comments
*975 Are sessions used or automatic time-out?
*939 The note about the mappings should go on the mapping page
*1068 Request to remove versions of SO-PHARM that were not loaded correctly
*1079 MOD should be in the group PSI
*1078 Ontology loading issues
*808 Concept 4525/PathologicalPhenomenon makes BP REST services crashed
*563 Mappings download seems to not work all the time
*1069 Unable to upload/submit new version of NCIT
*816 Add link back to NCBO
*605 OBO parse exception : LexBIG Ontology load failed
*851 Cannot specify Categories on the "Submit new ontology" page
*1004 General Issue on 1/21/09 - local ontologies now remote
*1187 Separate multiple values by new line rather than comma
*1183 Do not show inverse relations on the Details page
*1164 Resources - paging links to see list of resources from NextBio
*1162 Alpha next to Resources not visible in tab name in IE
*1160 Add project button should be more prominent
*1158 Help/about page doesn't have any margin
*1156 Virtual URLs for concepts don't work
*1155 Change "MarginNote" to "Note" in the message after a note is created
*1149 Semantic type - missing scroll bar
*1143 Projects and reviews not visible in Safari
*1142 Length of Subject field for Notes
*1140 Wrong field for ontology upload on "Submit new version"
*1139 The "*fields are required" string is in the wrong place

BioPortal 2.1 (Core 1014; UI 1019) Release Notes

2009-05-01T17:59:26Z

Benjamindai: Added bug fixes

BioPortal 2.1 consists of two NCBO software packages: BioPortal Core (Label 1014) and BioPortal UI (Label 1019).

=New Features=
* New Annotator service
* New All Resources UI
* New Search UI
* New BioPortal Look and Feel
* New labels on relations in the tree
* Adding reviews and projects
* Ontology list on the Browse page
* Add column on main page for group
* Add syndication for a specific ontology
* Filter out "[R].." relationships

=Resolved Bugs=
*1157 Need to add "alpha" to "All Resources" tab
*1159 Clicking on a Project in Projects tab results in an error
*1194 Request to remove ontology - carol
*1188 Need isFoundry added to /ontologies response XML
*1153 Navigation Visualization doesn't scale correctly in IE
*709 Additional inverse relationships gets introduced for OBO ontologies (has subclass and has part)
*1131 Explore button on home page should take you to the metadata page for ontologies that are not explorable
*1151 Full text name and/or description of resource
*1180 Wrong relations returned by a concept service in OBO ontologies
*1175 Category "Taxonomic Classification" has no instances
*1023 Ontology ID mismatch on metadata page and URL
*1154 Wrong hierarchy when going directly to a concept in OWL ontologies
*1171 The children hierarchy service returns children only at the specified level, rather than *up to* specified level
*1148 Ontology selection - missing scroll bar
*1150 Max Results slider
*1163 Gene ontology not explorable on stage
*1161 Gene ontology not explorable
*1132 Class details do not work in IE on Windows (hangs the browser)
*1145 OBO ontologies not explorable on the dev server
*1108 [R]regulates link appear as "regulates" link in FlexViz
*1097 Edit Metadata button - unable to add multiple categories
*1127 NPO ontology is stuck in parsing
*1118 Project page - updates needed for EFO project
*1109 Don't show "Thing" concept in Full FlexViz
*1110 Search of NCIT - not pointing to latest version
*1117 EFO - stuck in Parsing
*1098 Typo in message following ontology submission
*1121 Update the version number for NPO
*807 Ontology for disease genetic investigation Broken
*1092 Request to remove ontology - NIF Gross Anatomy
*1084 STAGE - Error with term Clarke's nuclei in Jump to and Search
*1095 Notes Column Overlap in IE and Safari
*999 MySQL exceptions when requesting too many services
*990 Update on ontologies with problem with the REST services
*801 Ontology 38633 does not support UI
*953 We should preserve namespaces with concepts in OWL ontologies, even when we use preferred names
*510 Adding ontologies to a project, maximize dialog doesn't use full screen
*1057 More concepts with problem (after processing of OBS DB)
*835 Plus/Minus sign usage in Visualization full window is inconsistent
*486 A spurious phone number appears after user registration
*991 Link to filter by group, should select menu highlight group filtered by?
*800 Ontology 28837 does not support UI
*961 Update on ontologies which has some conceptIDs as URL
*1032 Duplication of ontology abbreviation on Home page for Gene Regulation ontology
*984 Highly nested ontologies and tree-view
*1038 Notes expanded past note panel
*1006 DermLex - issue with display of preferred name
*974 Display of BioPortal metadata ontology?
*596 In the Visualization tree: a click a node doesn't take move to that node
*1043 Repeated labels in OBI - {definition, definition}
*511 Add Ontologies To Project dialog has too many scrollbars!!
*551 Ontology review display and editing use ontology ID instead of ontology name
*925 Mapping not reciprocal - not shown for mapped to term
*554 When editing marginal notes the create link button doesn't work
*613 Expanding tree view frame causing odd behaviour
*497 If I select a particular tab (e.g., Details), then this tab should open when I click on a different class
*547 Clicking on a node on the graph view should open the corresponding concept.
*543 Need to stay on the same tab when exploring an ontology
*648 Concept tree navigation should be centered on the concept of focus
*552 Ontology review feature is not working from the main ontology list
*587 When window width is reduced, columns jump to the bottom of it
*595 A clicked term has always the tab Details shown
*628 Marginal Note - Title Field in Comment Display is too short (i.e., Comment Editor is significantly longer than display) and Missing Comments
*975 Are sessions used or automatic time-out?
*939 The note about the mappings should go on the mapping page
*1068 Request to remove versions of SO-PHARM that were not loaded correctly
*1079 MOD should be in the group PSI
*1078 Ontology loading issues
*808 Concept 4525/PathologicalPhenomenon makes BP REST services crashed
*563 Mappings download seems to not work all the time
*1069 Unable to upload/submit new version of NCIT
*816 Add link back to NCBO
*605 OBO parse exception : LexBIG Ontology load failed
*851 Cannot specify Categories on the "Submit new ontology" page
*1004 General Issue on 1/21/09 - local ontologies now remote
*1187 Separate multiple values by new line rather than comma
*1183 Do not show inverse relations on the Details page
*1164 Resources - paging links to see list of resources from NextBio
*1162 Alpha next to Resources not visible in tab name in IE
*1160 Add project button should be more prominent
*1158 Help/about page doesn't have any margin
*1156 Virtual URLs for concepts don't work
*1155 Change "MarginNote" to "Note" in the message after a note is created
*1149 Semantic type - missing scroll bar
*1143 Projects and reviews not visible in Safari
*1142 Length of Subject field for Notes
*1140 Wrong field for ontology upload on "Submit new version"
*1139 The "*fields are required" string is in the wrong place
*1113 RSS feed for OBI has wrong id for URL
*1107 Send Feedback page
*1101 Email address usage for Support on BioPortal
*1100 Request to remove Group MSI
*1099 Explore button doesn't work on the new home page
*1096 Filter mappings doesn't work on stage
*1072 Need relationships on full path to root
*1060 Unable to subscribe to overall BioPortal RSS feed
*1059 OBO ontologies parse errors causing wrong search results
*1015 Need to add a note in order to see the past one
*971 When a user creates a note, it does not show up right away
*957 Concepts with IDs starting with "@_" cannot be visualized in the UI

BioPortal 2.1 (Core 1014; UI 1019) Release Notes

2009-05-01T17:56:37Z

Benjamindai:

BioPortal 2.1 consists of two NCBO software packages: BioPortal Core (Label 1014) and BioPortal UI (Label 1019).

=New Features=
* New Annotator service
* New All Resources UI
* New Search UI
* New BioPortal Look and Feel
* New labels on relations in the tree
* Adding reviews and projects
* Ontology list on the Browse page
* Add column on main page for group
* Add syndication for a specific ontology
* Filter out "[R].." relationships

=Resolved Bugs=
1157 Need to add "alpha" to "All Resources" tab
1159 Clicking on a Project in Projects tab results in an error
1194 Request to remove ontology - carol
1188 Need isFoundry added to /ontologies response XML
1153 Navigation Visualization doesn't scale correctly in IE
709 Additional inverse relationships gets introduced for OBO ontologies (has subclass and has part)
1131 Explore button on home page should take you to the metadata page for ontologies that are not explorable
1151 Full text name and/or description of resource
1180 Wrong relations returned by a concept service in OBO ontologies
1175 Category "Taxonomic Classification" has no instances
1023 Ontology ID mismatch on metadata page and URL
1154 Wrong hierarchy when going directly to a concept in OWL ontologies
1171 The children hierarchy service returns children only at the specified level, rather than *up to* specified level
1148 Ontology selection - missing scroll bar
1150 Max Results slider
1163 Gene ontology not explorable on stage
1161 Gene ontology not explorable
1132 Class details do not work in IE on Windows (hangs the browser)
1145 OBO ontologies not explorable on the dev server
1108 [R]regulates link appear as "regulates" link in FlexViz
1097 Edit Metadata button - unable to add multiple categories
1127 NPO ontology is stuck in parsing
1118 Project page - updates needed for EFO project
1109 Don't show "Thing" concept in Full FlexViz
1110 Search of NCIT - not pointing to latest version
1117 EFO - stuck in Parsing
1098 Typo in message following ontology submission
1121 Update the version number for NPO
807 Ontology for disease genetic investigation Broken
1092 Request to remove ontology - NIF Gross Anatomy
1084 STAGE - Error with term Clarke's nuclei in Jump to and Search
1095 Notes Column Overlap in IE and Safari
999 MySQL exceptions when requesting too many services
990 Update on ontologies with problem with the REST services
801 Ontology 38633 does not support UI
953 We should preserve namespaces with concepts in OWL ontologies, even when we use preferred names
510 Adding ontologies to a project, maximize dialog doesn't use full screen
1057 More concepts with problem (after processing of OBS DB)
835 Plus/Minus sign usage in Visualization full window is inconsistent
486 A spurious phone number appears after user registration
991 Link to filter by group, should select menu highlight group filtered by?
800 Ontology 28837 does not support UI
961 Update on ontologies which has some conceptIDs as URL
1032 Duplication of ontology abbreviation on Home page for Gene Regulation ontology
984 Highly nested ontologies and tree-view
1038 Notes expanded past note panel
1006 DermLex - issue with display of preferred name
974 Display of BioPortal metadata ontology?
596 In the Visualization tree: a click a node doesn't take move to that node
1043 Repeated labels in OBI - {definition, definition}
511 Add Ontologies To Project dialog has too many scrollbars!!
551 Ontology review display and editing use ontology ID instead of ontology name
925 Mapping not reciprocal - not shown for mapped to term
554 When editing marginal notes the create link button doesn't work
613 Expanding tree view frame causing odd behaviour
497 If I select a particular tab (e.g., Details), then this tab should open when I click on a different class
547 Clicking on a node on the graph view should open the corresponding concept.
543 Need to stay on the same tab when exploring an ontology
648 Concept tree navigation should be centered on the concept of focus
552 Ontology review feature is not working from the main ontology list
587 When window width is reduced, columns jump to the bottom of it
595 A clicked term has always the tab Details shown
628 Marginal Note - Title Field in Comment Display is too short (i.e., Comment Editor is significantly longer than display) and Missing Comments
975 Are sessions used or automatic time-out?
939 The note about the mappings should go on the mapping page
1068 Request to remove versions of SO-PHARM that were not loaded correctly
Trish Whetzel
1079 MOD should be in the group PSI
1078 Ontology loading issues
808 Concept 4525/PathologicalPhenomenon makes BP REST services crashed
563 Mappings download seems to not work all the time
1069 Unable to upload/submit new version of NCIT
816 Add link back to NCBO
605 OBO parse exception : LexBIG Ontology load failed
851 Cannot specify Categories on the "Submit new ontology" page
1004 General Issue on 1/21/09 - local ontologies now remote
1187 Separate multiple values by new line rather than comma
1183 Do not show inverse relations on the Details page
1164 Resources - paging links to see list of resources from NextBio
1162 Alpha next to Resources not visible in tab name in IE
1160 Add project button should be more prominent
1158 Help/about page doesn't have any margin
1156 Virtual URLs for concepts don't work
1155 Change "MarginNote" to "Note" in the message after a note is created
1149 Semantic type - missing scroll bar
1143 Projects and reviews not visible in Safari
1142 Length of Subject field for Notes
1140 Wrong field for ontology upload on "Submit new version"
1139 The "*fields are required" string is in the wrong place
1113 RSS feed for OBI has wrong id for URL
1107 Send Feedback page
1101 Email address usage for Support on BioPortal
1100 Request to remove Group MSI
1099 Explore button doesn't work on the new home page
1096 Filter mappings doesn't work on stage
1072 Need relationships on full path to root
1060 Unable to subscribe to overall BioPortal RSS feed
1059 OBO ontologies parse errors causing wrong search results
1015 Need to add a note in order to see the past one
971 When a user creates a note, it does not show up right away
957 Concepts with IDs starting with "@_" cannot be visualized in the UI

BioPortal 2.1 (Core 1014; UI 1019) Release Notes

2009-05-01T17:56:18Z

Benjamindai: New page: BioPortal 2.1 consists of two NCBO software packages: BioPortal Core (Label 1014) and BioPortal UI (Label 1019). =New Features= * New Annotator service * New All Resources UI * New Sear...

NCBO Developer Documentation

2009-05-01T17:07:28Z

Benjamindai: /* Release Notes */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Web Service Usage=
All NCBO REST web service calls '''MUST append a search query parameter''' with the pattern of "email=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. For example, ''benjamin.dai@stanford.edu'' would look like ''benjamin.dai%40stanford.edu''. This is critical to ensure we can maintain the quality of service expected for you as our customer. Later in 2009, we may start challenging REST service calls that do not have this parameter. In the meantime, please start adding this URL parameter to all your web service invocations.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

[[BioPortal 2.1 (Core 1014; UI 1019) Release Notes]] - 5/1/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-17T18:43:46Z

Benjamindai: /* NCBO REST Web Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Web Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. For example, ''benjamin.dai@stanford.edu'' would look like ''benjamin.dai%40stanford.edu''. This is critical to ensure we can maintain the quality of service expected for you as our customer. Later in 2009, we may start challenging REST service calls that do not have this parameter. In the meantime, please start adding this URL parameter to all your web service invocations.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-17T18:42:49Z

Benjamindai: /* NCBO REST Web Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Web Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. For example, ''benjamin.dai@stanford.edu'' would look like ''benjamin.dai%40stanford.edu''. This is critical to ensure we can maintain the quality of service expected for you as our customer. Later in 2009, we may start challenging REST service calls that do not have this parameter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-17T18:42:12Z

Benjamindai: /* NCBO REST Web Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Web Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. For example, ''benjamin.dai@stanford.edu'' would look like ''benjamin.dai%40stanford.edu''. This is critical to ensure we can maintain the quality of service expected for you as our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-17T18:41:59Z

Benjamindai: /* NCBO REST Web Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Web Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. For example,''benjamin.dai@stanford.edu'' would look like ''benjamin.dai%40stanford.edu''. This is critical to ensure we can maintain the quality of service expected for you as our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-17T18:41:17Z

Benjamindai: /* NCBO REST Web Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Web Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. For example,'benjamin.dai@stanford.edu' would look like 'benjamin.dai%40stanford.edu'. This is critical to ensure we can maintain the quality of service expected for you as our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:41:46Z

Benjamindai: /* NCBO REST Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Web Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. This is critical to ensure we can maintain the quality of service expected for you as our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:41:16Z

Benjamindai: /* NCBO REST Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. This is critical to ensure we can maintain the quality of service expected for you as our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:40:32Z

Benjamindai: /* NCBO REST Service Usage */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Service Usage=
All to NCBO REST web services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. This is critical to ensure we can maintain quality service to our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:40:10Z

Benjamindai:

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO REST Service Usage=
All REST web service calls to NCBO services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. This is critical to ensure we can maintain quality service to our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:39:35Z

Benjamindai: /* BioPortal */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==NCBO REST Service Usage==
All REST web service calls to NCBO services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. This is critical to ensure we can maintain quality service to our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:38:45Z

Benjamindai: /* BioPortal */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

All REST calls to NCBO services '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. This is critical to ensure we can maintain quality service to our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:38:26Z

Benjamindai: /* BioPortal */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

All REST calls described in this section '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. This is critical to ensure we can maintain quality service to our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:37:48Z

Benjamindai: /* BioPortal */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

All REST calls described in this section '''MUST append a search query parameter''' with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user email address. This is critical to ensure we can maintain quality service to our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Developer Documentation

2009-04-16T23:37:00Z

Benjamindai: /* BioPortal 2.0 */

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

All REST calls described in this section must append a search query parameter with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user email address. This is critical to ensure we can maintain quality service to our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

[[NCBO_REST_services|BioPortal 2.0 REST web service]] API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===Local Installation===
Please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO-OOR Development

2009-03-07T00:23:21Z

Benjamindai: /* OOR Developer Collaboration */

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the open source [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=OOR Developer Collaboration=
The OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect (Benjamin Dai) which includes communications channels, source control processes/practices, and NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome to the conferences, they focus primarily on how NCBO software can best serve biomedical communities.

Main Page

2009-03-07T00:22:25Z

Benjamindai: /* Software Development Area */

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

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

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

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

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

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

=== Ontology Development Area ===

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

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

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

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

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

*[[SO:Main_Page]] - Sequence Ontology

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

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

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

=== Software Development Area ===
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[NCBO_REST_services]] - Documentation on how to use our Ontology services
*[[UMLS_REST_Services]] - Documentation on how to use our prototype UMLS services
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
*[[Processing_OBR_Resources]] - Notes on resources being processed

Processing OBR Resources

2009-03-04T22:11:28Z

Benjamindai: /* Reprocessing: Simple re-run of an existing ResourceAccessTool */

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool=

1. Resource: PharmGKB
*Person responsible: Adrien
*Status: Completed
*Last processed: 3/3/2009

2. Resource: Uniprot
*Person responsible: Adrien
*Status: Completed
*Last processed: 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool =
Examples include GEO, ClinicalTrials, Pubmed.

=Writing a new ResourceAccessTools=
Examples include CaNanoLab.

=Ongoing Challenges=

=Other Updates=

Processing OBR Resources

2009-03-04T22:10:54Z

Benjamindai: /* Reprocessing: Simple re-run of an existing ResourceAccessTool */

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool=

#Resource: PharmGKB
Person responsible: Adrien

Status: Completed

Last processed: 3/3/2009

#Resource: Uniprot
Person responsible: Adrien

Status: Completed

Last processed: 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool =
Examples include GEO, ClinicalTrials, Pubmed.

=Writing a new ResourceAccessTools=
Examples include CaNanoLab.

=Ongoing Challenges=

=Other Updates=

Processing OBR Resources

2009-03-04T22:10:32Z

Benjamindai: /* Reprocessing: Simple re-run of an existing ResourceAccessTool */

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool=

#Resource: PharmGKB
Person responsible: Adrien
Status: Completed
Last processed: 3/3/2009

#Resource: Uniprot
Person responsible: Adrien
Status: Completed
Last processed: 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool =
Examples include GEO, ClinicalTrials, Pubmed.

=Writing a new ResourceAccessTools=
Examples include CaNanoLab.

=Ongoing Challenges=

=Other Updates=

Processing OBR Resources

2009-03-04T19:26:35Z

Benjamindai: /* Writing a new ResourceAccessTools) */

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool=
#PharmGKB - Adrien completed on 3/3/2009
#Uniprot - Adrien completed on 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool =
Examples include GEO, ClinicalTrials, Pubmed.

=Writing a new ResourceAccessTools=
Examples include CaNanoLab.

=Ongoing Challenges=

=Other Updates=

Processing OBR Resources

2009-03-04T19:26:23Z

Benjamindai: /* More updates here */

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool=
#PharmGKB - Adrien completed on 3/3/2009
#Uniprot - Adrien completed on 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool =
Examples include GEO, ClinicalTrials, Pubmed.

=Writing a new ResourceAccessTools)=
Examples include CaNanoLab.

=Ongoing Challenges=

=Other Updates=

Processing OBR Resources

2009-03-04T19:25:53Z

Benjamindai:

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool=
#PharmGKB - Adrien completed on 3/3/2009
#Uniprot - Adrien completed on 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool =
Examples include GEO, ClinicalTrials, Pubmed.

=Writing a new ResourceAccessTools)=
Examples include CaNanoLab.

=Ongoing Challenges=

=More updates here=

Processing OBR Resources

2009-03-04T19:25:19Z

Benjamindai:

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main reprocessing activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool=
#PharmGKB - Adrien completed on 3/3/2009
#Uniprot - Adrien completed on 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool =
Examples include GEO, ClinicalTrials, Pubmed.

=Reprocessing: Writing a new ResourceAccessTools)=
Examples include CaNanoLab.

=Ongoing Challenges=

=More updates here=

Processing OBR Resources

2009-03-04T19:24:31Z

Benjamindai:

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main reprocessing activities.

=Reprocessing: Simple re-run of an existing ResourceAccessTool (e.g. PharmGKB, Uniprot etc)=
#PharmGKB - Adrien completed on 3/3/2009
#Uniprot - Adrien completed on 3/3/2009

=Reprocessing: Modification of an existing ResourceAccessTool (e.g. GEO, ClinicalTrials, Pubmed)=

=Reprocessing: Writing a new ResourceAccessTools (e.g. CaNanoLab)=

=Ongoing Challenges=

=More updates here=

Processing OBR Resources

2009-03-04T19:23:17Z

Benjamindai: Minor reformatting

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities:

=Simple re-run of an existing ResourceAccessTool (e.g. PharmGKB, Uniprot etc)=
#PharmGKB - Adrien completed on 3/3/2009
#Uniprot - Adrien completed on 3/3/2009

=Modification of an existing ResourceAccessTool (e.g. GEO, ClinicalTrials, Pubmed)=

=Writing a new ResourceAccessTools (e.g. CaNanoLab)=

=Ongoing Challenges=

=More updates here=

NCBO-OOR Source Control Practices and Processes

2009-02-19T20:32:40Z

Benjamindai: /* Stage 1 – Start Simple - Initial Development */

=Stage 1 – Start Simple - Initial Development=
The entire OOR community has access to the NCBO-OOR source code (essentially the BioPortal source). Use your favorite SVN client tool to retrieve the latest source code.

The BioPortal server side source can be perused at the following NCBO GForge link:

https://bmir-gforge.stanford.edu/gf/project/bioportal_core/scmsvn/?action=browse&path=%2Ftrunk%2F

The BioPortal user interface source can be perused at the following NCBO GForge link:

https://bmir-gforge.stanford.edu/gf/project/bioportalui/scmsvn/?action=browse&path=%2Ftrunk%2F

In April 2009, a NCBO GForge branch will be created starting with an initial core pool of developers having commit access (including Michael Gruniger's graduate students). Read access will be entirely public.

=Stage 2 – Ramp-Up Collaboration=
As the developer community grows, there will quickly be a need for clear open source collaboration processes and practices. Mike Dean and Benjamin Dai will establish Open Source Collaboration policies (e.g., commit rights, trusted developers, external developers, etc). The NCBO GForge site will continue to be the primary source control mechanism for OOR.

As details of the NCBO-OOR open source collaboration policies are established, they will be updated on this wiki page.

NCBO-OOR Development

2009-02-19T19:37:56Z

Benjamindai: /* OOR Developer Collaboration */

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the open source [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=OOR Developer Collaboration=
The OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect (Benjamin Dai) which includes communications channels, source control processes/practices, and NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome to the conferences, they focuses primarily on how NCBO software can best serve biomedical communities.

NCBO-OOR Development

2009-02-19T19:37:35Z

Benjamindai: /* OOR Developer Collaboration */

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the open source [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=OOR Developer Collaboration=
The OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect (Benjamin Dai) which includes a communications channels, source control processes/practices, and NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome to the conferences, they focuses primarily on how NCBO software can best serve biomedical communities.

NCBO-OOR Development

2009-02-19T19:35:45Z

Benjamindai: /* NCBO-OOR Developer Collaboration */

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the open source [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=OOR Developer Collaboration=
The OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect (Benjamin Dai) which includes a NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome, the conference focuses primarily on how NCBO software can best serve the biomedical communities.

NCBO-OOR Development

2009-02-19T19:34:18Z

Benjamindai:

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the open source [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=NCBO-OOR Developer Collaboration=
The NCBO-OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect (Benjamin Dai) which includes a NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome, the conference focuses primarily on how NCBO software can best serve the biomedical communities.

NCBO-OOR Development

2009-02-19T19:30:45Z

Benjamindai: /* NCBO-OOR Developer Collaboration */

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=NCBO-OOR Developer Collaboration=
The NCBO-OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect (Benjamin Dai) which includes a NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome, the conference focuses primarily on how NCBO software can best serve the biomedical communities.

NCBO-OOR Architecture

2009-02-19T19:28:25Z

Benjamindai: /* Consolidating the Bioportal back-end */

The NCBO-OOR architecture (essentially the NCBO BioPortal architecture) uses a classic architecture layered approach, which decouples the logic and domain object models between each layer. This approach decouples the versioning and changes in one layer from another. Thus, as software modules evolve (which they always do), the impact on the rest of the software sub-systems is significantly reduced. Furthermore, the BioPortal enforces de-coupling through web services (e.g., REST and SOAP) and the enterprise pattern of “Dependency Injection.” Note that Protégé 3.x has been incorporated into business logic layer (in addition to pre-existing LexGrid) to enable full support of OWL ontologies and the capability to store ontology based meta data, mappings, and marginal notes. The following diagram presents a simple overview of the layers in the BioPortal architecture followed by a description of each.

[[Image:BP Simple Layered Diagram.jpg|frame|center|200x|||]]

The ''Presentation Tier'' delivers the BioPortal user-interface which currently uses the Ruby on Rails technology. Ruby on Rails is a leading mature UI framework supported by large software development communities. It enables rapid prototyping as well as solid integration with web services.

The ''Interface Tier'' consists of both REST and SOAP web services that present all BioPortal capabilities to the upper tiers (e.g., upload ontology, download ontology, display concept, administrative functions, etc). The Presentation Tier is primarly driven by the REST services (currently implemented with RESTlet libraries). Thus, the BioPortal Presentation Tier is just one vanilla consumer of the BioPortal REST services. In the principle of Service-Oriented Architecture, any number of partner developers could consume the set of existing REST services for any number of purposes. For example, one could implement a completely different UI than that currently exposed by the BioPortal. Or, one could simply want to consume a single REST services for integrating into a back-end workflow with no UI at all. Please see [[NCBO_REST_services | NCBO REST Services]] documentation to learn about consuming the BioPortal REST services.

The ''Business Logic Tier'' uses the Spring technology which enables a partner to insert any software implementation that abides to the NCBO-defined interfaces. This is achieved through the “Dependency Injection” enterprise pattern which is core to the Spring framework. For example, if NCI requires use of a different flavor of LexGrid, a module could be easily implemented by NCI using the NCBO interfaces and deployed without having to modify the core BioPortal software. This architectural approach enables incorporation of new capability into the BioPortal through packaging and configuration. The need to do a major BioPortal software release to support a customized implementation is significantly reduced. [[NCBO-OOR Server-Side Customization]] provides further details how such a customization can occur.

The ''Persistence Tier'' uses the Hibernate technology as a basic object-relational mapping to the back-end relational database. Hibernate is used for storing administrative (e.g., user information) and external ontology data (e.g., ontology attributes specified at upload time). All ontology content is stored in Protege and LexGrid as shown in the ''Business Logic'' layer.

