[bro-discuss] Release of Biomedical Resource Ontology BRO3.0 and request for comments

[Trish Whetzel]

The Biomedical Resource Ontology (BRO) development team would like to inform you of the release of BRO 3.0 (http://purl.bioontology.org/ontology/BRO-Core). The BRO is a classification of resource types and provides a source of annotation terms used in Biositemaps (http://www.biositemaps.org), an approach for identifying and querying biomedical resources on the Internet.
Major updates include the addition of definitions for most terms, significant re-structuring of the BRO:Data_Object section under BRO:Data_Resource (http://bioportal.bioontology.org/visualize/42483/BRO:Data_Resource), continued alignment with NIFSTD, and deprecation of terms. A list of deprecated terms and their replacement term(s) is listed below.
Many of the changes for this release were motivated by use cases and usability of BRO by the Biositemaps CTSA Inventory Resource Web Presence group. We encourage your feedback to continue to improve the BRO. For general comments on the release, please email me, if you would like to be more engaged please reply to this email to post to the bro-discuss mailing list (http://groups.google.com/group/bro-discuss).

Deprecated terms with a replacement term(s)

*   BRO:Averaging_and_Aglomeration            BRO:Averaging_and_Agglomeration
*   BRO:Backup_Archives_and_Disaster_Recovery            BRO:Disaster_Recovery_Service, BRO:Backup_Archive_Service
*   BRO:Centrality_Analsysis            BRO:Centrality_Analysis
*   BRO:Clinical_Data            BRO:Clinical_Care_Data
*   BRO:Data_Repository            BRO:Database
*   BRO:Data_Storage_Repository            BRO:Database_Software
*   BRO:EDA            BRO:Exploratory_Data_Analysis
*   BRO:Experimental_Measurement            BRO:Molecular_and_Cellular_Data
*   BRO:Knowledge_Environment            BRO:Structured_Knowledge_Resource
*   BRO:Molecular_Trajectory_Data                        BRO:Dynamic_Model
*   BRO:Structured_Data            BRO:Structured_File
*   BRO:Summarization            BRO:Language_Summarization
*   BRO:Support            BRO:Technical_Support
*   BRO:Unstructured_Data            BRO:Unstructured_Knowledge_Resource

Deprecated terms without a replacement term (reason for deprecation)

*   BRO:Anatomic_Atlas (This is the only child term of Atlas and Atlas also contains anatomy information)
*   BRO:Automated_Natural_Language_Output (This term is too granular)
*   BRO:Binary_Executable
*   BRO:Clinical_Chart
*   BRO:Connectivity_Matrix
*   BRO:Continuous_Data (Deprecated as part of Data_Object restructuring)
*   BRO:Clinical_Trial_Data (After adding new terms this term was redundant)
*   BRO:Data_Distribution (Deprecated as part of restructuring)
*   BRO:Data_Object (Deprecated as part of Data_Object restructuring)
*   BRO:Discrete_Data (Deprecated as part of Data_Object restructuring)
*   BRO:Document (Use as a class for organization not needed)
*   BRO:Four_Dimensional_Data (Deprecated as part of Data_Object restructuring)
*   BRO:Free_Text (Not needed in comparison to existing child terms of BRO:Narrative_Resource)
*   BRO:Heterogeneous_Funding_Resource (Removed since this is a mix of types)
*   BRO:High_Dimensional_Data (Deprecated as part of Data_Object restructuring)
*   BRO:License_and_Terms_for_Redistribution (Too specific)
*   BRO:License_and_Terms_for_Use (Too specific)
*   BRO:Matrix (Deprecated as part of Data_Object restructuring)
*   BRO:Modular_Component
*   BRO:Network_Editor (Too granular)
*   BRO:Nonhuman_Data (Not a kind of clinical data)
*   BRO:Pass_Through_License (Too granular)
*   BRO:Portlet_Component
*   BRO:Publication
*   BRO:Scalar_Data
*   BRO:Semantic_Network (This is the only subclass of Knowledgebase, it is not clear the origin of this term, and it is not currently used in annotation of BioSitemap files)
*   BRO:Server
*   BRO:Software_Distribution (By adopting the phraseology of “A resource that…” this term is redundant and was deprecated, however the children were moved to appropriate location in the Software branch)
*   BRO:Software_Documentation
*   BRO:Source_Code
*   BRO:Standalone_Application
*   BRO:Stochastic_Data (Deprecated as part of restructuring)
*   BRO:Three_Dimensional_Data (Deprecated as part of Data_Object restructuring)
*   BRO:Toolkit
*   BRO:Vector_Data (Deprecated as part of Data_Object restructuring)
*   BRO:Web_Service
*   BRO:Website