BIRNLex-OBI-proxy
type: Ontology
change note: 2008-02-21 (BB): Updated the sham control role classes.
contributor: Jeff Grethe
editorial note: Using birnlex IDs starting with 11000.
contributor: Carol Bean
definition: The BIRN Project lexicon uses this file as a temporary proxy for classes from the Ontology of Biomedical Investigation (OBI). These classes will be replaced by their OBI equivalents, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
modified date: 2008-02-21
contributor: Amarnath Gupta
creator: The BIRN Ontology Task Force
contributor: Christine Fennema-Notestine
default language: en
editorial note: next ID: birnlex_11049
contributor: Jessica Turner
contributor: David Kennedy
created date: 2007-10-05
contributor: Bill Bug
contributor: Maryann Martone
version info: 1.3.1
editorial note: ID use: 11000 - 11048
subject: The BIRN project lexicon

Detector role
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_323
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2007-10-05
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
subclass of: Reagent role

Reagent role
type: Class
modified date: 2007-10-05
subclass of: Role
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_328
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
nif ID: _1_3.2
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Source code
type: Class
external source id: OBI_0000039
comment: We need to have this in there somewhere, but it looks like OBI has something equivalent "source code module"; they have it classified as an information content entity, so I placed it here. (Maryann Martone)
has definition source: OBI
definition: A source code module is an information content entity that specifies, using a programming language, some algorithm.
created date: December 15, 2008
subclass of: Information entity

Information entity
type: Class
modified date: 2007-10-05
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_344
subclass of: GenericallyDependentContinuant
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Non-realizable information entity
type: Class
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_295
subclass of: GenericallyDependentContinuant
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
modified date: 2007-10-05

Entity of organismal origin
type: Class
synonym: Entity of organismal origin
nif ID: _1_3.5
synonym: In vitro anatomical object
subclass of: birnlex 6
modified date: March 15, 2010
label: Ex vivo anatomical object
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_133
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
has former parent class: http://www.ifomis.org/bfo/1.1/snap#Object

Microarray platform
type: Class
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_52
modified date: 2007-10-05
subclass of: Platform
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05
nif ID: _7_5.1

Platform
type: Class
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_50
modified date: 2007-10-05
created date: 2007-10-05
subclass of: ObjectAggregate
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Placebo treatment
type: Class
subclass of: Sham treatment
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2008-02-21
modified date: 2008-02-21
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#Placebo_treatment

Sham treatment
type: Class
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2008-02-21
modified date: 2008-02-21
birnlex definition: A subject group treatment identical to the experimental treatment but without the active agent under study.
subclass of: Reference treatment
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#Sham_treatment
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Cardinal part of instrument
type: Class
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_36
subclass of: Artefact object
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
modified date: 2007-10-05

Artefact object
type: Class
created date: 2007-10-05
modified date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
alternative label: manufactured_object
subclass of: MaterialEntity
label: Artefact entity
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
synonym: artefact object
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_47

Journal article
type: Class
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_275
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
modified date: 2007-10-05
synonym: Publication
definition: A written composition, usually nonfiction, on a specific topic, forming an independent part of a journal or other publication.
subclass of: Narrative object
synonym: Journal article resource

Narrative object
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_300
nif ID: _7_12
modified date: 2007-10-05
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
subclass of: Information content entity
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Information content entity
type: Class
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_342
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2007-10-05
subclass of: Non-realizable information entity
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Investigation administration role
type: Class
subclass of: Role
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_176
modified date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Software application
type: Class
modified date: December 15, 2008
synonym: software resource
subclass of: Digital entity
definition: Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
synonym: software program
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_351
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
synonym: Software application
external source id: OBI_0000222
created date: 2007-10-05
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
nif ID: _1_2
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
preferred label: Binary executable
modified date: 2007-10-05
synonym: program

Digital entity
type: Class
modified date: 2007-10-05
modified date: December 15, 2008
created date: 2007-10-05
external source id: OBI_0000261
subclass of: GenericallyDependentContinuant
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_306
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
definition: A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. (OBI)
comment: OBI has this as a child of "non realizable information entity"; we may need to update the entire hierarchy (Maryann Martone).

Comment
type: Class
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
subclass of: Narrative object
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
synonym: Note
nif ID: _4_6.3
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
modified date: 2007-10-10
nif ID: _7_12
created date: 2007-10-10

Protocol
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2007-10-05
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_272
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
subclass of: Information entity

Algorithm
type: Class
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2007-10-05
change note: Definition and defining source has been added.
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
subclass of: Information entity
modified date: December 15, 2008
modified date: 2007-10-05
definition: An algorithm is a plan which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_270
has definition source: OBI
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Planned process
type: Class
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_600062
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
subclass of: Process
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
modified date: 2007-10-05

Assay
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2007-10-05
subclass of: Protocol application
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_70
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.