=Consolidating the Bioportal back-end=
While architecturally it is preferable to have a single ontology/terminology back-end repository to reduce complexity, no single repository meets all NCBO requirements. The NCBO must support the OWL language and RDF/XML, OBO, RDF and RRF formats. As shown in the diagram, Protégé 3.x has been incorporated into the business-logic layer to enable full support of OWL ontologies and the capability to store ontology based meta-data, mappings, and marginal notes. LexGrid continues to support the diverse terminology formats required by NCBO (e.g., the RRF format used for UMLS is particularly critical). As shown in the above diagram, the combination of LexGrid and Protégé jointly provide sufficient support for the diverse standards and formats. All OWL ontology requests (e.g., get concept, find concept, and upload) will be routed to Protégé. All other ontology/terminology requests such as RRF and OBO will be routed to LexGrid. Long-term, the NCBO plans to rearchitect the BioPortal to leverage both normalized store and native OWL/RDF triple store in collaboration between Stanford University and Mayo Clinic.

With this in mind, adding, removing, and changing back-ends to the BioPortal is entirely customizable and adjustable by design. The server-side architecture leverages the principles of aspect-oriented programming. Thus, the majority of server-side component in the BioPortal can be more easily modified to meet the needs of OOR. Please see the [[NCBO-OOR Server-Side Customization]] page for descriptions and examples how this customization can be done.

NCBO-OOR Architecture

2009-02-19T19:27:33Z

Benjamindai: /* Consolidating the Bioportal back-end */

NCBO-OOR Architecture

2009-02-19T19:25:53Z

Benjamindai: /* Consolidating the Bioportal back-end */

The NCBO-OOR architecture (essentially the NCBO BioPortal architecture) uses a classic architecture layered approach, which decouples the logic and domain object models between each layer. This approach decouples the versioning and changes in one layer from another. Thus, as software modules evolve (which they always do), the impact on the rest of the software sub-systems is significantly reduced. Furthermore, the BioPortal enforces de-coupling through web services (e.g., REST and SOAP) and the enterprise pattern of “Dependency Injection.” Note that Protégé 3.x has been incorporated into business logic layer (in addition to pre-existing LexGrid) to enable full support of OWL ontologies and the capability to store ontology based meta data, mappings, and marginal notes. The following diagram presents a simple overview of the layers in the BioPortal architecture followed by a description of each.

[[Image:BP Simple Layered Diagram.jpg|frame|center|200x|||]]

The ''Presentation Tier'' delivers the BioPortal user-interface which currently uses the Ruby on Rails technology. Ruby on Rails is a leading mature UI framework supported by large software development communities. It enables rapid prototyping as well as solid integration with web services.

The ''Interface Tier'' consists of both REST and SOAP web services that present all BioPortal capabilities to the upper tiers (e.g., upload ontology, download ontology, display concept, administrative functions, etc). The Presentation Tier is primarly driven by the REST services (currently implemented with RESTlet libraries). Thus, the BioPortal Presentation Tier is just one vanilla consumer of the BioPortal REST services. In the principle of Service-Oriented Architecture, any number of partner developers could consume the set of existing REST services for any number of purposes. For example, one could implement a completely different UI than that currently exposed by the BioPortal. Or, one could simply want to consume a single REST services for integrating into a back-end workflow with no UI at all. Please see [[NCBO_REST_services | NCBO REST Services]] documentation to learn about consuming the BioPortal REST services.

The ''Business Logic Tier'' uses the Spring technology which enables a partner to insert any software implementation that abides to the NCBO-defined interfaces. This is achieved through the “Dependency Injection” enterprise pattern which is core to the Spring framework. For example, if NCI requires use of a different flavor of LexGrid, a module could be easily implemented by NCI using the NCBO interfaces and deployed without having to modify the core BioPortal software. This architectural approach enables incorporation of new capability into the BioPortal through packaging and configuration. The need to do a major BioPortal software release to support a customized implementation is significantly reduced. [[NCBO-OOR Server-Side Customization]] provides further details how such a customization can occur.

The ''Persistence Tier'' uses the Hibernate technology as a basic object-relational mapping to the back-end relational database. Hibernate is used for storing administrative (e.g., user information) and external ontology data (e.g., ontology attributes specified at upload time). All ontology content is stored in Protege and LexGrid as shown in the ''Business Logic'' layer.

=Consolidating the Bioportal back-end=
While architecturally it is preferable to have a single ontology/terminology back-end repository to reduce complexity, no single repository meets all NCBO requirements. The NCBO must support the OWL language and RDF/XML, OBO, RDF and RRF formats. As shown in the diagram, Protégé 3.x has been incorporated into the business-logic layer to enable full support of OWL ontologies and the capability to store ontology based meta-data, mappings, and marginal notes. LexGrid continues to support the diverse terminology formats required by NCBO (e.g., the RRF format used for UMLS is particularly critical). As shown in the above diagram, the combination of LexGrid and Protégé jointly provide sufficient support for the diverse standards and formats. All OWL ontology requests (e.g., get concept, find concept, and upload) will be routed to Protégé. All other ontology/terminology requests such as RRF and OBO will be routed to LexGrid. Long-term, the NCBO plans to rearchitect the BioPortal to leverage both normalized store and native OWL/RDF triple store in collaboration between Stanford University and Mayo Clinic.

