A flow cytometer. Material entity that is designed to have a function and play a role in scientific investigation. PERSON: Melissa Haendel See OBI listserv discussion for considerations in defining instrument. http://sourceforge.net/tracker/index.php?func=detail&aid=2894801&group_id=177891&atid=886178 http://en.wikipedia.org/wiki/Scientific_instrument instrument A DNA sequencing service performed by a core lab. An information content entity that describes a service performed by a person or organization with the objective of performing a technique, providing training, providing storage of data or material entities, or providing access to resources for another person or organization Coordinate with NIF. NIF ID: nlx_res_20090105 PERSON: Melissa Haendel PERSON: Melissa Haendel service A plasmid can be used as a reagent. PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). Processed material that is used in a chemical reaction or other experimental process to detect, measure, examine, or produce other substances. http://www.yourdictionary.com/reagent reagent A technique is a planned process used to accomplish a specific activity or task. Flow cytometry is a technique. PERSON: Melissa Haendel Protocol is added to eagle-i temporarily until a relationship between the informatio entity "protocol" and these planned processes is created. This class refers to the axtual process not the document http://en.wikipedia.org/wiki/Technique A role inhering in a person or organization that is realized when the bearer participates in providing a service to meet the need of another person or thing. A technician in a core laboratory. An role of an individual within his or her profession or institution; use outreach provider role for community service or other activities outside the profession. Member of the International Conference on Complex Systems Organizing Committee PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky A funded collection of investigations as described in a research proposal. A project to study the role of a specific protein in cell signaling. Maybe SameAs "Investigation" but is the subject of funding PERSON: Melissa Haendel PERSON: Melissa Haendel Heart tissue obtained from an organism. Material entity that is a portion or quantity of a biological material for use in testing, examination, or study. A biological specimen can be an individual animal, a population of organisms, or is a part of or derived from an animal, plant, part of a plant, or microorganism. When a taxon is described, it is typically based on a single specimen and is referred to as the holotype. PERSON: Melissa Haendel Should have relationship to Organism biological specimen biospecimen http://en.wikipedia.org/wiki/Specimen A general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers. IAO is a planned specification, in SWO is an Information artifact. In eagle-i, we have a need to collect material instances and is it thus currently classified as a material entity. Microsoft Word is commonly used word processing software. PERSON: Melissa Haendel http://en.wikipedia.org/wiki/Computer_software software A service offering that describes a service in which the consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. Allowing access to a microscope in a core lab. Coordinate with NIF PERSON: Matt Brush PERSON: Matthew Brush A computer server. A service offering that describes a service in which the consumer provides some material or data as input which a service provider stores and returns as output. PERSON: Matt Brush PERSON: Matthew Brush coordinate with NIF. NIF ID:nlx_res_20090419 A service offering that describes a service in which the provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer Coordinate with NIF. NIF ID: nlx_res_20090444 PERSON: Matt Brush PERSON: Matthew Brush Training a researcher to use a microscope. A service offering that describes a service in which the provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer Biopsy service. Coordinate with NIF: NIF ID: nlx_res_20090416 PERSON: Nicole Vasilevsky http://neurolex.org/wiki/Category:Production_service_resource An analysis service offering that describes a service in which the consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. Coordinate with NIF: NIF ID: nlx_res_20090420 Flow cytometry analysis of T cells. PERSON: Nicole Vasilevsky http://neurolex.org/wiki/Category:Analysis_service_resource A material processing service offering that describes a service in which the provider makes physical changes to a specified input material that produce a new entity as specified output that is returned the service consumer. The specified output of a material production service can be contained within, derived from, or synthesized from specified input materials, but it represents a material entity that is of a distinct type from any of the specified input materials. Coordinate with NIF. NIF ID: nlx_res_20090418 PERSON: Matthew Brush Production of monoclonal antibodies from a hybridoma. http://neurolex.org/wiki/Category:Material_service_resource A technique that authorizes a use (such as copying software or using a (patented) invention) to a licensee, sparing the licensee from a claim of infringement brought by the licensor. Licensing of a new technology. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/License A service offering that describes a service in which the provider facilitates the transport of some material entity to a specified destination for the service consumer. PERSON: Matt Brush PERSON: Matthew Brush Transport of a patient within a hospital. A service offering that describes a service in which the provider assists the consumer in activities directly or indirectly associated with the production and analysis or experimental research data. PERSON: Matt Brush PERSON: Matthew Brush Technical support. A storage service offering that describes a service in which the consumer provides some material as input which a service provider stores and returns as output Cryopreservation service. PERSON: Matt Brush PERSON: Matthew Brush A storage service offering that describes a service in which the consumer provides data as input, which a service provider stores and returns as output in its original form. PERSON: Matt Brush PERSON: Matthew Brush Storing data on a server. A service offering that describes a service in which the provider actively maintains a material or data resource (e.g. a model organism colony or database) for the service consumer. This may involved making physical alterations to the material or data with the goal of maintaining its integrity or features. PERSON: Matt Brush PERSON: Matthew Brush A maintenance service offering that describes a service in which the provider actively maintains a material resource (e.g. a model organism colony) for the service consumer. A material maintenance service may or may not include storage of the material input. Maintaining an animal coloy. PERSON: Matt Brush PERSON: Matthew Brush A maintenance service offering that describes a service in which the provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. Maintaining a database. PERSON: Matt Brush PERSON: Matthew Brush A service offering that describes a service in which the consumer provides some input material or data and a service provider returns data about the input material or data. Flow cytometry analysis service. PERSON: Matt Brush PERSON: Matthew Brush An analysis service offering that describes a service in which the consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output PERSON: Matt Brush PERSON: Matthew Brush Sequence data analysis. data processing service data transformation service A material processing service offering that describes a service in which the provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. Histology service. PERSON: Matt Brush PERSON: Matthew Brush A database is an organized collection of data, today typically in digital form. Just a place horder. It will probably be replaced by NIF term: http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Resource.owl#nlx_res_20090405 PERSON: Carlo Torniai http://en.wikipedia.org/wiki/Database 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) Bjoern Peters Injecting mice with a vaccine in order to test its efficacy branch derived planned process A processual entity that realizes a plan which is the concretization of a plan specification. planned process OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice. PlanAndPlannedProcess Branch Protocol a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. protocol GROUP: OBI Biomaterial Branch A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus