SBC Extension of the OBOE Measurement Ontology Margaret 1, O’Brien Shawn 1 UC Abstract: SBC’s EML datasets are part of an ontology research project called “Semtools, ” which is exploring how an observation ontology Text here can be applied to environmental and ecological data. Here we introduce some features and uses of the ontology. Using the Ontology Populate an EML <attribute> node <attribute id="sbc_ammonium_seawater_automated" system="sbc_attribute_dictonary" scope="system"> <attribute. Name>ammonium concentration</attribute. Name> <attribute. Label>NH 4 [umol/l]</attribute. Label> <attribute. Definition>concentration of ammonium in seawater measured by automated flow injection</attribute. Definition> <storage. Type type. System="http: //www. w 3. org/2001/XMLSchema-datatypes">float</storage. Type> <measurement. Scale> <ratio> <unit> <custom. Unit>micromole. Per. Liter</custom. Unit> </unit> <precision>0. 01</precision> <numeric. Domain> <number. Type>real</number. Type> </numeric. Domain> </ratio> </measurement. Scale> <missing. Value. Code> <code>99999. 00</code> <code. Explanation>no measurement collected at this point, or not available</code. Explanation> </missing. Value. Code> </attribute> 2, Bowers Matt The ontology can store the information necessary to convert between units, e. g. , the molecular weight of a compound. Data Integration The top data model shows two observations, both of tree diameter, but which are not described the same way. By aligning the observed entities (“Tree”) and characteristics (“Length”) with annotation, and knowing that “DBH” is a “Diameter, ” an application can compare these observations. Mark 3, Schildhauer Ben 3 Leinfelder Santa Barbara (SBC LTER), 2 Gonzaga University, 3 NCEAS https: //semtools. ecoinformatics. org/ SBC Extension: As part of the project, SBC is developing a dictionary of its ecological and environmental measurements as Text here an extension of the OBOE ontology, and is annotating its datasets with ontological terms. OBOE Model Observation of entity has measurement Entity Extension is a Ammonium has characteristic of Characteristic is a Concentration uses Protocol is a NH 4 in SW uses Standard has Measurement Precision is a Automated Flow injection Micromole. Per. Liter 0. 01 Example: Measurement Definition Concentration of Ammonium in Seawater 1. Entity: the ‘thing’ you observed The content of an EML <attribute> can come from the ontology. Unit Conversion 3, Jones Tools in Development Dataset Annotation <sms: annotation id="mobrien. 36. 62" eml. Package="mobrien. 50. 1" data. Table=“ 1"> <sms: observation label="o 2"> <sms: context observation="o 1"> <sms: relationship id="oboe-sbc. owl: Within"/> <sms: entity id="oboe-sbc. owl: Stream"/> <sms: entity id="oboe-sbc. owl: Discrete. Sample"/> </sms: context> <sms: measurement id="oboe-sbc. owl: SBC_Concentration. Of. Ammonium_Fresh. Water" label="m 3" precision="1. 0"> <sms: entity id="oboe-chemistry. owl: Ammonium"/> <sms: characteristic id="oboe-units. owl: Amount. Of. Substance. Concentration"/> <sms: standard id="oboe-units. owl: Micromole. Per. Liter"/> <sms: protocol id="oboe-sbc. owl: Melack. Lab. Ammonium. Concentration. Protocol. Freshwater. Automated"/> </sms: measurement> <sms: measurement id="oboe-sbc. owl: SBC_Concentration. Of. Nitrate_Fresh. Water" label="m 4" precision="1. 0"> <sms: entity id="oboe-chemistry. owl: Nitrate"/> <sms: characteristic id="oboe-units. owl: Amount. Of. Substance. Concentration"/> <sms: standard id="oboe-units. owl: Micromole. Per. Liter"/> <sms: protocol id="oboe-sbc. owl: Melack. Lab. Nitrate. Nitrite. Concentration. Protocol. Freshwater. Automated"/> </sms: measurement> <sms: measurement id="oboe-sbc. owl: SBC_Concentration. Of. Phosphate_Fresh. Water" label="m 5" precision="1. 0"> <sms: entity id="oboe-chemistry. owl: Phosphate"/> <sms: characteristic id="oboe-units. owl: Amount. Of. Substance. Concentration"/> <sms: standard id="oboe-units. owl: Micromole. Per. Liter"/> <sms: protocol id="oboe-sbc. owl: Melack. Lab. Phosphate. Concentration. Protocol. Freshwater. Automated"/> </sms: measurement> </sms: observation> <sms: map attribute="NH 4_u. M" measurement="m 1"/> <sms: map attribute="NO 3_u. M" measurement="m 2"/> <sms: map attribute="PO 4_u. M" measurement="m 3"/> </sms: annotation> Text here -- Ann manag from d -- Ann separa -- EML to the -- The separa be ann one on same reprod Ontology Creation Tools are in development to assist ontology authors. 4. Standard: a reference for comparing or naming Entities 2. Characteristic: a property of the Entity that can be measured “Context” associates this measurement with another Entity 3. Protocol: the procedure for generating data The OBOE group is creating a Other graphical plug-ins plug-in for this are already available for application to Protégé. assist authors designing OBOE Browse, Search and Discovery extensions. More specific and accurate searches can be conducted when datasets are annotated with ontological terms. This research was supported by the US National Science Foundation’s Long Term Ecological Research program and by DBI-0743429
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