Protocol application
type: Class
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_69
created date: 2007-10-05
modified date: 2007-10-05
subclass of: Planned process
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Clinical finding
type: Class
subclass of: Narrative object
created date: 2007-10-05
modified date: 2007-10-05
nif ID: _7_12.1
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_286
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Quantitative value
type: Class
subclass of: Value
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_147
modified date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05

Value
type: Class
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_18
subclass of: Data object
created date: 2007-10-05
modified date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Material transformation
type: Class
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_94
subclass of: Protocol application
modified date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05

Reference treatment
type: Class
modified date: 2008-02-21
subclass of: Reference
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2008-02-21
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#Reference_treatment
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.

Reference
type: Class
created date: 2008-02-21
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
subclass of: Role
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2008-02-21
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#Reference
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.

Role in protocol application
type: Class
modified date: 2008-02-21
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_343
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
subclass of: Role
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Instrument
type: Class
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: March 31, 2010
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_400003
definition: Any entity used to perform a measurement, e.g., a microscope, a test battery
subclass of: Device
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
nif ID: _1_3.1
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Device
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_400002
subclass of: Artefact object
modified date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.

Imaging assay
type: Class
modified date: 2007-10-05
created date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_185
subclass of: Assay
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Negative control role
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
modified date: 2008-02-21
has former parent class: Control role
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05
is replaced by class: Sham treatment
subclass of: birnlex retired class
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_173

Liquid chromatography mass spectrometry platform
type: Class
created date: 2007-10-05
subclass of: Platform
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_51
modified date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Mock surgery
type: Class
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
modified date: 2008-02-21
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#Mock_surgery
subclass of: Sham treatment
created date: 2008-02-21
synonym: Sham surgery

Disease
type: Class
modified date: 2007-10-05
created date: 2007-10-05
nif ID: _8.3
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_155
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
subclass of: Disposition

Data object
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_305
modified date: 2007-10-05
created date: 2007-10-05
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
subclass of: Information content entity
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Reporter role
type: Class
created date: 2007-10-05
modified date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_289
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
subclass of: Reagent role

Investigation design
type: Class
subclass of: Information entity
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_335
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2007-10-05
modified date: 2007-10-05

Data transformation
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
subclass of: Protocol application
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_95
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.

Image
type: Class
modified date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
subclass of: Data object
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_325
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
created date: 2007-10-05

Investigation record
type: Class
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
subclass of: Report
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_46
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
modified date: 2007-10-05
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Report
type: Class
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_322
subclass of: Narrative object
nif ID: _7_12
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05
modified date: 2007-10-05
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary

Cell line
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_129
subclass of: Entity of organismal origin
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
nif ID: _1_3.3

Investigator
type: Class
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
subclass of: Investigation administration role
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_288
modified date: 2007-10-05
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug

Control role
type: Class
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
has former parent class: Role in protocol application
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
created date: 2007-10-05
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_171
is replaced by class: Reference treatment
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2008-02-21
subclass of: birnlex retired class

Vehicle control treatment
type: Class
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#Vehicle_control_treatment
subclass of: Sham treatment
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
modified date: 2008-02-21
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary
created date: 2008-02-21

CHEBI_15765
definition: An amino acid precursor of dopamine with antiparkinsonian properties. L-DOPA is a prodrug that is converted to dopamine by DOPA decarboxylase and can cross the blood-brain barrier. When in the brain, L-DOPA is decarboxylated to dopamine and stimulates the dopaminergic receptors. (Adapted from NCI Thesaurus) Levodopa is naturally occurring form of dihydroxyphenylalanine and the immediate precursor of dopamine. Unlike dopamine itself, it can be taken orally and crosses the blood-brain barrier. It is rapidly taken up by dopaminergic neurons and converted to dopamine. It is used for the treatment of parkinsonian disorders and is usually given with agents that inhibit its conversion to dopamine outside of the central nervous system. (PubChem) Pharmacology: Levodopa (L-dopa) is used to replace dopamine lost in Parkinson's disease because dopamine itself cannot cross the blood-brain barrier where its precursor can. However, L-DOPA is converted to dopamine in the periphery as well as in the CNS, so it is administered with a peripheral DDC (dopamine decarboxylase) inhibitor such as carbidopa, without which 90% is metabolised in the gut wall, and with a COMT inhibitor if possible; this prevents about a 5% loss. The form given therapeutically is therefore a prodrug which avoids decarboxylation in the stomach and periphery, can cross the blood-brain barrier, and once in the brain is converted to the neurotransmitter dopamine by the enzyme aromatic-L-amino-acid decarboxylase. Mechanism of action: Striatal dopamine levels in symptomatic Parkinson's disease are decreased by 60 to 80%, striatal dopaminergic neurotransmission may be enhanced by exogenous supplementation of dopamine through administration of dopamine's precursor, levodopa. A small percentage of each levodopa dose crosses the blood-brain barrier and is decarboxylated to dopamine. This newly formed dopamine then is available to stimulate dopaminergic receptors, thus compensating for the depleted supply of endogenous do…
abbrev: L-Dopa

Data set
external source URI: http://obi.sourceforge.net/ontology/OBI.owl#OBI_43
has birnlex curator: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug
created date: 2007-10-05
modified date: 2007-10-05
editorial note: This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege.
subclass of: Data object
has curation status: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#graph_position_temporary