With this in mind, adding, removing, and changing back-ends to the BioPortal is modular by design. The server-side architecture implicitly is based on the principle of aspect-oriented programming. Thus, the majority of server-side component in the BioPortal can be modified to meet the needs of OOR.

NCBO-OOR Development

2009-02-19T19:18:04Z

Benjamindai:

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=NCBO-OOR Developer Collaboration=
The NCBO-OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect which includes a NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome, the conference focuses primarily on how NCBO software can best serve the biomedical communities.

NCBO-OOR Development

2009-02-19T19:17:35Z

Benjamindai:

Welcome to the OOR Project! This developer's guide provides an introduction to the OOR architecture and steps (with examples) of how to customize server-side components. The NCBO-OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "NCBO-OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the NCBO-OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=NCBO-OOR Developer Collaboration=
The NCBO-OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect which includes a NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome, the conference focuses primarily on how NCBO software can best serve the biomedical communities.

NCBO-OOR Source Control Practices and Processes

2009-02-19T19:15:08Z

Benjamindai: /* Stage 1 – Start Simple - Initial Development */

=Stage 1 – Start Simple - Initial Development=
The entire OOR community has access to the NCBO-OOR source code (essentially the BioPortal source). User your favorite SVN client tool to retrieve the latest source code.

The BioPortal server side source can be perused at the following NCBO GForge link:

https://bmir-gforge.stanford.edu/gf/project/bioportal_core/scmsvn/?action=browse&path=%2Ftrunk%2F

The BioPortal user interface source can be perused at the following NCBO GForge link:

https://bmir-gforge.stanford.edu/gf/project/bioportalui/scmsvn/?action=browse&path=%2Ftrunk%2F

In April 2009, a NCBO GForge branch will be created starting with an initial core pool of developers having commit access (including Michael Gruniger's graduate students). Read access will be entirely public.

=Stage 2 – Ramp-Up Collaboration=
As the developer community grows, there will quickly be a need for clear open source collaboration processes and practices. Mike Dean and Benjamin Dai will establish Open Source Collaboration policies (e.g., commit rights, trusted developers, external developers, etc). The NCBO GForge site will continue to be the primary source control mechanism for OOR.

As details of the NCBO-OOR open source collaboration policies are established, they will be updated on this wiki page.

NCBO-OOR Development

2009-02-19T19:11:23Z

Benjamindai: /* NCBO-OOR Developer Collaboration */

Welcome to the NCBO-OOR Project! This developer's guide provides an introduction to the NCBO-OOR architecture and steps (with examples) of how to customize server-side components. The NCBO-OOR project is a collaborative open source endeavor to meet the needs of the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR Open Ontology Repository (OOR) Initiative.] The Ontology Open Repository (OOR) initiative is using the BioPortal 2.0 software as a basis for their first "NCBO-OOR" deployment to begin serving its diverse communities. This page serves as a launch point for understanding the NCBO-OOR architecture and getting started with customizing the code to advance OOR goals and objectives.

* The [[NCBO-OOR Architecture]] page provides a general architecture and philosphy used in it's design and development. This page is geared for any reader who has a basic understanding of multi-tier software architecture.

* The [[NCBO-OOR Server-Side Customization]] page describes the design and approach to customization of NCBO-OOR server-side components. To fully execute the examples presented on this page requires that the readers have an understanding of the principles of Aspect of Oriented programming and the [http://www.springsource.org/ Spring technology framework]. The author strongly recommends reading the [[NCBO-OOR Architecture]] page before diving into this document to ensure the reader has a good context.

* The [[NCBO-OOR Source Control Practices and Processes]] page describes the practices and processes expected to encourage the open source collaboration of geographically dispersed development teams.

* The [[NCBO-OOR Sandbox]] describes the deployed NCBO-OOR software.

=OOR Charter=
The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

=Short-Term NCBO-OOR Plan=
The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployed for the February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the NCBO-OOR software in a server environment that mimics the NCBO BioPortal Production environment.

=NCBO-OOR Developer Collaboration=
The NCBO-OOR developer collaboration will leverage practices that have worked successfully for various OOR community participants. The collaboration approach is still under construction.

An example of practices that the OOR could leverage is the [[NCBO Developer Communications | NCBO developer communications infrastructure]]. This has been established and driven by the NCBO Chief Software Architect which includes a NCBO quarterly developer conferences for which all NCBO partners are invited. Though all NCBO partners are welcome, the conference focuses primarily on how NCBO software can best serve the biomedical communities.